* Re: [devel] I: итоги NMU по добавлению BR: texinfo
2015-12-11 11:45 ` Kirill Maslinsky
2015-12-11 12:33 ` Gleb Fotengauer-Malinovskiy
@ 2015-12-11 12:56 ` Igor Vlasenko
2015-12-11 13:10 ` Michael Shigorin
2 siblings, 0 replies; 11+ messages in thread
From: Igor Vlasenko @ 2015-12-11 12:56 UTC (permalink / raw)
To: kirill, ALT Linux Team development discussions, Igor Vlasenko
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прикладываю лог неудавшейся сборки
(в спеке добавлено BR: texinfo)
2015-12-11 13:45 GMT+02:00 Kirill Maslinsky <kirill@altlinux.org>:
> On Wed, Dec 09, 2015 at 07:43:25PM +0200, Igor Vlasenko wrote:
>> Уважаемые коллеги,
>> по итогам транзакции по добавлению BR: texinfo
>> 1) из 64 пакетов которым нужно было добавить BR: texinfo
>> и на которые у меня не было acl, осталось 49 пакетов.
>
> [...]
>
>> далее, 31 пакет, которые тоже нуждаются в NMU
>> но сломаны и я их сходу не смог починить:
>>
>> R-base kirill ldv @everybody
>
> А что именно в нем сломано? Я могу его обновить и попробовать починить,
> но пока не понимаю суть проблемы.
>
> --
> KM
--
С уважением,
Игорь Власенко.
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~/src/repo/foreign/MAKEINFONMU/OUT.gits/R-base.git ~/src/repo/foreign/MAKEINFONMU
gear --hasher -- hsh --apt-config=/etc/apt/apt.conf.SS --with-stuff --mountpoints=/proc --packager=Igor Vlasenko <viy@altlinux.ru> --number 2 /tmp/.private/igor/hasher2
deduce_number_from_directory: dir=/tmp/.private/igor/hasher2/chroot gid=517
deduce_number_from_directory: dir=/tmp/.private/igor/hasher2/chroot gid=517
debug:hsh-mkchroot:gid1=517 517:517=ugid1
deduce_number_from_directory: dir=/tmp/.private/igor/hasher2/chroot gid=517
<86>Dec 11 12:22:04 userdel[17466]: delete user 'rooter'
<86>Dec 11 12:22:04 userdel[17466]: removed group 'rooter' owned by 'rooter'
<86>Dec 11 12:22:04 userdel[17466]: removed shadow group 'rooter' owned by 'rooter'
<86>Dec 11 12:22:04 groupadd[17471]: group added to /etc/group: name=rooter, GID=517
<86>Dec 11 12:22:04 groupadd[17471]: group added to /etc/gshadow: name=rooter
<86>Dec 11 12:22:04 groupadd[17471]: new group: name=rooter, GID=517
<86>Dec 11 12:22:04 useradd[17475]: new user: name=rooter, UID=517, GID=517, home=/root, shell=/bin/bash
<86>Dec 11 12:22:04 userdel[17481]: delete user 'builder'
<86>Dec 11 12:22:04 userdel[17481]: removed group 'builder' owned by 'builder'
<86>Dec 11 12:22:04 userdel[17481]: removed shadow group 'builder' owned by 'builder'
<86>Dec 11 12:22:04 groupadd[17486]: group added to /etc/group: name=builder, GID=518
<86>Dec 11 12:22:04 groupadd[17486]: group added to /etc/gshadow: name=builder
<86>Dec 11 12:22:04 groupadd[17486]: new group: name=builder, GID=518
<86>Dec 11 12:22:04 useradd[17490]: new user: name=builder, UID=518, GID=518, home=/usr/src, shell=/bin/bash
deduce_number_from_directory: dir=/tmp/.private/igor/hasher2/chroot gid=517
warning: Macro %add_tcl_lib_path not found
deduce_number_from_directory: dir=/tmp/.private/igor/hasher2/chroot gid=517
<13>Dec 11 12:22:14 rpmi: tex-common-0.2-alt4 1244804096 installed
<13>Dec 11 12:22:14 rpmi: texlive-common-0.1-alt3 1244804816 installed
<13>Dec 11 12:22:14 rpmi: xorg-xproto-devel-7.0.28-alt1 1448272470 installed
<13>Dec 11 12:22:14 rpmi: libjpeg-2:1.3.1-alt0.1 1388074033 installed
<13>Dec 11 12:22:14 rpmi: perl-Encode-2.78-alt1.1 1448469971 installed
<13>Dec 11 12:22:14 rpmi: libpng15-1.5.25-alt1 1449329557 installed
<13>Dec 11 12:22:14 rpmi: libtiff5-4.0.3-alt1 1348347498 installed
<13>Dec 11 12:22:14 rpmi: libpng12-1.2.50-alt2 1347753407 installed
<13>Dec 11 12:22:14 rpmi: libexpat-2.1.0-alt1 1347469765 installed
<13>Dec 11 12:22:14 rpmi: libICE-1.0.9-alt1 1409902719 installed
<13>Dec 11 12:22:14 rpmi: libSM-1.2.2-alt1 1391072686 installed
<13>Dec 11 12:22:14 rpmi: perl-Term-ANSIColor-4.04-alt1 1449507765 installed
<13>Dec 11 12:22:14 rpmi: rpm-macros-info-install-6.0-alt2 1449157524 installed
<13>Dec 11 12:22:14 rpmi: libtcl-8.5.9-alt2 1351878901 installed
<13>Dec 11 12:22:14 rpmi: tcl-8.5.9-alt2 1351878901 installed
<13>Dec 11 12:22:14 rpmi: liblcms2-2.7-alt1 1428681013 installed
<13>Dec 11 12:22:14 rpmi: libopenblas-0.2.14-alt1.git20150324 1433158855 installed
<13>Dec 11 12:22:14 rpmi: zlib-devel-1.2.8-alt1 1371079009 installed
<13>Dec 11 12:22:14 rpmi: libwayland-client-1.9.0-alt1 1442913481 installed
<13>Dec 11 12:22:14 rpmi: libXau-1.0.8-alt1 1369565807 installed
<13>Dec 11 12:22:14 rpmi: libnspr-1:4.10.10-alt1 1447166548 installed
<13>Dec 11 12:22:14 rpmi: libkpathsea-2008.0-alt0.15.6 1449446882 installed
<13>Dec 11 12:22:14 rpmi: libquadmath0-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:14 rpmi: libgfortran3-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:14 rpmi: libgdbm-1.8.3-alt9 1297723357 installed
<13>Dec 11 12:22:15 rpmi: ca-certificates-2015.08.04-alt1 1441020102 installed
<13>Dec 11 12:22:15 rpmi: libcrypto10-1.0.1k-alt4 1436449862 installed
<13>Dec 11 12:22:15 rpmi: libssh2-1.4.3-alt2 1448445217 installed
<13>Dec 11 12:22:15 rpmi: perl-DBM-1:5.22.0-alt2 1448833096 installed
<13>Dec 11 12:22:15 rpmi: libquadmath5-devel-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:15 rpmi: libXau-devel-1.0.8-alt1 1369565807 installed
<13>Dec 11 12:22:15 rpmi: libpng-devel-1.5.25-alt1 1449329557 installed
<13>Dec 11 12:22:15 rpmi: libopenblas-devel-0.2.14-alt1.git20150324 1433158855 installed
<13>Dec 11 12:22:15 rpmi: texi2dvi-6.0-alt2 1449157524 installed
<13>Dec 11 12:22:15 rpmi: libICE-devel-1.0.9-alt1 1409902719 installed
<13>Dec 11 12:22:15 rpmi: libSM-devel-1.2.2-alt1 1391072686 installed
<13>Dec 11 12:22:15 rpmi: perl-libintl-1.24-alt1.1 1448485129 installed
<13>Dec 11 12:22:15 rpmi: libjasper-1.900.1-alt3 1391718482 installed
<13>Dec 11 12:22:15 rpmi: fonts-type1-tipa-tex-1.3-alt4 1246545601 installed
<13>Dec 11 12:22:15 rpmi: texlive-doc-base-2008.0-alt0.10 1238420746 installed
<13>Dec 11 12:22:15 rpmi: texmf-tex4ht-1.0.2009_06_11_1038-alt1 1328304130 installed
<13>Dec 11 12:22:15 rpmi: tcsh-6.18.01-alt2 1442313244 installed
<13>Dec 11 12:22:15 rpmi: t1lib-5.1.2-alt5 1326979643 installed
<13>Dec 11 12:22:15 rpmi: rpm-build-tcl-0.4-alt2 1445508295 installed
<13>Dec 11 12:22:15 rpmi: tcl-devel-8.5.9-alt2 1351878901 installed
<13>Dec 11 12:22:15 rpmi: perl-Term-Cap-1.17-alt1 1445018869 installed
<13>Dec 11 12:22:15 rpmi: perl-Unicode-EastAsianWidth-1.33-alt1 1383358357 installed
<13>Dec 11 12:22:15 rpmi: perl-Text-Unidecode-1.27-alt1 1445859908 installed
<13>Dec 11 12:22:15 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed
<13>Dec 11 12:22:15 rpmi: perl-Pod-Simple-3.32-alt1 1447205413 installed
<13>Dec 11 12:22:15 rpmi: libruby-2.0.0-alt10 1404231146 installed
<13>Dec 11 12:22:15 rpmi: ruby-2.0.0-alt10 1404231146 installed
<13>Dec 11 12:22:16 rpmi: poppler-data-0.4.7-alt1 1415971818 installed
<13>Dec 11 12:22:16 rpmi: libpcre16-8.38-alt1 1448366677 installed
<13>Dec 11 12:22:16 rpmi: pcretest-8.38-alt1 1448366677 installed
<13>Dec 11 12:22:16 rpmi: libopenjpeg-1.3-alt1.3 1349374484 installed
<13>Dec 11 12:22:16 rpmi: libxblas-1.0.248-alt1 1322010716 installed
<13>Dec 11 12:22:16 rpmi: liblapack-1:3.5.0-alt1 1401382194 installed
<13>Dec 11 12:22:16 rpmi: libdatrie-0.2.8-alt1_5 1410185969 installed
<13>Dec 11 12:22:16 rpmi: libthai-0.1.21-alt1_1 1410187251 installed
<13>Dec 11 12:22:16 rpmi: libidn-1.28-alt1 1374528190 installed
<13>Dec 11 12:22:16 rpmi: libpixman-3:0.32.8-alt1 1447610691 installed
<13>Dec 11 12:22:16 rpmi: xorg-renderproto-devel-0.11.1-alt3 1303465056 installed
<13>Dec 11 12:22:16 rpmi: xorg-xextproto-devel-2:7.3.0-alt1 1389258977 installed
<13>Dec 11 12:22:16 rpmi: xorg-kbproto-devel-1.0.6-alt1 1332531883 installed
<13>Dec 11 12:22:16 rpmi: libwayland-server-1.9.0-alt1 1442913481 installed
<13>Dec 11 12:22:16 rpmi: libxshmfence-1.2-alt1 1420972191 installed
<13>Dec 11 12:22:16 rpmi: libpciaccess-1:0.13.4-alt1 1431681688 installed
<13>Dec 11 12:22:16 rpmi: libdrm-1:2.4.63-alt1 1439650113 installed
<13>Dec 11 12:22:16 rpmi: libgbm-4:11.0.6-alt1 1448452293 installed
<13>Dec 11 12:22:16 rpmi: libX11-locales-3:1.6.3-alt1 1431956885 installed
<13>Dec 11 12:22:16 rpmi: libXdmcp-1.1.1-alt1 1334617699 installed
<13>Dec 11 12:22:16 rpmi: libxcb-1.11-alt1 1409047934 installed
<13>Dec 11 12:22:16 rpmi: libX11-3:1.6.3-alt1 1431956911 installed
<13>Dec 11 12:22:16 rpmi: libXext-1.3.3-alt1 1409902932 installed
<13>Dec 11 12:22:16 rpmi: libXt-1.1.4-alt1 1369984716 installed
<13>Dec 11 12:22:16 rpmi: libXrender-0.9.8-alt1 1371312110 installed
<13>Dec 11 12:22:16 rpmi: libXmu-1.1.2-alt1 1391072528 installed
<13>Dec 11 12:22:16 rpmi: libXpm-3.5.11-alt1 1391072398 installed
<13>Dec 11 12:22:17 rpmi: libxcb-devel-1.11-alt1 1409047934 installed
<13>Dec 11 12:22:17 rpmi: libX11-devel-3:1.6.3-alt1 1431956911 installed
<13>Dec 11 12:22:17 rpmi: libXrender-devel-0.9.8-alt1 1371312110 installed
<13>Dec 11 12:22:17 rpmi: libXext-devel-1.3.3-alt1 1409902932 installed
<13>Dec 11 12:22:17 rpmi: libXt-devel-1.1.4-alt1 1369984716 installed
<13>Dec 11 12:22:17 rpmi: libXaw-1.0.12-alt1 1391072621 installed
<13>Dec 11 12:22:17 rpmi: libXxf86vm-1.1.3-alt1 1369984824 installed
<13>Dec 11 12:22:17 rpmi: libXdamage-1.1.3-alt4 1297162596 installed
<13>Dec 11 12:22:17 rpmi: libXfixes-5.0.1-alt1 1369809606 installed
<13>Dec 11 12:22:17 rpmi: libGL-4:11.0.6-alt1 1448452293 installed
<13>Dec 11 12:22:17 rpmi: libEGL-4:11.0.6-alt1 1448452293 installed
<13>Dec 11 12:22:17 rpmi: libEGL-devel-4:11.0.6-alt1 1448452293 installed
<13>Dec 11 12:22:17 rpmi: libGL-devel-4:11.0.6-alt1 1448452293 installed
<13>Dec 11 12:22:17 rpmi: mailx-8.1.2-alt7 1366314831 installed
<13>Dec 11 12:22:17 rpmi: sharutils-4.6.3-alt1.1.qa2.1 1449219807 installed
<13>Dec 11 12:22:17 rpmi: libsqlite3-3.8.10.2-alt1 1432747242 installed
<13>Dec 11 12:22:17 rpmi: libnss-3.20.1-alt1 1447166823 installed
<13>Dec 11 12:22:17 rpmi: nss-utils-3.20.1-alt1 1447166823 installed
<13>Dec 11 12:22:17 rpmi: ncompress-4.2.4.4-alt1 1366160439 installed
<13>Dec 11 12:22:17 rpmi: libjbig-2.1-alt1 1401380921 installed
<13>Dec 11 12:22:17 rpmi: xorg-rgb-1.0.4-alt1.qa1 1366268675 installed
<13>Dec 11 12:22:17 rpmi: libnetpbm-10.35.97-alt1 1447854203 installed
<13>Dec 11 12:22:17 rpmi: netpbm-10.35.97-alt1 1447854203 installed
<13>Dec 11 12:22:18 rpmi: libicu50-1:5.1.1-alt3 1368393235 installed
<13>Dec 11 12:22:18 rpmi: icu-utils-1:5.1.1-alt3 1368393235 installed
<13>Dec 11 12:22:18 rpmi: xml-utils-1:2.9.3-alt1 1448028556 installed
<13>Dec 11 12:22:18 rpmi: rpm-build-gir-0.7.2-alt2 1390711550 installed
<13>Dec 11 12:22:18 rpmi: libpaper-1.1.24-alt4 1315383473 installed
<13>Dec 11 12:22:18 rpmi: liblz4-r131-alt1 1447866717 installed
<13>Dec 11 12:22:18 rpmi: libgpg-error-1.20-alt1.1 1449204243 installed
<13>Dec 11 12:22:18 rpmi: libgcrypt20-1.6.4-alt1.1 1449202893 installed
<13>Dec 11 12:22:18 rpmi: libsystemd-1:228-alt2 1449588193 installed
<13>Dec 11 12:22:18 rpmi: libdbus-1.10.6-alt1 1449475477 installed
<13>Dec 11 12:22:18 rpmi: libavahi-0.6.31-alt6 1447371819 installed
<13>Dec 11 12:22:18 rpmi: gcc-fortran-common-1.4.20-alt1 1432315196 installed
<13>Dec 11 12:22:18 rpmi: libgfortran5-devel-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:18 rpmi: gcc-c++-common-1.4.20-alt1 1432315196 installed
<13>Dec 11 12:22:18 rpmi: libstdc++5-devel-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:18 rpmi: libgraphite2-1.2.4-alt1 1393325247 installed
<13>Dec 11 12:22:18 rpmi: libtinfo-devel-5.9-alt7 1442415999 installed
<13>Dec 11 12:22:18 rpmi: libncurses-devel-5.9-alt7 1442415999 installed
<13>Dec 11 12:22:18 rpmi: python-modules-curses-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:18 rpmi: libverto-0.2.6-alt1_5 1442994337 installed
<13>Dec 11 12:22:18 rpmi: libkeyutils-1.5.9-alt1 1398435624 installed
<13>Dec 11 12:22:18 rpmi: libcom_err-1.42.13-alt2 1449075846 installed
<13>Dec 11 12:22:19 rpmi: gcc5-c++-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:19 rpmi: gcc5-fortran-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:19 rpmi: libicu-devel-1:5.1.1-alt3 1368393235 installed
<13>Dec 11 12:22:19 rpmi: libXmu-devel-1.1.2-alt1 1391072528 installed
<13>Dec 11 12:22:19 rpmi: liblapack-devel-1:3.5.0-alt1 1401382194 installed
<13>Dec 11 12:22:19 rpmi: libpcre-devel-8.38-alt1 1448366677 installed
<13>Dec 11 12:22:19 rpmi: libtiff-devel-4.0.3-alt1 1348347498 installed
<13>Dec 11 12:22:19 rpmi: libjpeg-devel-2:1.3.1-alt0.1 1388074033 installed
<13>Dec 11 12:22:19 rpmi: libreadline-devel-6.3.8-alt1 1418911064 installed
<13>Dec 11 12:22:19 rpmi: bzlib-devel-1:1.0.6-alt4 1449156902 installed
<13>Dec 11 12:22:19 rpmi: liblzma-devel-5.0.7-alt1 1416090478 installed
<13>Dec 11 12:22:20 rpmi: texlive-base-bin-2008.0-alt0.15.6 1449446882 installed
<13>Dec 11 12:22:21 rpmi: texlive-base-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:22 rpmi: texlive-latex-base-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:22 rpmi: texlive-font-utils-2008.0-alt0.15.6 1449446882 installed
<13>Dec 11 12:22:22 rpmi: perl-Pod-Usage-1.67-alt2 1445108310 installed
<13>Dec 11 12:22:23 rpmi: libssl10-1.0.1k-alt4 1436449862 installed
<13>Dec 11 12:22:23 rpmi: perl-Unicode-Normalize-1:5.22.0-alt2 1448833096 installed
<13>Dec 11 12:22:23 rpmi: libharfbuzz-1.1.1-alt1 1448577010 installed
<13>Dec 11 12:22:23 rpmi: libfreetype-2.6-alt1 1433953073 installed
<13>Dec 11 12:22:23 rpmi: fontconfig-2.11.1-alt4 1447161344 installed
Updating fonts cache: <29>Dec 11 12:22:24 fontconfig: Updating fonts cache: succeeded
[ DONE ]
<13>Dec 11 12:22:24 rpmi: libXft-2.3.2-alt1 1409902650 installed
<13>Dec 11 12:22:24 rpmi: libfreetype-devel-2.6-alt1 1433953073 installed
<13>Dec 11 12:22:24 rpmi: fontconfig-devel-2.11.1-alt4 1447161344 installed
<13>Dec 11 12:22:24 rpmi: libcairo-1:1.14.4-alt1 1447005495 installed
<13>Dec 11 12:22:24 rpmi: libkrb5-1.13.2-alt2 1447670694 installed
<13>Dec 11 12:22:24 rpmi: libcups-2.1.0-alt1 1447854832 installed
<13>Dec 11 12:22:24 rpmi: libgs-9.16-alt1 1444660003 installed
<13>Dec 11 12:22:24 rpmi: libcairo-devel-1:1.14.4-alt1 1447005495 installed
<13>Dec 11 12:22:24 rpmi: libpango-1.38.1-alt1 1444685285 installed
<13>Dec 11 12:22:24 rpmi: libXft-devel-2.3.2-alt1 1409902650 installed
<13>Dec 11 12:22:24 rpmi: libtk-8.5.9-alt3 1308047279 installed
<13>Dec 11 12:22:24 rpmi: tk-8.5.9-alt3 1308047279 installed
<13>Dec 11 12:22:24 rpmi: perl-Tk-804.033-alt1.1 1448484960 installed
<13>Dec 11 12:22:24 rpmi: fonts-type1-urw-3:1.0.7pre44-alt2 1419342366 installed
<13>Dec 11 12:22:25 rpmi: makeinfo-6.0-alt2 1449157524 installed
<13>Dec 11 12:22:25 rpmi: libcurl-7.46.0-alt1 1449521272 installed
<13>Dec 11 12:22:25 rpmi: libpoppler57-0.38.0-alt1 1449158942 installed
<13>Dec 11 12:22:25 rpmi: poppler-0.38.0-alt1 1449158942 installed
<13>Dec 11 12:22:25 rpmi: texlive-latex3-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:25 rpmi: texlive-lang-tibetan-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:25 rpmi: texlive-lang-polish-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:25 rpmi: texmf-latex-tipa-1.3-alt4 1246545601 installed
<13>Dec 11 12:22:25 rpmi: texlive-generic-extra-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:25 rpmi: perl-podlators-4.03-alt1 1449507577 installed
<13>Dec 11 12:22:25 rpmi: perl-unicore-1:5.22.0-alt2 1448833189 installed
<13>Dec 11 12:22:25 rpmi: texinfo-6.0-alt2 1449157516 installed
<13>Dec 11 12:22:25 rpmi: tk-devel-8.5.9-alt3 1308047279 installed
<13>Dec 11 12:22:25 rpmi: python-modules-compiler-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: ghostscript-common-9.16-alt1 1444660041 installed
<13>Dec 11 12:22:26 rpmi: ghostscript-classic-9.16-alt1 1444660003 installed
<13>Dec 11 12:22:26 rpmi: latex2html-2008-alt1 1244296992 installed
<13>Dec 11 12:22:26 rpmi: python-modules-email-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-unittest-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-xml-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-encodings-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-hotshot-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-bsddb-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-ctypes-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-multiprocessing-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-logging-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-dev-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: glib2-devel-2.46.2-alt1 1446853786 installed
<13>Dec 11 12:22:26 rpmi: libpango-devel-1.38.1-alt1 1444685285 installed
<13>Dec 11 12:22:29 rpmi: texlive-fonts-recommended-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:36 rpmi: texlive-latex-recommended-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:36 rpmi: texlive-generic-recommended-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:36 rpmi: texlive-math-extra-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:36 rpmi: texlive-lang-french-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:37 rpmi: texlive-extra-utils-2008.0-alt0.15.6 1449446882 installed
<13>Dec 11 12:22:37 rpmi: texlive-lang-german-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:37 rpmi: texlive-lang-cyrillic-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:37 rpmi: texmf-latex-xcolor-2.06-alt3 1244802289 installed
<13>Dec 11 12:22:38 rpmi: texmf-pgf-3.0.1-alt1 1439012888 installed
<13>Dec 11 12:22:43 rpmi: texlive-fonts-extra-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:50 rpmi: texlive-pstricks-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:50 rpmi: texlive-games-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:50 rpmi: texmf-latex-obsolete-0.1-alt1 1244748792 installed
<13>Dec 11 12:22:51 rpmi: texlive-lang-arab-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:51 rpmi: texlive-xetex-2008.0-alt0.15.6 1449446882 installed
<13>Dec 11 12:22:51 rpmi: texmf-latex-beamer-3.36-alt3 1445751824 installed
<13>Dec 11 12:22:53 rpmi: texlive-publishers-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:53 rpmi: texlive-pictures-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:54 rpmi: texlive-science-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:54 rpmi: texlive-humanities-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:23:00 rpmi: texlive-latex-extra-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:23:01 rpmi: texlive-bibtex-extra-2008.0-alt0.16 1300008623 installed
Building target platforms: x86_64
Building for target x86_64
Wrote: /usr/src/in/srpm/R-base-3.1.2-alt1.1.src.rpm
Installing R-base-3.1.2-alt1.1.src.rpm
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.13082
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ rm -rf R-3.1.2
+ echo 'Source #0 (R-3.1.2.tar):'
Source #0 (R-3.1.2.tar):
+ /bin/tar -xf /usr/src/RPM/SOURCES/R-3.1.2.tar
+ cd R-3.1.2
+ /bin/chmod -c -Rf u+rwX,go-w .
+ echo 'Patch #0 (R-3.1.2-alt1.1.patch):'
Patch #0 (R-3.1.2-alt1.1.patch):
+ /usr/bin/patch -p1
patching file .gear/rules
patching file .gear/tags/15fa18936deccebb8baa76357c7a902b06205ce0
patching file .gear/tags/a3506a8419eb2903e6d3ce37c465295a254fd1d5
patching file .gear/tags/c7dc0028771e7098f72fe8ac9e9575451d4fb020
patching file .gear/tags/list
patching file R-base.spec
patching file src/extra/blas/Makefile.in
patching file src/extra/bzip2/Makefile.in
patching file src/extra/pcre/Makefile.in
patching file src/extra/xdr/Makefile.in
patching file src/extra/zlib/Makefile.in
+ rm src/extra/zlib/adler32.c src/extra/zlib/compress.c src/extra/zlib/crc32.c src/extra/zlib/crc32.h src/extra/zlib/deflate.c src/extra/zlib/deflate.h src/extra/zlib/infback.c src/extra/zlib/inffast.c src/extra/zlib/inffast.h src/extra/zlib/inffixed.h src/extra/zlib/inflate.c src/extra/zlib/inflate.h src/extra/zlib/inftrees.c src/extra/zlib/inftrees.h src/extra/zlib/trees.c src/extra/zlib/trees.h src/extra/zlib/uncompr.c src/extra/zlib/zconf.h src/extra/zlib/zlib.h src/extra/zlib/zutil.c src/extra/zlib/zutil.h src/extra/bzip2/blocksort.c src/extra/bzip2/bzcompress.c src/extra/bzip2/bzlib.c src/extra/bzip2/bzlib.h src/extra/bzip2/bzlib_private.h src/extra/bzip2/crctable.c src/extra/bzip2/decompress.c src/extra/bzip2/huffman.c src/extra/bzip2/randtable.c src/extra/pcre/pcre.h src/extra/pcre/pcre_chartables.c src/extra/pcre/pcre_compile.c src/extra/pcre/pcre_config.c src/extra/pcre/pcre_exec.c src/extra/pcre/pcre_fullinfo.c src/extra/pcre/pcre_get.c src/extra/pcre/pcre_globals.c src/extra/pcre/pcre_internal.h src/extra/pcre/pcre_jit_compile.c src/extra/pcre/pcre_maketables.c src/extra/pcre/pcre_newline.c src/extra/pcre/pcre_ord2utf8.c src/extra/pcre/pcre_refcount.c src/extra/pcre/pcre_study.c src/extra/pcre/pcre_tables.c src/extra/pcre/pcre_ucd.c src/extra/pcre/pcre_valid_utf8.c src/extra/pcre/pcre_version.c src/extra/pcre/pcre_xclass.c src/extra/pcre/ucp.h
+ rm src/extra/xz/api/lzma.h src/extra/xz/check/check.c src/extra/xz/check/check.h src/extra/xz/check/crc32_fast.c src/extra/xz/check/crc32_small.c src/extra/xz/check/crc32_table.c src/extra/xz/check/crc32_table_be.h src/extra/xz/check/crc32_table_le.h src/extra/xz/check/crc32_tablegen.c src/extra/xz/check/crc64_fast.c src/extra/xz/check/crc64_small.c src/extra/xz/check/crc64_table.c src/extra/xz/check/crc64_table_be.h src/extra/xz/check/crc64_table_le.h src/extra/xz/check/crc64_tablegen.c src/extra/xz/check/crc_macros.h src/extra/xz/check/sha256.c src/extra/xz/common/alone_decoder.c src/extra/xz/common/alone_decoder.h src/extra/xz/common/alone_encoder.c src/extra/xz/common/auto_decoder.c src/extra/xz/common/block_buffer_decoder.c src/extra/xz/common/block_buffer_encoder.c src/extra/xz/common/block_decoder.c src/extra/xz/common/block_decoder.h src/extra/xz/common/block_encoder.c src/extra/xz/common/block_encoder.h src/extra/xz/common/block_header_decoder.c src/extra/xz/common/block_header_encoder.c src/extra/xz/common/block_util.c src/extra/xz/common/bsr.h src/extra/xz/common/bswap.h src/extra/xz/common/common.c src/extra/xz/common/common.h src/extra/xz/common/easy_buffer_encoder.c src/extra/xz/common/easy_decoder_memusage.c src/extra/xz/common/easy_encoder.c src/extra/xz/common/easy_encoder_memusage.c src/extra/xz/common/easy_preset.c src/extra/xz/common/easy_preset.h src/extra/xz/common/filter_buffer_decoder.c src/extra/xz/common/filter_buffer_encoder.c src/extra/xz/common/filter_common.c src/extra/xz/common/filter_common.h src/extra/xz/common/filter_decoder.c src/extra/xz/common/filter_decoder.h src/extra/xz/common/filter_encoder.c src/extra/xz/common/filter_encoder.h src/extra/xz/common/filter_flags_decoder.c src/extra/xz/common/filter_flags_encoder.c src/extra/xz/common/index.c src/extra/xz/common/index.h src/extra/xz/common/index_decoder.c src/extra/xz/common/index_encoder.c src/extra/xz/common/index_encoder.h src/extra/xz/common/index_hash.c src/extra/xz/common/local.h src/extra/xz/common/mythread.h src/extra/xz/common/stream_buffer_decoder.c src/extra/xz/common/stream_buffer_encoder.c src/extra/xz/common/stream_decoder.c src/extra/xz/common/stream_decoder.h src/extra/xz/common/stream_encoder.c src/extra/xz/common/stream_encoder.h src/extra/xz/common/stream_flags_common.c src/extra/xz/common/stream_flags_common.h src/extra/xz/common/stream_flags_decoder.c src/extra/xz/common/stream_flags_encoder.c src/extra/xz/common/sysdefs.h src/extra/xz/common/tuklib_common.h src/extra/xz/common/tuklib_config.h src/extra/xz/common/tuklib_integer.h src/extra/xz/common/vli_decoder.c src/extra/xz/common/vli_encoder.c src/extra/xz/common/vli_size.c src/extra/xz/delta/delta_common.c src/extra/xz/delta/delta_common.h src/extra/xz/delta/delta_decoder.c src/extra/xz/delta/delta_decoder.h src/extra/xz/delta/delta_encoder.c src/extra/xz/delta/delta_encoder.h src/extra/xz/delta/delta_private.h src/extra/xz/lz/lz_decoder.c src/extra/xz/lz/lz_decoder.h src/extra/xz/lz/lz_encoder.c src/extra/xz/lz/lz_encoder.h src/extra/xz/lz/lz_encoder_hash.h src/extra/xz/lz/lz_encoder_hash_table.h src/extra/xz/lz/lz_encoder_mf.c src/extra/xz/lzma/fastpos.h src/extra/xz/lzma/fastpos_table.c src/extra/xz/lzma/fastpos_tablegen.c src/extra/xz/lzma/lzma2_decoder.c src/extra/xz/lzma/lzma2_decoder.h src/extra/xz/lzma/lzma2_encoder.c src/extra/xz/lzma/lzma2_encoder.h src/extra/xz/lzma/lzma_common.h src/extra/xz/lzma/lzma_decoder.c src/extra/xz/lzma/lzma_decoder.h src/extra/xz/lzma/lzma_encoder.c src/extra/xz/lzma/lzma_encoder.h src/extra/xz/lzma/lzma_encoder_optimum_fast.c src/extra/xz/lzma/lzma_encoder_optimum_normal.c src/extra/xz/lzma/lzma_encoder_presets.c src/extra/xz/lzma/lzma_encoder_private.h src/extra/xz/rangecoder/price.h src/extra/xz/rangecoder/price_table.c src/extra/xz/rangecoder/price_tablegen.c src/extra/xz/rangecoder/range_common.h src/extra/xz/rangecoder/range_decoder.h src/extra/xz/rangecoder/range_encoder.h src/extra/xz/simple/arm.c src/extra/xz/simple/armthumb.c src/extra/xz/simple/ia64.c src/extra/xz/simple/powerpc.c src/extra/xz/simple/simple_coder.c src/extra/xz/simple/simple_coder.h src/extra/xz/simple/simple_decoder.c src/extra/xz/simple/simple_decoder.h src/extra/xz/simple/simple_encoder.c src/extra/xz/simple/simple_encoder.h src/extra/xz/simple/simple_private.h src/extra/xz/simple/sparc.c src/extra/xz/simple/x86.c
+ rm src/extra/blas/blas.f src/extra/blas/cmplxblas.f src/modules/lapack/cmplx.f src/modules/lapack/dlamch.f src/modules/lapack/dlapack.f src/modules/lapack/vecLibg95f.f
+ exit 0
Executing(%build): /bin/sh -e /usr/src/tmp/rpm-tmp.13082
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.1.2
+ export lt_cv_prog_cc_static_works=no ac_cv_path_R_ZIPCMD=zip ac_cv_path_R_UNZIPCMD=unzip ac_cv_path_R_BROWSER=firefox ac_cv_path_R_PDFVIEWER=evince 'ac_cv_path_PAGER=less -isR' ac_cv_prog_R_PRINTCMD=lpr
+ lt_cv_prog_cc_static_works=no
+ ac_cv_path_R_ZIPCMD=zip
+ ac_cv_path_R_UNZIPCMD=unzip
+ ac_cv_path_R_BROWSER=firefox
+ ac_cv_path_R_PDFVIEWER=evince
+ ac_cv_path_PAGER='less -isR'
+ ac_cv_prog_R_PRINTCMD=lpr
+ CFLAGS='-pipe -Wall -g -O2 -fno-strict-aliasing'
+ export CFLAGS
+ CXXFLAGS='-pipe -Wall -g -O2 -fno-strict-aliasing'
+ export CXXFLAGS
+ FFLAGS='-pipe -Wall -g -O2 -fno-strict-aliasing'
+ export FFLAGS
+ '[' -n '' ']'
++ printf %s '-pipe -Wall -g -O2 -fno-strict-aliasing'
++ sed -r 's/(^|[[:space:]]+)-[^m][^[:space:]]*//g'
+ ASFLAGS=
+ export ASFLAGS
+ export lt_cv_deplibs_check_method=pass_all
+ lt_cv_deplibs_check_method=pass_all
+ readlink -e -- ./configure
+ xargs -ri dirname -- '{}'
+ xargs -ri find '{}' -type f '(' -name config.sub -or -name config.guess ')' -printf '%h/\n'
+ xargs -rn1 install -pm755 -- /usr/share/gnu-config/config.sub /usr/share/gnu-config/config.guess
+ sort -u
+ ./configure --build=x86_64-alt-linux --host=x86_64-alt-linux --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/lib --localstatedir=/var/lib --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --disable-dependency-tracking --without-included-gettext --enable-prebuilt-html --enable-R-shlib --with-x --with-system-zlib --with-system-bzlib --with-system-pcre --with-system-xz --with-blas=openblas --with-lapack=lapack --with-tcl-config=/usr/lib64/tclConfig.sh --with-tk-config=/usr/lib64/tkConfig.sh '--libdir=${prefix}/lib64' 'rincludedir=${prefix}/include/R' 'rdocdir=${prefix}/share/doc/R-3.1'
configure: WARNING: unrecognized options: --disable-dependency-tracking
checking build system type... x86_64-alt-linux-gnu
checking host system type... x86_64-alt-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
checking for working autoheader... found
checking for gawk... gawk
checking whether ln -s works... yes
checking for bison... bison -y
checking for ar... ar
checking for a BSD-compatible install... /bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... (cached) less -isR
checking for gtar... /usr/bin/gtar
checking for tex... /usr/bin/tex
checking for pdftex... /usr/bin/pdftex
checking for pdflatex... /usr/bin/pdflatex
checking for makeindex... /usr/bin/makeindex
checking for makeinfo... /usr/bin/makeinfo
checking whether makeinfo version is at least 4.7... no
checking for ginstall-info... no
checking for install-info... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... /usr/bin/kpsewhich
checking for latex inconsolata package... missing
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
checking for unzip... (cached) unzip
checking for zip... (cached) zip
checking for gzip... /bin/gzip
checking for bzip2... /bin/bzip2
checking for firefox... (cached) firefox
using default browser ... firefox
checking for acroread... (cached) evince
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-alt-linux-gcc accepts -g... yes
checking for x86_64-alt-linux-gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... x86_64-alt-linux-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether x86_64-alt-linux-gcc needs -traditional... no
checking how to run the C preprocessor... x86_64-alt-linux-gcc -E
checking for f95... f95
checking for x86_64-alt-linux-g77... (cached) f95
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether f95 accepts -g... yes
checking for x86_64-alt-linux-g++... x86_64-alt-linux-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-alt-linux-g++ accepts -g... yes
checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether x86_64-alt-linux-gcc accepts -fvisibility... yes
checking whether f95 accepts -fvisibility... yes
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc
checking whether we are using the GNU Objective C compiler... no
checking whether x86_64-alt-linux-gcc accepts -g... no
checking for Objective C++ compiler... trying some possibilities
checking whether x86_64-alt-linux-g++ can compile ObjC++... no
no working ObjC++ compiler found
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for x86_64-alt-linux-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... (cached) pass_all
checking for x86_64-alt-linux-ar... (cached) ar
checking for x86_64-alt-linux-strip... no
checking for strip... strip
checking for x86_64-alt-linux-ranlib... no
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from x86_64-alt-linux-gcc object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether x86_64-alt-linux-g++ accepts -g... (cached) yes
checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E
checking for x86_64-alt-linux-g77... (cached) f95
checking whether we are using the GNU Fortran 77 compiler... (cached) yes
checking whether f95 accepts -g... (cached) yes
checking for objdir... .libs
checking if x86_64-alt-linux-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-alt-linux-gcc option to produce PIC... -fPIC -DPIC
checking if x86_64-alt-linux-gcc PIC flag -fPIC -DPIC works... yes
checking if x86_64-alt-linux-gcc static flag -static works... no
checking if x86_64-alt-linux-gcc supports -c -o file.o... yes
checking if x86_64-alt-linux-gcc supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by x86_64-alt-linux-g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for x86_64-alt-linux-g++ option to produce PIC... -fPIC -DPIC
checking if x86_64-alt-linux-g++ PIC flag -fPIC -DPIC works... yes
checking if x86_64-alt-linux-g++ static flag -static works... no
checking if x86_64-alt-linux-g++ supports -c -o file.o... yes
checking if x86_64-alt-linux-g++ supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for f95 option to produce PIC... -fPIC
checking if f95 PIC flag -fPIC works... yes
checking if f95 static flag -static works... no
checking if f95 supports -c -o file.o... yes
checking if f95 supports -c -o file.o... (cached) yes
checking whether the f95 linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking whether rl_completion_matches exists and is declared... yes
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for sys/wait.h that is POSIX.1 compatible... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking dl.h usability... no
checking dl.h presence... no
checking for dl.h... no
checking for dlfcn.h... (cached) yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking floatingpoint.h usability... no
checking floatingpoint.h presence... no
checking for floatingpoint.h... no
checking fpu_control.h usability... yes
checking fpu_control.h presence... yes
checking for fpu_control.h... yes
checking glob.h usability... yes
checking glob.h presence... yes
checking for glob.h... yes
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking for strings.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
checking for utime.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for GNU C library with version >= 2... yes
checking return type of signal handlers... void
checking for uint64_t... yes
checking for int64_t... yes
checking for int_fast64_t... yes
checking for pid_t... yes
checking for size_t... yes
checking whether SIZE_MAX is declared... yes
checking for blkcnt_t... yes
checking for type of socket length... socklen_t *
checking for stack_t... yes
checking for intptr_t... yes
checking for uintptr_t... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for x86_64-alt-linux-gcc option to accept ISO C99... none needed
checking for x86_64-alt-linux-gcc option to accept ISO Standard C... (cached) none needed
checking for inline... inline
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of double... 8
checking size of size_t... 8
checking size of long double... 16
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether x86_64-alt-linux-gcc supports -c -o FILE.lo... yes
checking for x86_64-alt-linux-gcc option to support OpenMP... unsupported
checking how to get verbose linking output from f95... -v
checking for Fortran 77 libraries of f95... -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../.. -lgfortran -lm -lquadmath
checking how to get verbose linking output from x86_64-alt-linux-gcc... -v
checking for C libraries of x86_64-alt-linux-gcc... -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../.. -lgcc_s
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking whether f95 appends underscores to external names... yes
checking whether f95 appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether f95 and x86_64-alt-linux-gcc agree on int and double... yes
checking whether f95 and x86_64-alt-linux-gcc agree on double complex... yes
checking for f95 option to support OpenMP... unsupported
checking whether x86_64-alt-linux-g++ accepts -M for generating dependencies... yes
checking for x86_64-alt-linux-g++ option to support OpenMP... unsupported
checking whether we can compute ObjC Make dependencies... no
checking for ObjC runtime library...
checking whether x86_64-alt-linux-gcc accepts -fobjc-exceptions... no
checking whether C runtime needs -D__NO_MATH_INLINES... no
checking for xmkmf... no
checking whether x86_64-alt-linux-g++ supports C++11 features by default... no
checking whether x86_64-alt-linux-g++ supports C++11 features with -std=c++11... yes
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
checking whether expm1 exists and is declared... yes
checking whether hypot exists and is declared... yes
checking whether log1p exists and is declared... yes
checking whether log1pl exists and is declared... yes
checking whether log2 exists and is declared... yes
checking whether log10 exists and is declared... yes
checking whether nearbyint exists and is declared... yes
checking whether nearbyintl exists and is declared... yes
checking whether powl exists and is declared... yes
checking whether rint exists and is declared... yes
checking whether rintl exists and is declared... yes
checking whether va_copy exists and is declared... yes
checking for isblank... yes
checking sunmath.h usability... no
checking sunmath.h presence... no
checking for sunmath.h... no
checking for cospi in -lsunmath... no
checking for atanpi... no
checking for atan2pi... no
checking for cospi... no
checking for exp10... yes
checking for pown... no
checking for sinpi... no
checking for tanpi... no
checking for fseeko... yes
checking for ftello... yes
checking for matherr... yes
checking whether fcntl exists and is declared... yes
checking whether getgrgid exists and is declared... yes
checking whether getpwuid exists and is declared... yes
checking whether kill exists and is declared... yes
checking whether sigaction exists and is declared... yes
checking whether sigaltstack exists and is declared... yes
checking whether sigemptyset exists and is declared... yes
checking whether fdopen exists and is declared... yes
checking whether popen exists and is declared... yes
checking whether setenv exists and is declared... yes
checking whether unsetenv exists and is declared... yes
checking whether getrlimit exists and is declared... yes
checking whether getrusage exists and is declared... yes
checking whether getpriority exists and is declared... yes
checking whether chmod exists and is declared... yes
checking whether mkfifo exists and is declared... yes
checking whether stat exists and is declared... yes
checking whether umask exists and is declared... yes
checking whether gettimeofday exists and is declared... yes
checking whether utimes exists and is declared... yes
checking whether times exists and is declared... yes
checking whether gmtime_r exists and is declared... yes
checking whether localtime_r exists and is declared... yes
checking whether nl_langinfo exists and is declared... yes
checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether execv exists and is declared... yes
checking whether ftruncate exists and is declared... yes
checking whether getcwd exists and is declared... yes
checking whether geteuid exists and is declared... yes
checking whether getuid exists and is declared... yes
checking whether link exists and is declared... yes
checking whether readlink exists and is declared... yes
checking whether symlink exists and is declared... yes
checking whether sysconf exists and is declared... yes
checking whether sched_setaffinity exists and is declared... yes
checking whether sched_getaffinity exists and is declared... yes
checking whether utime exists and is declared... yes
checking for clock_gettime in -lrt... yes
checking whether clock_gettime exists and is declared... yes
checking whether timespec_get exists and is declared... yes
checking for putenv... yes
checking whether putenv is declared... yes
checking for vasprintf... yes
checking whether vasprintf is declared... yes
checking for mempcpy... yes
checking for realpath... yes
checking whether realpath is declared... yes
checking whether glob exists and is declared... yes
checking for isnan... yes
checking whether isfinite is declared... yes
checking whether isnan is declared... yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking whether putenv("FOO") can unset an environment variable... yes
checking whether putenv("FOO=") can unset an environment variable... no
checking for nl_langinfo and CODESET... yes
checking for mkdtemp... yes
checking for strdup... yes
checking for strncasecmp... yes
checking whether mkdtemp is declared... yes
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for library containing xdr_string... none required
checking for __setfpucw... no
checking for working calloc... yes
checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether mktime sets errno... yes
checking whether mktime works correctly outside 1902-2037... yes
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
checking whether carg exists and is declared... yes
checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
checking whether cacos exists and is declared... yes
checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
checking whether ctanh exists and is declared... yes
checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for cblas_cdotu_sub in Accelerate framework... no
checking for dgemm_ in -lopenblas... yes
checking whether double complex BLAS can be used... yes
checking whether the BLAS is complete... yes
checking for dpstrf_... no
checking for dpstrf_ in -llapack... yes
checking iconv.h usability... yes
checking iconv.h presence... yes
checking for iconv.h... yes
checking for iconv... yes
checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
checking for iconvlist... no
checking for iconv... yes
checking for iconv declaration...
extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking wctype.h usability... yes
checking wctype.h presence... yes
checking for wctype.h... yes
checking whether mbrtowc exists and is declared... yes
checking whether wcrtomb exists and is declared... yes
checking whether wcscoll exists and is declared... yes
checking whether wcsftime exists and is declared... yes
checking whether wcstod exists and is declared... yes
checking whether mbstowcs exists and is declared... yes
checking whether wcstombs exists and is declared... yes
checking whether wctrans exists and is declared... yes
checking whether iswblank exists and is declared... yes
checking whether wctype exists and is declared... yes
checking whether iswctype exists and is declared... yes
checking for wctrans_t... yes
checking for mbstate_t... yes
checking for ICU... yes
checking for X... libraries , headers
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... yes
checking for X11/Intrinsic.h... yes
checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
checking for KeySym... yes
checking X11/Xmu/Atoms.h usability... yes
checking X11/Xmu/Atoms.h presence... yes
checking for X11/Xmu/Atoms.h... yes
checking for XmuInternAtom in -lXmu... yes
checking whether pkg-config knows about cairo and pango... yes
checking whether cairo including pango is >= 1.2 and works... yes
checking for /usr/lib64/tclConfig.sh... /usr/lib64/tclConfig.sh
checking for /usr/lib64/tkConfig.sh... /usr/lib64/tkConfig.sh
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
checking tk.h usability... yes
checking tk.h presence... yes
checking for tk.h... yes
checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking if jpeglib version >= 6b... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking for main in -lz... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... yes
checking tiffio.h usability... yes
checking tiffio.h presence... yes
checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking rpc/types.h usability... yes
checking rpc/types.h presence... yes
checking for rpc/types.h... yes
checking for rpc/xdr.h... yes
checking for XDR support... yes
checking for inflateInit2_ in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... yes
checking whether zlib support needs to be compiled... no
checking for BZ2_bzlibVersion in -lbz2... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking if bzip2 version >= 1.0.6... yes
checking whether bzip2 support needs to be compiled... no
checking for lzma_version_number in -llzma... yes
checking lzma.h usability... yes
checking lzma.h presence... yes
checking for lzma.h... yes
checking if lzma version >= 5.0.3... yes
checking for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... no
checking pcre.h presence... no
checking for pcre.h... no
checking pcre/pcre.h usability... yes
checking pcre/pcre.h presence... yes
checking for pcre/pcre.h... yes
checking if PCRE version >= 8.10... yes
checking whether PCRE support needs to be compiled... no
checking whether leap seconds are treated according to POSIX... yes
checking for inline... inline
checking for sys/time.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for struct stat.st_atim.tv_nsec... yes
checking whether struct stat.st_atim is of type struct timespec... yes
checking for setitimer... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether KERN_USRSTACK sysctl is supported... no
checking for visible __lib_stack_end... yes
checking for lpr... (cached) lpr
checking for paperconf... /usr/bin/paperconf
checking for x86_64-alt-linux-gfortran... x86_64-alt-linux-gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether x86_64-alt-linux-gfortran accepts -g... yes
checking for x86_64-alt-linux-gfortran... (cached) x86_64-alt-linux-gfortran
checking whether we are using the GNU Fortran compiler... (cached) yes
checking whether x86_64-alt-linux-gfortran accepts -g... (cached) yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for x86_64-alt-linux-gfortran option to produce PIC... -fPIC
checking if x86_64-alt-linux-gfortran PIC flag -fPIC works... yes
checking if x86_64-alt-linux-gfortran static flag -static works... no
checking if x86_64-alt-linux-gfortran supports -c -o file.o... yes
checking if x86_64-alt-linux-gfortran supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-gfortran linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... none
checking for x86_64-alt-linux-gfortran option to support OpenMP... unsupported
checking for recommended packages... yes
checking whether NLS is requested... yes
Configuring src/extra/intl directory
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether we are using the GNU C Library 2 or newer... yes
checking for x86_64-alt-linux-ranlib... ranlib
checking for simple visibility declarations... yes
checking for stdint.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... yes
checking for inttypes.h... yes
checking for unsigned long long int... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking whether imported symbols can be declared weak... yes
checking for multithread API to use... none
checking argz.h usability... yes
checking argz.h presence... yes
checking for argz.h... yes
checking for inttypes.h... (cached) yes
checking for limits.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getcwd... yes
checking for getegid... yes
checking for geteuid... yes
checking for getgid... yes
checking for getuid... yes
checking for mempcpy... (cached) yes
checking for munmap... yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strdup... (cached) yes
checking for strtoul... yes
checking for tsearch... yes
checking for argz_count... yes
checking for argz_stringify... yes
checking for argz_next... yes
checking for __fsetlocking... yes
checking whether feof_unlocked is declared... yes
checking whether fgets_unlocked is declared... yes
checking for iconv... (cached) yes
checking for iconv declaration... (cached)
extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for NL_LOCALE_NAME macro... yes
checking for bison... bison
checking version of bison... 3.0.4.0.14.8, ok
checking for long long int... yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for intmax_t... yes
checking whether printf() supports POSIX/XSI format strings... yes
checking whether we are using the GNU C Library 2.1 or newer... yes
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
checking for CFPreferencesCopyAppValue... no
checking for CFLocaleCopyCurrent... no
checking for ptrdiff_t... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for asprintf... yes
checking for fwprintf... yes
checking for putenv... (cached) yes
checking for setenv... yes
checking for setlocale... yes
checking for snprintf... yes
checking for wcslen... yes
checking whether _snprintf is declared... no
checking whether _snwprintf is declared... no
checking whether getc_unlocked is declared... yes
checking for nl_langinfo and CODESET... (cached) yes
checking for LC_MESSAGES... yes
checking for shared library run path origin... done
checking for CFPreferencesCopyAppValue... (cached) no
checking for CFLocaleCopyCurrent... (cached) no
checking whether included gettext is requested... no
checking for GNU gettext in libc... yes
checking whether to use NLS... yes
checking where the gettext function comes from... libc
Finished configuring src/extra/intl directory
using as R_SHELL for scripts ... /bin/sh
configure: creating ./config.status
config.status: creating Makeconf
config.status: creating Makefile
config.status: creating doc/Makefile
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configure: WARNING: unrecognized options: --disable-dependency-tracking
R is now configured for x86_64-alt-linux-gnu
Source directory: .
Installation directory: /usr
C compiler: x86_64-alt-linux-gcc -pipe -Wall -g -O2 -fno-strict-aliasing
Fortran 77 compiler: f95 -pipe -Wall -g -O2 -fno-strict-aliasing
C++ compiler: x86_64-alt-linux-g++ -pipe -Wall -g -O2 -fno-strict-aliasing
C++ 11 compiler: x86_64-alt-linux-g++ -std=c++11 -pipe -Wall -g -O2 -fno-strict-aliasing
Fortran 90/95 compiler: x86_64-alt-linux-gfortran -g -O2
Obj-C compiler: x86_64-alt-linux-gcc
Interfaces supported: X11, tcltk
External libraries: readline, BLAS(OpenBLAS), LAPACK(generic), lzma
Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
Options enabled: shared R library, R profiling, static HTML
Capabilities skipped:
Options not enabled: shared BLAS, memory profiling
Recommended packages: yes
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
+ '[' -n '' ']'
+ NPROCS=4
+ make -j4
make: Entering directory `/usr/src/RPM/BUILD/R-3.1.2'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/m4'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/m4'
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make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tools'
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make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/html'
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make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/share'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
creating src/scripts/R.fe
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
mkdir -p -- ../../bin
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/include'
mkdir -p -- ../../include
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/include/R_ext'
mkdir -p -- ../../../include/R_ext
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/include/R_ext'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/include'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
making regcomp.d from regcomp.c
making regerror.d from regerror.c
making regexec.d from regexec.c
making tre-ast.d from tre-ast.c
making tre-compile.d from tre-compile.c
making tre-match-approx.d from tre-match-approx.c
making tre-match-backtrack.d from tre-match-backtrack.c
making tre-match-parallel.d from tre-match-parallel.c
making tre-mem.d from tre-mem.c
making tre-stack.d from tre-stack.c
making tre-parse.d from tre-parse.c
making xmalloc.d from xmalloc.c
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regcomp.c -o regcomp.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regerror.c -o regerror.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regexec.c -o regexec.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-ast.c -o tre-ast.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-compile.c -o tre-compile.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-mem.c -o tre-mem.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-parse.c -o tre-parse.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-stack.c -o tre-stack.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c xmalloc.c -o xmalloc.o
rm -f libtre.a
ar cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o
ranlib libtre.a
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
making integrate.d from integrate.c
making interv.d from interv.c
making maxcol.d from maxcol.c
making optim.d from optim.c
making pretty.d from pretty.c
making uncmin.d from uncmin.c
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c integrate.c -o integrate.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c interv.c -o interv.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c maxcol.c -o maxcol.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c optim.c -o optim.o
In file included from /usr/include/math.h:26:0,
from ../../src/include/R_ext/Arith.h:37,
from maxcol.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pretty.c -o pretty.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c uncmin.c -o uncmin.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dchdc.f -o dchdc.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpbfa.f -o dpbfa.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpbsl.f -o dpbsl.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpoco.f -o dpoco.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpodi.f -o dpodi.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpofa.f -o dpofa.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dposl.f -o dposl.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dqrdc.f -o dqrdc.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dqrdc2.f -o dqrdc2.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dqrls.f -o dqrls.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dqrsl.f -o dqrsl.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dqrutl.f -o dqrutl.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dsvdc.f -o dsvdc.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtrco.f -o dtrco.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtrsl.f -o dtrsl.o
rm -f libappl.a
ar cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o
ranlib libappl.a
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making ftrunc.d from ftrunc.c
making fround.d from fround.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making expm1.d from expm1.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making bessel_k.d from bessel_k.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making plnorm.d from plnorm.c
making dlnorm.d from dlnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making rcauchy.d from rcauchy.c
making qcauchy.d from qcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mlutils.c -o mlutils.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c d1mach.c -o d1mach.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c i1mach.c -o i1mach.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fmax2.c -o fmax2.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fmin2.c -o fmin2.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fprec.c -o fprec.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fround.c -o fround.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ftrunc.c -o ftrunc.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sign.c -o sign.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fsign.c -o fsign.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c imax2.c -o imax2.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c imin2.c -o imin2.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chebyshev.c -o chebyshev.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c log1p.c -o log1p.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c expm1.c -o expm1.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lgammacor.c -o lgammacor.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gammalims.c -o gammalims.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stirlerr.c -o stirlerr.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bd0.c -o bd0.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gamma.c -o gamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lgamma.c -o lgamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gamma_cody.c -o gamma_cody.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c beta.c -o beta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lbeta.c -o lbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c polygamma.c -o polygamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cospi.c -o cospi.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bessel_i.c -o bessel_i.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bessel_j.c -o bessel_j.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bessel_k.c -o bessel_k.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bessel_y.c -o bessel_y.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c choose.c -o choose.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c snorm.c -o snorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sexp.c -o sexp.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgamma.c -o dgamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pgamma.c -o pgamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qgamma.c -o qgamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rgamma.c -o rgamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dbeta.c -o dbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pbeta.c -o pbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qbeta.c -o qbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rbeta.c -o rbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dunif.c -o dunif.o
qbeta.c: In function 'Rf_qbeta':
qbeta.c:58:14: warning: variable 'warned' set but not used [-Wunused-but-set-variable]
Rboolean warned = FALSE;
^
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c punif.c -o punif.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qunif.c -o qunif.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c runif.c -o runif.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnorm.c -o dnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnorm.c -o pnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnorm.c -o qnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rnorm.c -o rnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dlnorm.c -o dlnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plnorm.c -o plnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qlnorm.c -o qlnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rlnorm.c -o rlnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c df.c -o df.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pf.c -o pf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qf.c -o qf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rf.c -o rf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnf.c -o dnf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dt.c -o dt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pt.c -o pt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qt.c -o qt.o
dt.c: In function 'Rf_dt':
dt.c:80:44: warning: 'ax' may be used uninitialized in this function [-Wmaybe-uninitialized]
double I_sqrt_ = (lrg_x2n ? sqrt(n)/ax : exp(-l_x2n));
^
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rt.c -o rt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnt.c -o dnt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dchisq.c -o dchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pchisq.c -o pchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qchisq.c -o qchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rchisq.c -o rchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rnchisq.c -o rnchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dbinom.c -o dbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pbinom.c -o pbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qbinom.c -o qbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rbinom.c -o rbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rmultinom.c -o rmultinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dcauchy.c -o dcauchy.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pcauchy.c -o pcauchy.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qcauchy.c -o qcauchy.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rcauchy.c -o rcauchy.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dexp.c -o dexp.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pexp.c -o pexp.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qexp.c -o qexp.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rexp.c -o rexp.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgeom.c -o dgeom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pgeom.c -o pgeom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qgeom.c -o qgeom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rgeom.c -o rgeom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dhyper.c -o dhyper.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c phyper.c -o phyper.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qhyper.c -o qhyper.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rhyper.c -o rhyper.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnbinom.c -o dnbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnbinom.c -o pnbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnbinom.c -o qnbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rnbinom.c -o rnbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpois.c -o dpois.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ppois.c -o ppois.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qpois.c -o qpois.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpois.c -o rpois.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dweibull.c -o dweibull.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pweibull.c -o pweibull.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qweibull.c -o qweibull.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rweibull.c -o rweibull.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dlogis.c -o dlogis.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plogis.c -o plogis.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qlogis.c -o qlogis.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rlogis.c -o rlogis.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnchisq.c -o dnchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnchisq.c -o pnchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnchisq.c -o qnchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnbeta.c -o dnbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnbeta.c -o pnbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnbeta.c -o qnbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnf.c -o pnf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnt.c -o pnt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnf.c -o qnf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnt.c -o qnt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ptukey.c -o ptukey.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qtukey.c -o qtukey.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c toms708.c -o toms708.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c wilcox.c -o wilcox.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c signrank.c -o signrank.o
rm -rf libnmath.a
ar cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o
ranlib libnmath.a
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
config.status: creating src/unix/Makefile
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
making Rembedded.d from Rembedded.c
making dynload.d from dynload.c
making system.d from system.c
making sys-unix.d from sys-unix.c
making sys-std.d from sys-std.c
making X11.d from X11.c
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rembedded.c -o Rembedded.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dynload.c -o dynload.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c system.c -o system.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sys-unix.c -o sys-unix.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sys-std.c -o sys-std.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c X11.c -o X11.o
rm -rf libunix.a
ar cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o
ranlib libunix.a
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -L/usr/local/lib64 -DR_HOME='"/usr/src/RPM/BUILD/R-3.1.2"' \
-o Rscript ./Rscript.c
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
config.status: creating src/main/Makefile
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
making CommandLineArgs.d from CommandLineArgs.c
making Rdynload.d from Rdynload.c
making Renviron.d from Renviron.c
making RNG.d from RNG.c
making agrep.d from agrep.c
making apply.d from apply.c
making arithmetic.d from arithmetic.c
making array.d from array.c
making attrib.d from attrib.c
making bind.d from bind.c
making builtin.d from builtin.c
making character.d from character.c
making coerce.d from coerce.c
making colors.d from colors.c
making complex.d from complex.c
making connections.d from connections.c
making context.d from context.c
making cum.d from cum.c
making dcf.d from dcf.c
making datetime.d from datetime.c
making debug.d from debug.c
making deparse.d from deparse.c
making devices.d from devices.c
making dotcode.d from dotcode.c
making dounzip.d from dounzip.c
making dstruct.d from dstruct.c
making duplicate.d from duplicate.c
making edit.d from edit.c
making engine.d from engine.c
making envir.d from envir.c
making errors.d from errors.c
making eval.d from eval.c
making format.d from format.c
making gevents.d from gevents.c
making gram.d from gram.c
making gram-ex.d from gram-ex.c
making graphics.d from graphics.c
making grep.d from grep.c
making identical.d from identical.c
making inlined.d from inlined.c
making inspect.d from inspect.c
making internet.d from internet.c
making iosupport.d from iosupport.c
making lapack.d from lapack.c
making list.d from list.c
making localecharset.d from localecharset.c
making logic.d from logic.c
making main.d from main.c
making mapply.d from mapply.c
making match.d from match.c
making memory.d from memory.c
making names.d from names.c
making objects.d from objects.c
making options.d from options.c
making paste.d from paste.c
making platform.d from platform.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making plotmath.d from plotmath.c
making print.d from print.c
making printarray.d from printarray.c
making printvector.d from printvector.c
making printutils.d from printutils.c
making qsort.d from qsort.c
making random.d from random.c
making raw.d from raw.c
making registration.d from registration.c
making relop.d from relop.c
making rlocale.d from rlocale.c
making saveload.d from saveload.c
making scan.d from scan.c
making seq.d from seq.c
making serialize.d from serialize.c
making sort.d from sort.c
making source.d from source.c
making split.d from split.c
making sprintf.d from sprintf.c
making startup.d from startup.c
making subassign.d from subassign.c
making subscript.d from subscript.c
making subset.d from subset.c
making summary.d from summary.c
making sysutils.d from sysutils.c
making times.d from times.c
making unique.d from unique.c
making util.d from util.c
making version.d from version.c
making vfonts.d from vfonts.c
making Rmain.d from Rmain.c
making alloca.d from alloca.c
making mkdtemp.d from mkdtemp.c
making strdup.d from strdup.c
making strncasecmp.d from strncasecmp.c
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c CommandLineArgs.c -o CommandLineArgs.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rdynload.c -o Rdynload.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Renviron.c -o Renviron.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c RNG.c -o RNG.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agrep.c -o agrep.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c apply.c -o apply.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c arithmetic.c -o arithmetic.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c array.c -o array.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c attrib.c -o attrib.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bind.c -o bind.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c builtin.c -o builtin.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c character.c -o character.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coerce.c -o coerce.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c colors.c -o colors.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c complex.c -o complex.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c connections.c -o connections.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c context.c -o context.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cum.c -o cum.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dcf.c -o dcf.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c datetime.c -o datetime.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c debug.c -o debug.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c deparse.c -o deparse.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devices.c -o devices.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dotcode.c -o dotcode.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dounzip.c -o dounzip.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dstruct.c -o dstruct.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c duplicate.c -o duplicate.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c edit.c -o edit.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c engine.c -o engine.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c envir.c -o envir.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c errors.c -o errors.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c eval.c -o eval.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c format.c -o format.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gevents.c -o gevents.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gram.c -o gram.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gram-ex.c -o gram-ex.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c graphics.c -o graphics.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c grep.c -o grep.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c identical.c -o identical.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c inlined.c -o inlined.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c inspect.c -o inspect.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c internet.c -o internet.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c iosupport.c -o iosupport.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lapack.c -o lapack.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c list.c -o list.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c localecharset.c -o localecharset.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c logic.c -o logic.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c main.c -o main.o
main.c: In function 'dummy_ii':
main.c:1594:12: warning: function returns address of local variable [-Wreturn-local-addr]
return (uintptr_t) ⅈ
^
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mapply.c -o mapply.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c match.c -o match.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c memory.c -o memory.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c names.c -o names.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c objects.c -o objects.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c options.c -o options.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c paste.c -o paste.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c platform.c -o platform.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plot.c -o plot.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plot3d.c -o plot3d.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plotmath.c -o plotmath.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c print.c -o print.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c printarray.c -o printarray.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c printvector.c -o printvector.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c printutils.c -o printutils.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qsort.c -o qsort.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c random.c -o random.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c raw.c -o raw.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c registration.c -o registration.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c relop.c -o relop.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rlocale.c -o rlocale.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c saveload.c -o saveload.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c scan.c -o scan.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c seq.c -o seq.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c serialize.c -o serialize.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sort.c -o sort.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c source.c -o source.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c split.c -o split.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sprintf.c -o sprintf.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c startup.c -o startup.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c subassign.c -o subassign.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c subscript.c -o subscript.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c subset.c -o subset.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c summary.c -o summary.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sysutils.c -o sysutils.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c times.c -o times.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c unique.c -o unique.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c util.c -o util.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c version.c -o version.o
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c vfonts.c -o vfonts.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c xxxpr.f -o xxxpr.o
x86_64-alt-linux-gcc -shared -L/usr/local/lib64 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o vfonts.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -lopenblas -lgfortran -lm -lquadmath -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
mkdir -p -- /usr/src/RPM/BUILD/R-3.1.2/bin/exec
mkdir -p -- /usr/src/RPM/BUILD/R-3.1.2/lib
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rmain.c -o Rmain.o
x86_64-alt-linux-gcc -Wl,--export-dynamic -L../../lib -L/usr/local/lib64 -o R.bin Rmain.o -lR
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
making g_alab_her.d from g_alab_her.c
making Lapack.d from Lapack.c
making Rhttpd.d from Rhttpd.c
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
making devX11.d from devX11.c
making Rsock.d from Rsock.c
making g_cntrlify.d from g_cntrlify.c
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Lapack.c -o Lapack.o
making g_fontdb.d from g_fontdb.c
making rotated.d from rotated.c
making internet.d from internet.c
making rbitmap.d from rbitmap.c
making g_her_glyph.d from g_her_glyph.c
making nanoftp.d from nanoftp.c
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c g_alab_her.c -o g_alab_her.o
making nanohttp.d from nanohttp.c
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devX11.c -o devX11.o
making sock.d from sock.c
making sockconn.d from sockconn.c
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c g_cntrlify.c -o g_cntrlify.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c g_fontdb.c -o g_fontdb.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c g_her_glyph.c -o g_her_glyph.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c Rsock.c -o Rsock.o
x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o vfonts.so g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o -lR -lm
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
mkdir -p -- /usr/src/RPM/BUILD/R-3.1.2/modules
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c internet.c -o internet.o
x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o lapack.so Lapack.o -lR -llapack -lopenblas -lgfortran -lm -lquadmath
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c nanoftp.c -o nanoftp.o
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c nanohttp.c -o nanohttp.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c sock.c -o sock.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c sockconn.c -o sockconn.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rotated.c -o rotated.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rbitmap.c -o rbitmap.o
x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o sockconn.o -lR
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dataentry.c -o dataentry.o
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o R_X11.so devX11.o rotated.o rbitmap.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -ltiff -ljpeg -lpng -lz -lR -lm
x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
mkdir -p -- ../../library
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/profile'
building system startup profile
mkdir -p -- ../../../library/base/R
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/profile'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/translations'
building package 'translations'
mkdir -p -- ../../../library/translations
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/translations'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/translations'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/translations'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
building package 'base'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
mkdir -p -- ../../../library/base/demo
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
building package 'tools'
mkdir -p -- ../../../library/tools
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
mkdir -p -- ../../../library/tools/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools/src'
making text.d from text.c
making init.d from init.c
making Rmd5.d from Rmd5.c
making md5.d from md5.c
making signals.d from signals.c
making install.d from install.c
making getfmts.d from getfmts.c
making http.d from http.c
making gramLatex.d from gramLatex.c
making gramRd.d from gramRd.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c text.c -o text.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rmd5.c -o Rmd5.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c md5.c -o md5.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c signals.c -o signals.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c install.c -o install.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c getfmts.c -o getfmts.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c http.c -o http.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gramLatex.c -o gramLatex.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gramRd.c -o gramRd.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
building package 'compiler'
mkdir -p -- ../../../library/compiler
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
mkdir -p -- ../../../library/compiler/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
byte-compiling package 'compiler'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
byte-compiling package 'base'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
byte-compiling package 'tools'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
building package 'utils'
mkdir -p -- ../../../library/utils
mkdir -p -- ../../../library/utils/doc
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
mkdir -p -- ../../../library/utils/R
mkdir -p -- ../../../library/utils/Sweave
mkdir -p -- ../../../library/utils/misc
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils/src'
making init.d from init.c
making io.d from io.c
making size.d from size.c
making sock.d from sock.c
making stubs.d from stubs.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
making utils.d from utils.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c io.c -o io.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c size.c -o size.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sock.c -o sock.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stubs.c -o stubs.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c utils.c -o utils.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils/src'
mkdir -p -- ../../../../library/utils/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
byte-compiling package 'utils'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
building package 'grDevices'
mkdir -p -- ../../../library/grDevices
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
mkdir -p -- ../../../library/grDevices/R
mkdir -p -- ../../../library/grDevices/afm
mkdir -p -- ../../../library/grDevices/enc
mkdir -p -- ../../../library/grDevices/icc
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src'
making axis_scales.d from axis_scales.c
making devices.d from devices.c
making chull.d from chull.c
making init.d from init.c
making stubs.d from stubs.c
making colors.d from colors.c
making devCairo.d from devCairo.c
making devPicTeX.d from devPicTeX.c
making devPS.d from devPS.c
making devQuartz.d from devQuartz.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c axis_scales.c -o axis_scales.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chull.c -o chull.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devices.c -o devices.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stubs.c -o stubs.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c colors.c -o colors.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devCairo.c -o devCairo.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devPicTeX.c -o devPicTeX.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devPS.c -o devPS.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devQuartz.c -o devQuartz.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src'
mkdir -p -- ../../../../library/grDevices/libs
make[7]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
making cairoBM.d from cairoBM.c
make[8]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
make[9]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
x86_64-alt-linux-gcc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cairoBM.c -o cairoBM.o
x86_64-alt-linux-gcc -shared -L../../../../../lib -L/usr/local/lib64 -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -ltiff -ljpeg -lpng -lz -L../../../../../lib -lR -lm
make[9]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
make[8]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
make[7]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
byte-compiling package 'grDevices'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
building package 'graphics'
mkdir -p -- ../../../library/graphics
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
mkdir -p -- ../../../library/graphics/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics/src'
making init.d from init.c
making base.d from base.c
making graphics.d from graphics.c
making par.d from par.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making stem.d from stem.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c base.c -o base.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c graphics.c -o graphics.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c par.c -o par.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plot.c -o plot.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plot3d.c -o plot3d.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stem.c -o stem.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics/src'
mkdir -p -- ../../../../library/graphics/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
byte-compiling package 'graphics'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
building package 'stats'
mkdir -p -- ../../../library/stats
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
mkdir -p -- ../../../library/stats/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats/src'
making init.d from init.c
making kmeans.d from kmeans.c
making ansari.d from ansari.c
making bandwidths.d from bandwidths.c
making chisqsim.d from chisqsim.c
making d2x2xk.d from d2x2xk.c
making fexact.d from fexact.c
making kendall.d from kendall.c
making ks.d from ks.c
making line.d from line.c
making smooth.d from smooth.c
making prho.d from prho.c
making swilk.d from swilk.c
making ksmooth.d from ksmooth.c
making loessc.d from loessc.c
making monoSpl.d from monoSpl.c
making isoreg.d from isoreg.c
making Srunmed.d from Srunmed.c
making dblcen.d from dblcen.c
making distance.d from distance.c
making hclust-utils.d from hclust-utils.c
making nls.d from nls.c
making rWishart.d from rWishart.c
making HoltWinters.d from HoltWinters.c
making PPsum.d from PPsum.c
making arima.d from arima.c
making burg.d from burg.c
making filter.d from filter.c
making mAR.d from mAR.c
making pacf.d from pacf.c
making starma.d from starma.c
making port.d from port.c
making family.d from family.c
making sbart.d from sbart.c
making approx.d from approx.c
making loglin.d from loglin.c
making lowess.d from lowess.c
making massdist.d from massdist.c
making splines.d from splines.c
making lm.d from lm.c
making complete_cases.d from complete_cases.c
making cov.d from cov.c
making deriv.d from deriv.c
making fft.d from fft.c
making fourier.d from fourier.c
making model.d from model.c
making optim.d from optim.c
making optimize.d from optimize.c
making integrate.d from integrate.c
making random.d from random.c
making distn.d from distn.c
making zeroin.d from zeroin.c
making rcont.d from rcont.c
making influence.d from influence.c
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c kmeans.c -o kmeans.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ansari.c -o ansari.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bandwidths.c -o bandwidths.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chisqsim.c -o chisqsim.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c d2x2xk.c -o d2x2xk.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fexact.c -o fexact.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c kendall.c -o kendall.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ks.c -o ks.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c line.c -o line.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c smooth.c -o smooth.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c prho.c -o prho.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c swilk.c -o swilk.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ksmooth.c -o ksmooth.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c loessc.c -o loessc.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c monoSpl.c -o monoSpl.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c isoreg.c -o isoreg.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Srunmed.c -o Srunmed.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dblcen.c -o dblcen.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c distance.c -o distance.o
In file included from /usr/include/math.h:26:0,
from ../../../include/R_ext/Arith.h:37,
from distance.c:26:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c hclust-utils.c -o hclust-utils.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nls.c -o nls.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rWishart.c -o rWishart.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c HoltWinters.c -o HoltWinters.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c PPsum.c -o PPsum.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c arima.c -o arima.o
In file included from /usr/include/math.h:26:0,
from ../../../include/R_ext/Arith.h:37,
from arima.c:25:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c burg.c -o burg.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c filter.c -o filter.o
In file included from /usr/include/math.h:26:0,
from ../../../include/R_ext/Arith.h:37,
from filter.c:25:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mAR.c -o mAR.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pacf.c -o pacf.o
In file included from /usr/include/math.h:26:0,
from ../../../include/R_ext/Arith.h:37,
from pacf.c:29:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c starma.c -o starma.o
In file included from /usr/include/math.h:26:0,
from ../../../include/R_ext/Arith.h:37,
from starma.c:24:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c port.c -o port.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c family.c -o family.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sbart.c -o sbart.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c approx.c -o approx.o
In file included from /usr/include/math.h:26:0,
from ../../../include/R_ext/Arith.h:37,
from approx.c:25:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c loglin.c -o loglin.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lowess.c -o lowess.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c massdist.c -o massdist.o
In file included from /usr/include/math.h:26:0,
from ../../../include/R_ext/Arith.h:37,
from massdist.c:31:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c splines.c -o splines.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lm.c -o lm.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c complete_cases.c -o complete_cases.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cov.c -o cov.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c deriv.c -o deriv.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fft.c -o fft.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fourier.c -o fourier.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c model.c -o model.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c optim.c -o optim.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c optimize.c -o optimize.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c integrate.c -o integrate.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c random.c -o random.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c distn.c -o distn.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c zeroin.c -o zeroin.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rcont.c -o rcont.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c influence.c -o influence.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bsplvd.f -o bsplvd.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bvalue.f -o bvalue.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bvalus.f -o bvalus.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c loessf.f -o loessf.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ppr.f -o ppr.o
loessf.f:59:14:
j=DBLE(j)/2.D0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1896:14:
m=DBLE(l+u)/2.D0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1398:20:
i=phi(pi(ii))
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:927:12:
lg=DBLE(lg)/2.D0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:522:22:
if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1204:13:
ifloor=x
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:834:22:
if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1582:18:
i1=dble((d+2)*(d+1))/2.d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:472:25:
subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
1
Warning: Unused dummy argument 'n' at (1) [-Wunused-dummy-argument]
loessf.f:472:39:
subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
1
Warning: Unused dummy argument 'nc' at (1) [-Wunused-dummy-argument]
loessf.f:827:31:
subroutine ehg197(deg,tau,d,f,dk,trl)
1
Warning: Unused dummy argument 'tau' at (1) [-Wunused-dummy-argument]
loessf.f:1987:31:
subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
1
Warning: Unused dummy argument 'kappa' at (1) [-Wunused-dummy-argument]
loessf.f:1987:47:
subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
1
Warning: Unused dummy argument 'nv' at (1) [-Wunused-dummy-argument]
loessf.f:1987:53:
subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
1
Warning: Unused dummy argument 'nvmax' at (1) [-Wunused-dummy-argument]
loessf.f:1856:22:
logical i1,i2,i3,leaf
1
Warning: Unused variable 'i3' declared at (1) [-Wunused-variable]
loessf.f:1497:50:
subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)
1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1497:53:
subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)
1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1648:30:
subroutine lowese(iv,liv,lv,wv,m,z,s)
1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1648:33:
subroutine lowese(iv,liv,lv,wv,m,z,s)
1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1667:39:
subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)
1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1667:42:
subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)
1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1699:30:
subroutine lowesl(iv,liv,lv,wv,m,z,l)
1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1699:33:
subroutine lowesl(iv,liv,lv,wv,m,z,l)
1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1721:33:
subroutine lowesr(yy,iv,liv,lv,wv)
1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1721:36:
subroutine lowesr(yy,iv,liv,lv,wv)
1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
ppr.f:1323:8:
t=a(ij)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1328:8:
t=a(ij)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1336:8:
t=a(ij)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1343:8:
t=a(ij)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1354:9:
tt=a(l)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1379:8:
t=a(i+1)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:370:10:
k=sc(j,1)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1088:10:
ibw=0.5d0*span*n+0.5d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:396:10:
k=sc(j,1)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:404:10:
k=sc(j,1)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:115:8:
l=sc(lm,1)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:844:14:
k=sp(j,1)
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:860:8:
m=smod(1)+0.1d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:861:8:
p=smod(2)+0.1d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:862:8:
q=smod(3)+0.1d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:863:8:
n=smod(4)+0.1d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:864:9:
mu=smod(5)+0.1d0
1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1229:42:
integer iparms(3), i, nk, ip, isetup,ier
1
Warning: Unused variable 'isetup' declared at (1) [-Wunused-variable]
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qsbart.f -o qsbart.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sgram.f -o sgram.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sinerp.f -o sinerp.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sslvrg.f -o sslvrg.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stxwx.f -o stxwx.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c hclust.f -o hclust.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c kmns.f -o kmns.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c eureka.f -o eureka.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stl.f -o stl.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -ffloat-store -c portsrc.f -o portsrc.o
f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lminfl.f -o lminfl.o
portsrc.f:6340:0:
* MAXLST,NCOMP,NUMINC,NUMLST,NUMORD,NUMWGT
^
Warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:6339:0:
INTEGER DEG,HEAD,IC,IP,IPL,IPU,IR,JCOL,JP,JPL,JPU,L,MAXINC,
^
Warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:5328:0:
IF (ALPHAK .LE. ZERO .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
^
Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:5463:0:
IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310
^
Warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10090:0:
V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA)
^
Warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10008:0:
IF (-V(DST0) .GE. ALPHAK .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
^
Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10003:0:
LK = DMAX1(LK, PHI*W(PHIPIN))
^
Warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10144:0:
IF (KA .GE. KAMIN) GO TO 340
^
Warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11900:0:
V(NREDUC) = NRED
^
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11903:0:
V(DST0) = DNWTST
^
Warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:2390:0:
V(NREDUC) = NRED
^
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:2389:0:
60 V(DST0) = DS0
^
Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:7892:0:
V(NREDUC) = NRED
^
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:7891:0:
90 V(DST0) = DS0
^
Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:8370:0:
210 IV(FDH) = HES
^
Warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:3456:0:
IF (LIV .LT. MIV2) GO TO 300
^
Warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11737:0:
270 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
^
Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11694:0:
CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
^
Warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11694:0: Warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:440:0:
300 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
^
Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:348:0:
CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
^
Warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:348:0: Warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized]
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -llapack -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats/src'
mkdir -p -- ../../../../library/stats/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
byte-compiling package 'stats'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/datasets'
building package 'datasets'
mkdir -p -- ../../../library/datasets
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/datasets'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/datasets'
mkdir -p -- ../../../library/datasets/data
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/datasets'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
building package 'methods'
mkdir -p -- ../../../library/methods
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
mkdir -p -- ../../../library/methods/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods/src'
making do_substitute_direct.d from do_substitute_direct.c
making init.d from init.c
making methods_list_dispatch.d from methods_list_dispatch.c
making slot.d from slot.c
making class_support.d from class_support.c
making tests.d from tests.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c do_substitute_direct.c -o do_substitute_direct.o
making utils.d from utils.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c methods_list_dispatch.c -o methods_list_dispatch.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c slot.c -o slot.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c class_support.c -o class_support.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c tests.c -o tests.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c utils.c -o utils.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods/src'
mkdir -p -- ../../../../library/methods/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
byte-compiling 'methods'
initializing class and method definitions ... done
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
building package 'grid'
mkdir -p -- ../../../library/grid
mkdir -p -- ../../../library/grid/doc
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
mkdir -p -- ../../../library/grid/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid/src'
making gpar.d from gpar.c
making grid.d from grid.c
making just.d from just.c
making layout.d from layout.c
making matrix.d from matrix.c
making register.d from register.c
making state.d from state.c
making unit.d from unit.c
making util.d from util.c
making viewport.d from viewport.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gpar.c -o gpar.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c grid.c -o grid.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c just.c -o just.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c layout.c -o layout.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c register.c -o register.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c state.c -o state.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c unit.c -o unit.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c util.c -o util.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c viewport.c -o viewport.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid/src'
mkdir -p -- ../../../../library/grid/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
byte-compiling package 'grid'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
building package 'splines'
mkdir -p -- ../../../library/splines
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
mkdir -p -- ../../../library/splines/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines/src'
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c splines.c -o splines.o
making splines.d from splines.c
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o splines.so splines.o -L../../../../lib -lR
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building package 'stats4'
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x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/include -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
making init.d from init.c
making tcltk.d from tcltk.c
making tcltk_unix.d from tcltk_unix.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/include -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c tcltk.c -o tcltk.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/include -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c tcltk_unix.c -o tcltk_unix.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib64 -ltcl8.5 -L/usr/lib64 -ltk8.5 -lX11 -lm -L../../../../lib -lR
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tcltk/src'
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make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel'
building package 'parallel'
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make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel/src'
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
making init.d from init.c
making rngstream.d from rngstream.c
making fork.d from fork.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rngstream.c -o rngstream.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fork.c -o fork.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel/src'
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byte-compiling package 'parallel'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel'
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you should 'make docs' now ...
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2'
configuring Java ...
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
*** Cannot find any Java interpreter
*** Please make sure 'java' is on your PATH or set JAVA_HOME correspondingly
make[1]: [stamp-java] Error 1 (ignored)
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2'
creating NEWS
creating NEWS.pdf
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'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
file R-FAQ.html will be missing
creating doc/manual/version.texi
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file R-admin.html will be missing
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file R-exts.html will be missing
'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
file R-intro.html will be missing
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make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/html'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/html'
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make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
installing parsed Rd
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
methods
utils
graphics
datasets
grDevices
grid
tools
splines
tcltk
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stats4
parallel
stats
base
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writing package indices
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building all R object docs
converting help for package 'base'
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allnames html
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assign html
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c html
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copyright html
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debug html
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det html
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diff html
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do.call html
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dput html
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droplevels html
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eigen html
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environment html
eval html
exists html
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license html
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ns-hooks html
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ns-load html
ns-reflect html
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numeric html
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octmode html
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options html
order html
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parse html
paste html
path.expand html
pmatch html
polyroot html
pos.to.env html
pretty html
print html
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print.dataframe html
print.default html
prmatrix html
proc.time html
prod html
prop.table html
pushBack html
qr html
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rapply html
raw html
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readBin html
readChar html
readLines html
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reg.finalizer html
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rev html
rle html
rm html
round.POSIXt html
row html
row.names html
rowsum html
sQuote html
sample html
save html
scale html
scan html
search html
seek html
seq.Date html
seq.POSIXt html
seq html
sequence html
serialize html
setTimeLimit html
sets html
shQuote html
showConnections html
sign html
sink html
slice.index html
slotOp html
socketSelect html
solve html
sort html
source html
split html
sprintf html
srcfile html
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stop html
stopifnot html
strptime html
strsplit html
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strtrim html
structure html
strwrap html
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substr html
sum html
summary html
svd html
sweep html
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sys.parent html
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table html
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tempfile html
textconnections html
tilde html
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try html
typeof html
unique html
unlink html
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userhooks html
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vector html
warning html
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which html
which.min html
with html
withVisible html
write html
writeLines html
xtfrm html
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zapsmall html
zpackages html
zutils html
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QC html
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bibstyle html
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charsets html
checkFF html
checkMD5sums html
checkPoFiles html
checkRd html
checkRdaFiles html
checkTnF html
checkVignettes html
check_packages_in_dir html
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codoc html
compactPDF html
delimMatch html
dependsOnPkgs html
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fileutils html
find_gs_cmd html
getDepList html
getVignetteInfo html
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md5sum html
package.dependencies html
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parseLatex html
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pskill html
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read.00Index html
showNonASCII html
startDynamicHelp html
testInstalledPackage html
texi2dvi html
toHTML html
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tools-defunct html
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undoc html
update_pkg_po html
vignetteDepends html
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writePACKAGES html
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converting help for package 'utils'
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PkgUtils html
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Rprof html
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available.packages html
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bug.report html
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citEntry html
citation html
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combn html
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contrib.url html
count.fields html
create.post html
data html
dataentry html
debugger html
demo html
download.file html
download.packages html
edit html
edit.data.frame html
example html
file.edit html
filetest html
findLineNum html
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glob2rx html
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ls_str html
maintainer html
make.packages.html html
make.socket html
menu html
methods html
mirrorAdmin html
modifyList html
news html
object.size html
package.skeleton html
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page html
person html
process.events html
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rcompgen html
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rtags html
savehistory html
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sessionInfo html
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sourceutils html
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str html
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tar html
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untar html
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update.packages html
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zip html
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memory.size html
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grDevices-package html
gray html
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hcl html
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n2mfrow html
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quartz html
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converting help for package 'graphics'
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arrows html
assocplot html
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axis html
barplot html
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clip html
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coplot html
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frame html
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identify html
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locator html
matplot html
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sunflowerplot html
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binom.test html
biplot html
biplot.princomp html
birthday html
box.test html
cancor html
case.names html
checkMFClasses html
chisq.test html
cmdscale html
coef html
complete.cases html
confint html
constrOptim html
contrast html
contrasts html
convolve html
cophenetic html
cor html
cor.test html
cov.wt html
cpgram html
cutree html
decompose html
delete.response html
dendrapply html
dendrogram html
density html
deriv html
deviance html
df.residual html
diffinv html
dist html
dummy.coef html
ecdf html
eff.aovlist html
effects html
embed html
expand.model.frame html
extractAIC html
factanal html
factor.scope html
family html
fft html
filter html
fisher.test html
fitted.values html
fivenum html
fligner.test html
formula html
formula.nls html
friedman.test html
ftable html
ftable.formula html
getInitial html
glm html
glm.control html
glm.summaries html
hclust html
heatmap html
identify.hclust html
influence.measures html
integrate html
interaction.plot html
is.empty html
isoreg html
kernapply html
kernel html
kmeans html
kruskal.test html
ks.test html
ksmooth html
lag html
lag.plot html
line html
listof html
lm html
lm.influence html
lm.summaries html
lmfit html
loadings html
loess html
loess.control html
logLik html
loglin html
lowess html
ls.diag html
ls.print html
lsfit html
mad html
mahalanobis html
make.link html
makepredictcall html
manova html
mantelhaen.test html
mauchly.test html
mcnemar.test html
median html
medpolish html
model.extract html
model.frame html
model.matrix html
model.tables html
monthplot html
mood.test html
na.action html
na.contiguous html
na.fail html
nafns html
naprint html
nextn html
nlm html
nlminb html
nls html
nls.control html
nobs html
numericDeriv html
offset html
oneway.test html
optim html
optimize html
order.dendrogram html
p.adjust html
pairwise.prop.test html
pairwise.t.test html
pairwise.table html
pairwise.wilcox.test html
plot.HoltWinters html
plot.acf html
plot.density html
plot.isoreg html
plot.lm html
plot.ppr html
plot.profile.nls html
plot.spec html
plot.stepfun html
plot.ts html
poisson.test html
poly html
power html
power.anova.test html
power.prop.test html
power.t.test html
pp.test html
ppoints html
ppr html
prcomp html
predict.HoltWinters html
predict html
predict.arima html
predict.glm html
predict.lm html
predict.loess html
predict.nls html
predict.smooth.spline html
preplot html
princomp html
print.power.htest html
print.ts html
printCoefmat html
profile html
profile.nls html
proj html
prop.test html
prop.trend.test html
qqnorm html
quade.test html
quantile html
r2dtable html
rWishart html
read.ftable html
rect.hclust html
relevel html
reorder.dendrogram html
reorder.factor html
replications html
reshape html
residuals html
runmed html
scatter.smooth html
screeplot html
sd html
se.contrast html
selfStart html
setNames html
shapiro.test html
simulate html
smooth html
smooth.spline html
smoothEnds html
sortedXyData html
spec.ar html
spec.pgram html
spec.taper html
spectrum html
splinefun html
start html
stat.anova html
stats-defunct html
stats-deprecated html
stats-package html
step html
stepfun html
stl html
stlmethods html
summary.aov html
summary.glm html
summary.lm html
summary.manova html
summary.nls html
summary.princomp html
supsmu html
symnum html
t.test html
termplot html
terms html
terms.formula html
terms.object html
time html
toeplitz html
ts-methods html
ts html
ts.plot html
ts.union html
tsSmooth html
tsdiag html
tsp html
uniroot html
update html
update.formula html
var.test html
varimax html
vcov html
weighted.mean html
weighted.residuals html
weights html
wilcox.test html
window html
xtabs html
zC html
converting help for package 'datasets'
AirPassengers html
BJsales html
BOD html
ChickWeight html
DNase html
EuStockMarkets html
Formaldehyde html
HairEyeColor html
Harman23.cor html
Harman74.cor html
Indometh html
InsectSprays html
JohnsonJohnson html
LakeHuron html
LifeCycleSavings html
Loblolly html
Nile html
Orange html
OrchardSprays html
PlantGrowth html
Puromycin html
Theoph html
Titanic html
ToothGrowth html
UCBAdmissions html
UKDriverDeaths html
UKLungDeaths html
UKgas html
USAccDeaths html
USArrests html
USJudgeRatings html
USPersonalExpenditure html
VADeaths html
WWWusage html
WorldPhones html
ability.cov html
airmiles html
airquality html
anscombe html
attenu html
attitude html
austres html
beavers html
cars html
chickwts html
co2 html
crimtab html
datasets-package html
discoveries html
esoph html
euro html
eurodist html
faithful html
freeny html
infert html
iris html
islands html
lh html
longley html
lynx html
morley html
mtcars html
nhtemp html
nottem html
npk html
occupationalStatus html
precip html
presidents html
pressure html
quakes html
randu html
rivers html
rock html
sleep html
stackloss html
state html
sunspot.month html
sunspot.year html
sunspots html
swiss html
treering html
trees html
uspop html
volcano html
warpbreaks html
women html
zCO2 html
converting help for package 'methods'
BasicClasses html
Classes html
Documentation html
EmptyMethodsList-class html
EnvironmentClass html
GenericFunctions html
LanguageClasses html
LinearMethodsList-class html
MethodDefinition-class html
MethodSupport html
MethodWithNext-class html
Methods html
MethodsList-class html
MethodsList html
NextMethod html
ObjectsWithPackage-class html
RClassUtils html
RMethodUtils html
S3Part html
S4groupGeneric html
SClassExtension-class html
StructureClasses html
TraceClasses html
as html
callGeneric html
canCoerce html
cbind2 html
className html
classRepresentation-class html
classesToAM html
dotsMethods html
evalSource html
findClass html
findMethods html
fixPrevious html
genericFunction-class html
getClass html
getMethod html
getPackageName html
hasArg html
implicitGeneric html
inheritedSlotNames html
initialize-methods html
is html
isSealedMethod html
languageEl html
localRefClass html
method.skeleton html
methodUtilities html
methods-defunct html
methods-deprecated html
methods-package html
new html
nonStructure-class html
promptClass html
promptMethods html
refClass html
representation html
selectSuperClasses html
setClass html
setClassUnion html
setGeneric html
setLoadActions html
setMethod html
setOldClass html
setSClass html
show html
showMethods html
signature-class html
slot html
stdRefClass html
substituteDirect html
testInheritedMethods html
validObject html
zBasicFunsList html
converting help for package 'grid'
Grid html
absolute.size html
arrow html
calcStringMetric html
current.viewport html
dataViewport html
depth html
drawDetails html
editDetails html
explode html
gEdit html
gPath html
getNames html
gpar html
grid-defunct html
grid-internal html
grid-package html
grid.DLapply html
grid.add html
grid.bezier html
grid.cap html
grid.circle html
grid.clip html
grid.convert html
grid.copy html
grid.curve html
grid.delay html
grid.display.list html
grid.draw html
grid.edit html
grid.force html
grid.frame html
grid.function html
grid.get html
grid.grab html
grid.grep html
grid.grill html
grid.grob html
grid.layout html
grid.lines html
grid.locator html
grid.ls html
grid.move.to html
grid.newpage html
grid.null html
grid.pack html
grid.path html
grid.place html
grid.plot.and.legend html
grid.points html
grid.polygon html
grid.pretty html
grid.raster html
grid.record html
grid.rect html
grid.refresh html
grid.remove html
grid.reorder html
grid.roundrect html
grid.segments html
grid.set html
grid.show.layout html
grid.show.viewport html
grid.text html
grid.xaxis html
grid.xspline html
grid.yaxis html
grobName html
grobWidth html
grobX html
legendGrob html
makeContent html
plotViewport html
resolveRasterSize html
showGrob html
showViewport html
stringWidth html
unit html
unit.c html
unit.length html
unit.pmin html
unit.rep html
valid.just html
validDetails html
viewport html
viewports html
vpPath html
widthDetails html
xDetails html
xsplinePoints html
converting help for package 'splines'
asVector html
backSpline html
bs html
interpSpline html
ns html
periodicSpline html
polySpline html
predict.bSpline html
predict.bs html
splineDesign html
finding level-2 HTML links ... done
Rd warning: /usr/src/RPM/BUILD/R-3.1.2/src/library/splines/man/splineDesign.Rd:39: missing link 'sparseMatrix-class'
splineKnots html
splineOrder html
splines-package html
xyVector html
converting help for package 'stats4'
coef-methods html
confint-methods html
logLik-methods html
mle-class html
mle html
plot-methods html
profile-methods html
profile.mle-class html
show-methods html
stats4-package html
summary-methods html
summary.mle-class html
update-methods html
vcov-methods html
converting help for package 'tcltk'
TclInterface html
TkCommands html
TkWidgetcmds html
TkWidgets html
tclServiceMode html
tcltk-defunct html
tcltk-package html
tkProgressBar html
tkStartGUI html
tk_choose.dir html
tk_choose.files html
tk_messageBox html
tk_select.list html
tkpager html
converting help for package 'compiler'
compile html
converting help for package 'parallel'
RngStream html
clusterApply html
detectCores html
makeCluster html
parallel-package html
splitIndices html
children html
mcaffinity html
mcfork html
mclapply html
mcparallel html
pvec html
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/Recommended'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/Recommended'
begin installing recommended package codetools
begin installing recommended package MASS
begin installing recommended package lattice
begin installing recommended package survival
* installing *source* package 'codetools' ...
** package 'codetools' successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'codetools'
finding HTML links ... done
checkUsage html
codetools html
findGlobals html
showTree html
** building package indices
** testing if installed package can be loaded
* DONE (codetools)
Making 'packages.html' ... done
begin installing recommended package foreign
* installing *source* package 'foreign' ...
** package 'foreign' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpCXZ01p/R.INSTALL183351f8fce9/foreign/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c R_systat.c -o R_systat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rdbfread.c -o Rdbfread.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rdbfwrite.c -o Rdbfwrite.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c SASxport.c -o SASxport.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c avl.c -o avl.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dbfopen.c -o dbfopen.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c file-handle.c -o file-handle.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c format.c -o format.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c minitab.c -o minitab.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pfm-read.c -o pfm-read.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sfm-read.c -o sfm-read.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c spss.c -o spss.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stataread.c -o stataread.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpCXZ01p/R.INSTALL183351f8fce9/foreign/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/foreign/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'foreign'
finding HTML links ... done
lookup.xport html
read.S html
read.arff html
read.dbf html
read.dta html
read.epiinfo html
read.mtp html
read.octave html
read.spss html
read.ssd html
read.systat html
read.xport html
write.arff html
write.dbf html
write.dta html
write.foreign html
** building package indices
** testing if installed package can be loaded
* DONE (foreign)
Making 'packages.html' ... done
begin installing recommended package KernSmooth
* installing *source* package 'KernSmooth' ...
** package 'KernSmooth' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmppjNSXA/R.INSTALL18f921c1be17/KernSmooth/src'
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c blkest.f -o blkest.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cp.f -o cp.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgedi.f -o dgedi.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgefa.f -o dgefa.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgesl.f -o dgesl.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c linbin.f -o linbin.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c linbin2D.f -o linbin2D.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c locpoly.f -o locpoly.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rlbin.f -o rlbin.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sdiag.f -o sdiag.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sstdiag.f -o sstdiag.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lopenblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmppjNSXA/R.INSTALL18f921c1be17/KernSmooth/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/KernSmooth/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'KernSmooth'
finding HTML links ... done
bkde html
bkde2D html
bkfe html
dpih html
dpik html
dpill html
locpoly html
** building package indices
** testing if installed package can be loaded
* DONE (KernSmooth)
Making 'packages.html' ... done
begin installing recommended package rpart
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpM8ujGi/R.INSTALL1805c3a5958/MASS/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c MASS.c -o MASS.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lqs.c -o lqs.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpM8ujGi/R.INSTALL1805c3a5958/MASS/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/MASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MASS'
finding HTML links ... done
Aids2 html
Animals html
Boston html
Cars93 html
Cushings html
DDT html
GAGurine html
Insurance html
MASS-internal html
Melanoma html
Null html
OME html
Pima.tr html
Rabbit html
Rubber html
SP500 html
Sitka html
Sitka89 html
Skye html
Traffic html
UScereal html
UScrime html
VA html
abbey html
accdeaths html
addterm html
anorexia html
anova.negbin html
area html
bacteria html
bandwidth.nrd html
bcv html
beav1 html
beav2 html
biopsy html
birthwt html
boxcox html
cabbages html
caith html
cats html
cement html
chem html
con2tr html
confint html
contr.sdif html
coop html
corresp html
cov.rob html
cov.trob html
cpus html
crabs html
deaths html
denumerate html
dose.p html
drivers html
dropterm html
eagles html
epil html
eqscplot html
farms html
fgl html
fitdistr html
forbes html
fractions html
galaxies html
gamma.dispersion html
gamma.shape.glm html
gehan html
genotype html
geyser html
gilgais html
ginv html
glm.convert html
glm.nb html
glmmPQL html
hills html
hist.scott html
housing html
huber html
hubers html
immer html
isoMDS html
kde2d html
lda html
ldahist html
leuk html
lm.gls html
lm.ridge html
loglm html
loglm1 html
logtrans html
lqs html
mammals html
mca html
mcycle html
menarche html
michelson html
minn38 html
motors html
muscle html
mvrnorm html
negative.binomial html
newcomb html
nlschools html
npk html
npr1 html
oats html
painters html
pairs.lda html
parcoord html
petrol html
phones html
plot.lda html
plot.mca html
plot.profile html
polr html
predict.glmmPQL html
predict.lda html
predict.lqs html
predict.mca html
predict.qda html
profile.glm html
qda html
quine html
rational html
renumerate html
rlm html
rms.curv html
rnegbin html
road html
rotifer html
sammon html
ships html
shoes html
shrimp html
shuttle html
snails html
stdres html
steam html
stepAIC html
stormer html
studres html
summary.loglm html
summary.negbin html
summary.rlm html
survey html
synth.tr html
theta.md html
topo html
truehist html
ucv html
waders html
whiteside html
width.SJ html
write.matrix html
wtloss html
** building package indices
** testing if installed package can be loaded
* DONE (MASS)
Making 'packages.html' ... done
begin installing recommended package nnet
* installing *source* package 'lattice' ...
** package 'lattice' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpNgnT2h/R.INSTALL17ff1ea6c29f/lattice/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c threeDplot.c -o threeDplot.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpNgnT2h/R.INSTALL17ff1ea6c29f/lattice/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/lattice/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'lattice'
finding HTML links ... done
Lattice html
Rows html
axis.default html
banking html
barchart.table html
barley html
cloud html
draw.colorkey html
draw.key html
environmental html
ethanol html
histogram html
interaction html
lattice.options html
latticeParseFormula html
level.colors html
levelplot html
llines html
lset html
make.groups html
melanoma html
oneway html
packet.panel.default html
panel.axis html
panel.barchart html
panel.bwplot html
panel.cloud html
panel.densityplot html
panel.dotplot html
panel.functions html
panel.histogram html
panel.levelplot html
panel.loess html
panel.number html
panel.pairs html
panel.parallel html
panel.qqmath html
panel.qqmathline html
panel.smoothScatter html
panel.spline html
panel.stripplot html
panel.superpose html
panel.violin html
panel.xyplot html
prepanel.default html
prepanel.functions html
print.trellis html
qq html
qqmath html
rfs html
shingles html
simpleKey html
simpleTheme html
singer html
splom html
strip.default html
tmd html
trellis.device html
trellis.object html
trellis.par.get html
update.trellis html
utilities.3d html
xyplot html
xyplot.ts html
** building package indices
** testing if installed package can be loaded
* DONE (lattice)
Making 'packages.html' ... done
begin installing recommended package spatial
* installing *source* package 'nnet' ...
** package 'nnet' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpFmxuxb/R.INSTALL198a388bbc40/nnet/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nnet.c -o nnet.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpFmxuxb/R.INSTALL198a388bbc40/nnet/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/nnet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'nnet'
finding HTML links ... done
class.ind html
multinom html
nnet.Hess html
nnet html
predict.nnet html
which.is.max html
** building package indices
** testing if installed package can be loaded
* DONE (nnet)
Making 'packages.html' ... done
begin installing recommended package Matrix
* installing *source* package 'rpart' ...
** package 'rpart' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/Rtmpr5AKj6/R.INSTALL193369270043/rpart/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c anova.c -o anova.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c anovapred.c -o anovapred.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c branch.c -o branch.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bsplit.c -o bsplit.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c choose_surg.c -o choose_surg.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fix_cp.c -o fix_cp.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c free_tree.c -o free_tree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gini.c -o gini.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c graycode.c -o graycode.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c insert_split.c -o insert_split.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c make_cp_list.c -o make_cp_list.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c make_cp_table.c -o make_cp_table.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mysort.c -o mysort.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nodesplit.c -o nodesplit.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c partition.c -o partition.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c poisson.c -o poisson.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pred_rpart.c -o pred_rpart.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c print_tree.c -o print_tree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpart.c -o rpart.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpart_callback.c -o rpart_callback.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpartexp.c -o rpartexp.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpartexp2.c -o rpartexp2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpcountup.c -o rpcountup.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpmatrix.c -o rpmatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rundown.c -o rundown.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rundown2.c -o rundown2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c surrogate.c -o surrogate.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c usersplit.c -o usersplit.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c xpred.c -o xpred.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c xval.c -o xval.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/Rtmpr5AKj6/R.INSTALL193369270043/rpart/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/rpart/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rpart'
finding HTML links ... done
car.test.frame html
car90 html
cu.summary html
kyphosis html
labels.rpart html
meanvar.rpart html
na.rpart html
path.rpart html
plot.rpart html
plotcp html
post.rpart html
predict.rpart html
print.rpart html
printcp html
prune.rpart html
residuals.rpart html
rpart-internal html
rpart html
rpart.control html
rpart.exp html
rpart.object html
rsq.rpart html
snip.rpart html
solder html
stagec html
summary.rpart html
text.rpart html
xpred.rpart html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rpart)
Making 'packages.html' ... done
begin installing recommended package nlme
* installing *source* package 'spatial' ...
** package 'spatial' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpP7V0Hj/R.INSTALL19bf2d03356c/spatial/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c krc.c -o krc.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pps.c -o pps.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpP7V0Hj/R.INSTALL19bf2d03356c/spatial/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/spatial/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'spatial'
finding HTML links ... done
Kaver html
Kenvl html
Kfn html
Psim html
SSI html
Strauss html
anova.trls html
correlogram html
expcov html
ppgetregion html
ppinit html
pplik html
ppregion html
predict.trls html
prmat html
semat html
surf.gls html
surf.ls html
trls.influence html
trmat html
variogram html
** building package indices
** testing if installed package can be loaded
* DONE (spatial)
Making 'packages.html' ... done
begin installing recommended package cluster
* installing *source* package 'survival' ...
** package 'survival' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpQaB70h/R.INSTALL18021d920041/survival/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agexact.c -o agexact.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agfit4.c -o agfit4.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agfit5.c -o agfit5.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agmart.c -o agmart.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agmart2.c -o agmart2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agscore.c -o agscore.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agsurv3.c -o agsurv3.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agsurv4.c -o agsurv4.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agsurv5.c -o agsurv5.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chinv2.c -o chinv2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chinv3.c -o chinv3.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cholesky2.c -o cholesky2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cholesky3.c -o cholesky3.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chsolve2.c -o chsolve2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chsolve3.c -o chsolve3.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c concordance1.c -o concordance1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cox_Rcallback.c -o cox_Rcallback.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxcount1.c -o coxcount1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxdetail.c -o coxdetail.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxexact.c -o coxexact.o
coxexact.c: In function 'coxexact':
coxexact.c:303:22: warning: 'sstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
d0 = coxd0(ndeath, nrisk, score+sstart, dmem0, maxdeath);
^
coxexact.c:191:18: warning: 'nrisk' may be used uninitialized in this function [-Wmaybe-uninitialized]
nrisk++;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxfit5.c -o coxfit5.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxfit6.c -o coxfit6.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxmart.c -o coxmart.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxmart2.c -o coxmart2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxph_wtest.c -o coxph_wtest.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxsafe.c -o coxsafe.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxscho.c -o coxscho.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxscore.c -o coxscore.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dmatrix.c -o dmatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c doloop.c -o doloop.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c msurv.c -o msurv.o
msurv.c: In function 'msurv':
msurv.c:16:12: warning: unused variable 'ntime' [-Wunused-variable]
int ntime, nstate, n;
^
msurv.c:50:42: warning: 'k2' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (eflag==1 && i2>=0 && etime[k2] >=time) {
^
msurv.c:13:19: warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized]
int eflag, i2, k2;
^
msurv.c:12:21: warning: 'isort' may be used uninitialized in this function [-Wmaybe-uninitialized]
int *dsort, *isort;
^
msurv.c:50:42: warning: 'etime' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (eflag==1 && i2>=0 && etime[k2] >=time) {
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pyears1.c -o pyears1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pyears2.c -o pyears2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pyears3b.c -o pyears3b.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pystep.c -o pystep.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survConcordance.c -o survConcordance.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survdiff2.c -o survdiff2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survfit4.c -o survfit4.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survfitci.c -o survfitci.o
survfitci.c: In function 'survfitci':
survfitci.c:189:33: warning: 'umat' may be used uninitialized in this function [-Wmaybe-uninitialized]
umat[j][k] -= (p[kk]/ws[kk])* hmat[kk][k];
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survpenal.c -o survpenal.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survreg6.c -o survreg6.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survreg7.c -o survreg7.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survregc1.c -o survregc1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survregc2.c -o survregc2.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o concordance1.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o init.o msurv.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpQaB70h/R.INSTALL18021d920041/survival/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'survival'
finding HTML links ... done
Surv html
aareg html
agreg.fit html
aml html
anova.coxph html
attrassign html
basehaz html
bladder html
cch html
cgd html
clogit html
cluster html
colon html
cox.zph html
coxph html
coxph.control html
coxph.detail html
coxph.object html
coxph.wtest html
dsurvreg html
flchain html
frailty html
heart html
is.ratetable html
kidney html
lines.survfit html
logan html
lung html
mgus html
model.frame.coxph html
model.matrix.coxph html
nwtco html
ovarian html
pbc html
pbcseq html
plot.aareg html
plot.cox.zph html
plot.survfit html
predict.coxph html
predict.survreg html
print.aareg html
print.summary.coxph html
print.summary.survexp html
print.summary.survfit html
print.survfit html
pspline html
pyears html
quantile.survfit html
ratetable html
ratetableDate html
rats html
rats2 html
residuals.coxph html
residuals.survreg html
ridge html
stanford2 html
strata html
summary.aareg html
summary.coxph html
summary.survexp html
summary.survfit html
survConcordance html
survSplit html
survdiff html
survexp html
survexp.fit html
survexp.us html
survfit html
survfit.coxph html
survfit.formula html
survfit.object html
survfitcoxph.fit html
survival-internal html
survobrien html
survreg html
survreg.control html
survreg.distributions html
survreg.object html
survregDtest html
tcut html
tobin html
untangle.specials html
uspop2 html
veteran html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)
Making 'packages.html' ... done
begin installing recommended package class
* installing *source* package 'cluster' ...
** package 'cluster' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c clara.c -o clara.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c daisy.f -o daisy.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dysta.f -o dysta.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fanny.c -o fanny.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mona.f -o mona.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pam.c -o pam.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sildist.c -o sildist.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c spannel.c -o spannel.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c twins.c -o twins.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/cluster/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cluster'
finding HTML links ... done
agnes html
agnes.object html
agriculture html
animals html
bannerplot html
chorSub html
clara html
clara.object html
clusGap html
clusplot.default html
Rd warning: /usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/man/clusplot.default.Rd:208: missing file link 'cov.mve'
clusplot.partition html
cluster-internal html
coef.hclust html
daisy html
diana html
dissimilarity.object html
ellipsoidhull html
Rd warning: /usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/man/ellipsoidhull.Rd:36: missing file link 'cov.mve'
Rd warning: /usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/man/ellipsoidhull.Rd:86: missing file link 'cov.mve'
fanny html
fanny.object html
flower html
lower.to.upper.tri.inds html
mona html
mona.object html
pam html
pam.object html
partition.object html
plantTraits html
plot.agnes html
Rd warning: /usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/man/plot.agnes.Rd:73: missing file link 'plot.dendrogram'
plot.diana html
plot.mona html
plot.partition html
pltree html
pltree.twins html
pluton html
predict.ellipsoid html
print.agnes html
print.clara html
print.diana html
print.dissimilarity html
Rd warning: /usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/man/print.dissimilarity.Rd:27: missing file link 'print.dist'
print.fanny html
print.mona html
print.pam html
ruspini html
silhouette html
sizeDiss html
summary.agnes html
summary.clara html
summary.diana html
summary.mona html
summary.pam html
twins.object html
volume.ellipsoid html
votes.repub html
xclara html
** building package indices
** testing if installed package can be loaded
* DONE (cluster)
Making 'packages.html' ... done
begin installing recommended package boot
* installing *source* package 'class' ...
** package 'class' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/Rtmp021oNH/R.INSTALL1ad0799d6abd/class/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c class.c -o class.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o class.so class.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/Rtmp021oNH/R.INSTALL1ad0799d6abd/class/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/class/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'class'
finding HTML links ... done
SOM html
batchSOM html
condense html
knn html
knn.cv html
knn1 html
lvq1 html
lvq2 html
lvq3 html
lvqinit html
lvqtest html
multiedit html
olvq1 html
reduce.nn html
somgrid html
** building package indices
** testing if installed package can be loaded
* DONE (class)
Making 'packages.html' ... done
* installing *source* package 'boot' ...
** package 'boot' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'boot'
finding HTML links ... done
EEF.profile html
Imp.Estimates html
abc.ci html
acme html
aids html
aircondit html
amis html
aml html
beaver html
bigcity html
boot-practicals html
boot html
boot.array html
boot.ci html
brambles html
breslow html
calcium html
cane html
capability html
catsM html
cav html
cd4 html
cd4.nested html
censboot html
channing html
claridge html
cloth html
co.transfer html
coal html
control html
corr html
cum3 html
cv.glm html
darwin html
dogs html
downs.bc html
ducks html
empinf html
envelope html
exp.tilt html
fir html
freq.array html
frets html
glm.diag html
glm.diag.plots html
gravity html
hirose html
imp.weights html
inv.logit html
islay html
jack.after.boot html
k3.linear html
linear.approx html
lines.saddle.distn html
logit html
manaus html
melanoma html
motor html
neuro html
nitrofen html
nodal html
norm.ci html
nuclear html
paulsen html
plot.boot html
poisons html
polar html
print.boot html
print.bootci html
print.saddle.distn html
print.simplex html
remission html
saddle html
saddle.distn html
saddle.distn.object html
salinity html
simplex html
simplex.object html
smooth.f html
sunspot html
survival html
tau html
tilt.boot html
tsboot html
tuna html
urine html
var.linear html
wool html
** building package indices
** testing if installed package can be loaded
* DONE (boot)
Making 'packages.html' ... done
* installing *source* package 'nlme' ...
** package 'nlme' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpRs3bjG/R.INSTALL19f357052816/nlme/src'
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chol.f -o chol.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c corStruct.c -o corStruct.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gnls.c -o gnls.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nlOptimizer.c -o nlOptimizer.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nlme.c -o nlme.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nlmefit.c -o nlmefit.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nls.c -o nls.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pdMat.c -o pdMat.o
f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rs.f -o rs.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o nls.o pdMat.o rs.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpRs3bjG/R.INSTALL19f357052816/nlme/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'nlme'
finding HTML links ... done
ACF html
ACF.gls html
ACF.lme html
Alfalfa html
Assay html
BodyWeight html
Cefamandole html
Coef html
Covariate html
Covariate.varFunc html
Dialyzer html
Dim html
Dim.corSpatial html
Dim.corStruct html
Dim.pdMat html
Earthquake html
Extract.pdMat html
Fatigue html
Gasoline html
Glucose html
Glucose2 html
Gun html
IGF html
Initialize html
Initialize.corStruct html
Initialize.glsStruct html
Initialize.lmeStruct html
Initialize.reStruct html
Initialize.varFunc html
LDEsysMat html
Machines html
MathAchSchool html
MathAchieve html
Matrix html
Matrix.pdMat html
Matrix.reStruct html
Meat html
Milk html
Muscle html
Names html
Names.formula html
Names.pdBlocked html
Names.pdMat html
Names.reStruct html
Nitrendipene html
Oats html
Orthodont html
Ovary html
Oxboys html
Oxide html
PBG html
Phenobarb html
Pixel html
Quinidine html
Rail html
RatPupWeight html
Relaxin html
Remifentanil html
Soybean html
Spruce html
Tetracycline1 html
Tetracycline2 html
VarCorr html
Variogram html
Variogram.corExp html
Variogram.corGaus html
Variogram.corLin html
Variogram.corRatio html
Variogram.corSpatial html
Variogram.corSpher html
Variogram.default html
Variogram.gls html
Variogram.lme html
Wafer html
Wheat html
Wheat2 html
allCoef html
anova.gls html
anova.lme html
as.matrix.corStruct html
as.matrix.pdMat html
as.matrix.reStruct html
asOneFormula html
asTable html
augPred html
balancedGrouped html
bdf html
coef.corStruct html
coef.gnls html
coef.lmList html
coef.lme html
coef.modelStruct html
coef.pdMat html
coef.reStruct html
coef.varFunc html
collapse html
collapse.groupedData html
compareFits html
comparePred html
corAR1 html
corARMA html
corCAR1 html
corClasses html
corCompSymm html
corExp html
corFactor html
corFactor.corStruct html
corGaus html
corLin html
corMatrix html
corMatrix.corStruct html
corMatrix.pdMat html
corMatrix.reStruct html
corNatural html
corRatio html
corSpatial html
corSpher html
corSymm html
ergoStool html
fdHess html
fitted.glsStruct html
fitted.gnlsStruct html
fitted.lmList html
fitted.lme html
fitted.lmeStruct html
fitted.nlmeStruct html
fixed.effects html
fixef.lmList html
formula.pdBlocked html
formula.pdMat html
formula.reStruct html
gapply html
getCovariate html
getCovariate.corStruct html
getCovariate.data.frame html
getCovariate.varFunc html
getCovariateFormula html
getData html
getData.gls html
getData.lmList html
getData.lme html
getGroups html
getGroups.corStruct html
getGroups.data.frame html
getGroups.gls html
getGroups.lmList html
getGroups.lme html
getGroups.varFunc html
getGroupsFormula html
getResponse html
getResponseFormula html
getVarCov html
gls-internal html
gls html
glsControl html
glsObject html
glsStruct html
gnls html
gnlsControl html
gnlsObject html
gnlsStruct html
groupedData html
gsummary html
intervals html
intervals.gls html
intervals.lmList html
intervals.lme html
isBalanced html
isInitialized html
lmList html
lmList.groupedData html
lme html
lme.groupedData html
lme.lmList html
lmeControl html
lmeObject html
lmeStruct html
logDet html
logDet.corStruct html
logDet.pdMat html
logDet.reStruct html
logLik.corStruct html
logLik.glsStruct html
logLik.gnls html
logLik.gnlsStruct html
logLik.lmList html
logLik.lme html
logLik.lmeStruct html
logLik.reStruct html
logLik.varFunc html
model.matrix.reStruct html
needUpdate html
needUpdate.modelStruct html
nlme html
nlme.nlsList html
nlmeControl html
nlmeObject html
nlmeStruct html
nlsList html
nlsList.selfStart html
pairs.compareFits html
pairs.lmList html
pairs.lme html
pdBlocked html
pdClasses html
pdCompSymm html
pdConstruct html
pdConstruct.pdBlocked html
pdDiag html
pdFactor html
pdFactor.reStruct html
pdIdent html
pdLogChol html
pdMat html
pdMatrix html
pdMatrix.reStruct html
pdNatural html
pdSymm html
phenoModel html
plot.ACF html
plot.Variogram html
plot.augPred html
plot.compareFits html
plot.gls html
plot.intervals.lmList html
plot.lmList html
plot.lme html
plot.nffGroupedData html
plot.nfnGroupedData html
plot.nmGroupedData html
plot.ranef.lmList html
plot.ranef.lme html
pooledSD html
predict.gls html
predict.gnls html
predict.lmList html
predict.lme html
predict.nlme html
print.summary.pdMat html
print.varFunc html
qqnorm.gls html
qqnorm.lme html
quinModel html
random.effects html
ranef.lmList html
ranef.lme html
reStruct html
recalc html
recalc.corStruct html
recalc.modelStruct html
recalc.reStruct html
recalc.varFunc html
residuals.gls html
residuals.glsStruct html
residuals.gnlsStruct html
residuals.lmList html
residuals.lme html
residuals.lmeStruct html
residuals.nlmeStruct html
simulate.lme html
solve.pdMat html
solve.reStruct html
splitFormula html
summary.corStruct html
summary.gls html
summary.lmList html
summary.lme html
summary.modelStruct html
summary.nlsList html
summary.pdMat html
summary.varFunc html
update.modelStruct html
update.varFunc html
varClasses html
varComb html
varConstPower html
varExp html
varFixed html
varFunc html
varIdent html
varPower html
varWeights html
varWeights.glsStruct html
varWeights.lmeStruct html
** building package indices
** testing if installed package can be loaded
* DONE (nlme)
Making 'packages.html' ... done
* installing *source* package 'Matrix' ...
** package 'Matrix' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c CHMfactor.c -o CHMfactor.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Csparse.c -o Csparse.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c TMatrix_as.c -o TMatrix_as.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Tsparse.c -o Tsparse.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Mutils.c -o Mutils.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chm_common.c -o chm_common.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cs.c -o cs.o
cs.c: In function 'cs_qr':
cs.c:1408:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai,
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cs_utils.c -o cs_utils.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dense.c -o dense.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgCMatrix.c -o dgCMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgTMatrix.c -o dgTMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgeMatrix.c -o dgeMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpoMatrix.c -o dpoMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dppMatrix.c -o dppMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dsCMatrix.c -o dsCMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dsyMatrix.c -o dsyMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dspMatrix.c -o dspMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtCMatrix.c -o dtCMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtTMatrix.c -o dtTMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtrMatrix.c -o dtrMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtpMatrix.c -o dtpMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c factorizations.c -o factorizations.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ldense.c -o ldense.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lgCMatrix.c -o lgCMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sparseQR.c -o sparseQR.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c abIndex.c -o abIndex.o
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD'
( cd Lib ; make clean )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD/Lib'
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD'
( cd Source ; make clean )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD/Source'
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD/Source'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD'
( cd Source ; make clean )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD/Source'
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD/Source'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/SuiteSparse_config'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/SuiteSparse_config'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD'
( cd Lib ; make )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_aat.c -o cholmod_aat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_add.c -o cholmod_add.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_band.c -o cholmod_band.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:0:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^
In file included from ../Core/cholmod_change_factor.c:118:0:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
Int nsuper, xsize, ssize ;
^
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
Int *Lp, *Li, *Lnz ;
^
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
Int *Lp, *Li, *Lnz ;
^
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
Int *Ls, *Lpi, *Lpx, *Super, *Li ;
^
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
Int *Ls, *Lpi, *Lpx, *Super, *Li ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_common.c -o cholmod_common.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_complex.c -o cholmod_complex.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_copy.c -o cholmod_copy.o
../Core/cholmod_copy.c: In function 'cholmod_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
Int nrow, ncol, up, lo, values, diag, astype ;
^
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
Int nrow, ncol, up, lo, values, diag, astype ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_dense.c -o cholmod_dense.o
In file included from ../Core/cholmod_dense.c:48:0:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
In file included from ../Core/cholmod_dense.c:50:0:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^
In file included from ../Core/cholmod_dense.c:52:0:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^
../Core/cholmod_dense.c: In function 'cholmod_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
Int i, n, nz ;
^
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_error.c -o cholmod_error.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_factor.c -o cholmod_factor.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_memory.c -o cholmod_memory.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
../Core/cholmod_sparse.c: In function 'cholmod_copy_sparse':
../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
In file included from ../Core/cholmod_transpose.c:124:0:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
In file included from ../Core/cholmod_transpose.c:126:0:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
In file included from ../Core/cholmod_transpose.c:128:0:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
In file included from ../Core/cholmod_transpose.c:131:0:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
In file included from ../Core/cholmod_transpose.c:133:0:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
In file included from ../Core/cholmod_transpose.c:136:0:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
In file included from ../Core/cholmod_triplet.c:108:0:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
In file included from ../Core/cholmod_triplet.c:110:0:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
In file included from ../Core/cholmod_triplet.c:112:0:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
Int i, j, p, k, stype, nrow, ncol, nz, ok ;
^
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_version.c -o cholmod_version.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Check/cholmod_check.c -o cholmod_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
^
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
^
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
^
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
^
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Check/cholmod_read.c -o cholmod_read.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Check/cholmod_write.c -o cholmod_write.o
../Check/cholmod_write.c: In function 'cholmod_write_sparse':
../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
^
../Check/cholmod_check.c: In function 'check_factor.constprop':
../Check/cholmod_check.c:1934:48: warning: 'psxend' may be used uninitialized in this function [-Wmaybe-uninitialized]
|| (for_cholesky && psxend - psx != nsrow * nscol))
^
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_analyze_p2':
../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
^
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
^
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_factorize_p':
../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
In file included from ../Cholesky/cholmod_rowfac.c:164:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
In file included from ../Cholesky/cholmod_rowfac.c:166:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
In file included from ../Cholesky/cholmod_rowfac.c:168:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
In file included from ../Cholesky/cholmod_rowfac.c:172:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
In file included from ../Cholesky/cholmod_rowfac.c:174:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
In file included from ../Cholesky/cholmod_rowfac.c:176:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
In file included from ../Cholesky/cholmod_solve.c:66:0:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Lx, *Yx, *Yz ;
^
In file included from ../Cholesky/cholmod_solve.c:69:0:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Lx, *Yx, *Yz ;
^
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
In file included from ../MatrixOps/cholmod_sdmult.c:48:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
In file included from ../MatrixOps/cholmod_sdmult.c:50:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Modify/cholmod_updown.c -o cholmod_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
*Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^
In file included from ../Supernodal/cholmod_super_numeric.c:80:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:0:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
In file included from ../Supernodal/cholmod_super_solve.c:30:0:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
Int totsize ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:0:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^
In file included from ../Core/cholmod_change_factor.c:118:0:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
Int nsuper, xsize, ssize ;
^
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
Int *Lp, *Li, *Lnz ;
^
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
Int *Lp, *Li, *Lnz ;
^
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
double *Lx, *Lz ;
^
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
Int *Ls, *Lpi, *Lpx, *Super, *Li ;
^
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
Int *Ls, *Lpi, *Lpx, *Super, *Li ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_copy.c -o cholmod_l_copy.o
../Core/cholmod_copy.c: In function 'cholmod_l_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
Int nrow, ncol, up, lo, values, diag, astype ;
^
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
Int nrow, ncol, up, lo, values, diag, astype ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o
In file included from ../Core/cholmod_dense.c:48:0:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
In file included from ../Core/cholmod_dense.c:50:0:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^
In file included from ../Core/cholmod_dense.c:52:0:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Xx, *Az, *Xz ;
^
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Cx, *Xz, *Cz ;
^
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz, *Yx, *Yz ;
^
../Core/cholmod_dense.c: In function 'cholmod_l_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
Int i, n, nz ;
^
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Xx, *Xz ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
../Core/cholmod_sparse.c: In function 'cholmod_l_copy_sparse':
../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
^
In file included from ../Core/cholmod_transpose.c:124:0:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
In file included from ../Core/cholmod_transpose.c:126:0:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
In file included from ../Core/cholmod_transpose.c:128:0:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
In file included from ../Core/cholmod_transpose.c:131:0:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Fx, *Fz ;
^
In file included from ../Core/cholmod_transpose.c:133:0:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
In file included from ../Core/cholmod_transpose.c:136:0:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
^
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
In file included from ../Core/cholmod_triplet.c:108:0:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
In file included from ../Core/cholmod_triplet.c:110:0:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
In file included from ../Core/cholmod_triplet.c:112:0:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
double *Rx, *Rz, *Tx, *Tz ;
^
../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
Int i, j, p, k, stype, nrow, ncol, nz, ok ;
^
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_check.c -o cholmod_l_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
^
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
^
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
^
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
^
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_write.c -o cholmod_l_write.o
../Check/cholmod_write.c: In function 'cholmod_l_write_sparse':
../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
^
../Check/cholmod_check.c: In function 'check_factor.constprop':
../Check/cholmod_check.c:1934:48: warning: 'psxend' may be used uninitialized in this function [-Wmaybe-uninitialized]
|| (for_cholesky && psxend - psx != nsrow * nscol))
^
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_l_analyze_p2':
../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
^
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
^
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_l_factorize_p':
../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
In file included from ../Cholesky/cholmod_rowfac.c:166:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
In file included from ../Cholesky/cholmod_rowfac.c:168:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
In file included from ../Cholesky/cholmod_rowfac.c:172:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
In file included from ../Cholesky/cholmod_rowfac.c:174:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
^
In file included from ../Cholesky/cholmod_rowfac.c:176:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
In file included from ../Cholesky/cholmod_solve.c:66:0:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Lx, *Yx, *Yz ;
^
In file included from ../Cholesky/cholmod_solve.c:69:0:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Lx, *Yx, *Yz ;
^
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
In file included from ../MatrixOps/cholmod_sdmult.c:48:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
^
In file included from ../MatrixOps/cholmod_sdmult.c:50:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^
In file included from ../Supernodal/cholmod_super_numeric.c:80:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
^
../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
*Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:0:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
In file included from ../Supernodal/cholmod_super_solve.c:30:0:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
nsrow2, n, ps2, j, i, d, nrhs ;
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_l_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
Int totsize ;
^
ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD'
( cd Source ; make lib )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c colamd_global.c -o colamd_global.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c colamd.c -o colamd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD/Source'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD'
( cd Source ; make lib )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_1.c -o amd_i_1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_2.c -o amd_i_2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_order.c -o amd_i_order.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_control.c -o amd_i_control.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_info.c -o amd_i_info.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_global.c -o amd_i_global.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_global.c -o amd_l_global.o
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD/Source'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/SuiteSparse_config'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/SuiteSparse_config'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'image' from package 'graphics' in package 'Matrix'
Creating a generic function for 'solve' from package 'base' in package 'Matrix'
Creating a generic function for 'chol2inv' from 'base' in package 'Matrix'
(from the saved implicit definition)
Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix'
Creating a generic function for 'determinant' from package 'base' in package 'Matrix'
Creating a generic function for 'update' from package 'stats' in package 'Matrix'
Creating a generic function for 'as.vector' from package 'base' in package 'Matrix'
Creating a generic function for 't' from package 'base' in package 'Matrix'
Creating a generic function for 'diag' from package 'base' in package 'Matrix'
Creating a generic function for 'as.matrix' from package 'base' in package 'Matrix'
Creating a generic function for 'as.array' from package 'base' in package 'Matrix'
Creating a generic function for 'head' from package 'utils' in package 'Matrix'
Creating a generic function for 'tail' from package 'utils' in package 'Matrix'
Creating a generic function for 'drop' from package 'base' in package 'Matrix'
Creating a generic function for 'mean' from package 'base' in package 'Matrix'
Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix'
Creating a generic function for 'isSymmetric' from package 'base' in package 'Matrix'
Creating a generic function for 'unname' from package 'base' in package 'Matrix'
Creating a generic function for 'chol' from package 'base' in package 'Matrix'
Creating a generic function for 'norm' from package 'base' in package 'Matrix'
Creating a generic function for 'rcond' from 'base' in package 'Matrix'
(from the saved implicit definition)
Creating a generic function for 'rcond' from package 'base' in package 'Matrix'
Creating a generic function for 'all.equal' from package 'base' in package 'Matrix'
Creating a generic function for 'diff' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc"
Creating a generic function for 'colSums' from package 'base' in package 'Matrix'
Creating a generic function for 'colMeans' from package 'base' in package 'Matrix'
Creating a generic function for 'rowSums' from package 'base' in package 'Matrix'
Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix'
in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix'
Creating a generic function for 'qr' from package 'base' in package 'Matrix'
Creating a generic function for 'diag<-' from package 'base' in package 'Matrix'
Creating a generic function for 'crossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'print' from package 'base' in package 'Matrix'
Creating a generic function for 'summary' from package 'base' in package 'Matrix'
Creating a generic function for 'which' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM"
in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph"
in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph"
in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL"
in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL"
Creating a generic function for 'format' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.R' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix'
** help
*** installing help indices
converting help for package 'Matrix'
finding HTML links ... done
BunchKaufman-methods html
CAex html
CHMfactor-class html
Cholesky-class html
Cholesky html
CsparseMatrix-class html
Diagonal html
Hilbert html
KNex html
KhatriRao html
LU-class html
Matrix-class html
Matrix html
MatrixFactorization-class html
RsparseMatrix-class html
Schur-class html
Schur html
SparseM-conv html
Subassign-methods html
TsparseMatrix-class html
USCounties html
Xtrct-methods html
abIndex-class html
Rd warning: /usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/man/abIndex-class.Rd:81: missing file link 'Ops'
abIseq html
all-methods html
all.equal-methods html
atomicVector-class html
band html
bandSparse html
bdiag html
cBind html
chol html
chol2inv-methods html
colSums html
compMatrix-class html
condest html
dMatrix-class html
ddenseMatrix-class html
ddiMatrix-class html
denseMatrix-class html
dgCMatrix-class html
dgRMatrix-class html
dgTMatrix-class html
dgeMatrix-class html
diagU2N html
diagonalMatrix-class html
dpoMatrix-class html
drop0 html
dsCMatrix-class html
dsRMatrix-class html
dsparseMatrix-class html
dsyMatrix-class html
dtCMatrix-class html
dtRMatrix-class-def html
dtpMatrix-class html
dtrMatrix-class html
expand html
expm html
externalFormats html
facmul html
forceSymmetric html
formatSparseM html
generalMatrix-class html
graph2T html
image-methods html
Rd warning: /usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/man/image-methods.Rd:48: missing file link 'panel.levelplot.raster'
indMatrix-class html
index-class html
invPerm html
is.na-methods html
is.null.DN html
isSymmetric-methods html
isTriangular html
kronecker-methods html
ldenseMatrix-class html
ldiMatrix-class html
lgeMatrix-class html
lsparseMatrix-classes html
lsyMatrix-class html
ltrMatrix-class html
lu html
matrix-products html
Rd warning: /usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/man/matrix-products.Rd:325: missing file link 'tcrossprod'
nMatrix-class html
ndenseMatrix-class html
nearPD html
ngeMatrix-class html
nnzero html
norm html
nsparseMatrix-classes html
nsyMatrix-class html
ntrMatrix-class html
number-class html
pMatrix-class html
printSpMatrix html
qr-methods html
rankMatrix html
rcond html
rep2abI html
replValue-class html
rleDiff-class html
rsparsematrix html
solve-methods html
spMatrix html
sparse.model.matrix html
sparseLU-class html
sparseMatrix-class html
sparseMatrix html
sparseQR-class html
sparseVector-class html
sparseVector html
symmetricMatrix-class html
symmpart html
triangularMatrix-class html
unpack html
unused-classes html
updown html
** building package indices
Loading required package: Matrix
** installing vignettes
'Comparisons.Rnw'
'Design-issues.Rnw'
'Intro2Matrix.Rnw'
'Introduction.Rnw'
'sparseModels.Rnw'
** testing if installed package can be loaded
* DONE (Matrix)
Making 'packages.html' ... done
begin installing recommended package mgcv
* installing *source* package 'mgcv' ...
** package 'mgcv' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmprNiBIc/R.INSTALL1c8e1a8e1901/mgcv/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxph.c -o coxph.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gdi.c -o gdi.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c magic.c -o magic.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mat.c -o mat.o
coxph.c: In function 'coxlpl':
coxph.c:309:39: warning: 'd2ldA_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
d2ldA_p[l + off * *p] += d2gamma[i+ off * *n] * X[i + *n * l] * X[ i + *n *l];
^
coxph.c:302:47: warning: 'd1A_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
d1A_p[k + *p * l + m * *p * *p] += xx * X[i + *n * k] * X[i + *n * l];
^
coxph.c:381:27: warning: 'd1b_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
R_chk_free(d1gamma_p);R_chk_free(d1b_p);
^
coxph.c:380:5: warning: 'd1eta' may be used uninitialized in this function [-Wmaybe-uninitialized]
R_chk_free(d1eta);R_chk_free(d1gamma);
^
coxph.c:381:5: warning: 'd1gamma_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
R_chk_free(d1gamma_p);R_chk_free(d1b_p);
^
coxph.c:380:23: warning: 'd1gamma' may be used uninitialized in this function [-Wmaybe-uninitialized]
R_chk_free(d1eta);R_chk_free(d1gamma);
^
coxph.c:293:35: warning: 'd2b_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
d2b_p[l + off * *p] += d2gamma[i+ off * *n] * X[i + *n * l];
^
coxph.c:195:22: warning: 'd2gamma_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
*d2eta,*d2gamma,*d2gamma_p,*d2b_p,
^
coxph.c:309:50: warning: 'd2gamma' may be used uninitialized in this function [-Wmaybe-uninitialized]
d2ldA_p[l + off * *p] += d2gamma[i+ off * *n] * X[i + *n * l] * X[ i + *n *l];
^
coxph.c:386:5: warning: 'd2eta' may be used uninitialized in this function [-Wmaybe-uninitialized]
R_chk_free(d2eta);R_chk_free(d2gamma);
^
coxph.c:348:36: warning: 'A_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
d2H[l + off * *p] += xx3 * (A_p[l + *p *l] * d1gamma_p[k] +
^
coxph.c:192:6: warning: 'b_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
*b_p,*A_p,*p1,*p2,*p3,*p4,
^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mgcv.c -o mgcv.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c misc.c -o misc.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mvn.c -o mvn.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qp.c -o qp.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c soap.c -o soap.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sparse-smooth.c -o sparse-smooth.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c tprs.c -o tprs.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o mgcv.so coxph.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmprNiBIc/R.INSTALL1c8e1a8e1901/mgcv/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mgcv'
finding HTML links ... done
Beta html
Predict.matrix html
Predict.matrix.cr.smooth html
Predict.matrix.soap.film html
Rrank html
Tweedie html
anova.gam html
bam html
Rd warning: /usr/src/tmp/RtmprNiBIc/R.INSTALL1c8e1a8e1901/mgcv/man/bam.Rd:13: missing file link 'parallel'
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fs.test html
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gam.selection html
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gamm html
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get.var html
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initial.sp html
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linear.functional.terms html
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mgcv-package html
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ocat html
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predict.bam html
Rd warning: /usr/src/tmp/RtmprNiBIc/R.INSTALL1c8e1a8e1901/mgcv/man/predict.bam.Rd:71: missing file link 'parLapply'
predict.gam html
print.gam html
qq.gam html
rTweedie html
random.effects html
residuals.gam html
rig html
s html
scat html
slanczos html
smooth.construct html
smooth.construct.ad.smooth.spec html
smooth.construct.cr.smooth.spec html
smooth.construct.ds.smooth.spec html
smooth.construct.fs.smooth.spec html
smooth.construct.mrf.smooth.spec html
smooth.construct.ps.smooth.spec html
smooth.construct.re.smooth.spec html
smooth.construct.so.smooth.spec html
smooth.construct.sos.smooth.spec html
smooth.construct.t2.smooth.spec html
smooth.construct.tensor.smooth.spec html
smooth.construct.tp.smooth.spec html
smooth.terms html
smoothCon html
sp.vcov html
spasm.construct html
step.gam html
summary.gam html
t2 html
te html
tensor.prod.model.matrix html
uniquecombs html
vcov.gam html
vis.gam html
ziP html
ziplss html
** building package indices
** testing if installed package can be loaded
* DONE (mgcv)
Making 'packages.html' ... done
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[17 Chapter 9 [30]] [18] [31] Chapter 4 [19
[32]] Appendix A [33] [20 [34]] Chapter 5 [21] [35] [22] [36] [23] [37] [24] [25] [38] Chapter 6
[26] [39 [27]] Chapter 7 [28 [40]] [41] [29] Appendix B
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[59] Chapter 10 [46] [47 [60]] )</
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] Appendix D [64] [65] [66]
(Function and variable index) [67] (Concept index) [68]
(Environment variable index) [69]. [70] )
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[31]
[32] Appendix A [33] [34] [35] [36] [37] [38] [39] [40] [41] Appendix B
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[1] [2] Chapter 1 [3
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[]@textrm You can tar-get spe-cific Sparc ar-chi-tec-tures for (slightly) highe
r per-for-mance:
[59]] [60] [5] [61] [62] [6] [63] Appendix D [64] Chapter 2 [7 [65]] [8] [9 [66]]
(Function and variable index) [67] (./R-admin.vrs [10) (Concept index) [68]]
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[16] [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] Chapter 7 [23.]
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[]@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R
.framework/Resources/etc/Makeconf[]
[23]] [5] [24] [6] [25] Chapter 7 Chapter 2 [26 [7]] [8] [9] [27] [10 [28]] Chapter 8 [29] [11] Chapter 9 [30] [12] [31]
Chapter 3 [13]
[32] Appendix A [33] [34] [14] Chapter 4 [15] [35] [16] [36] [17] [37] [38] [18] [19] [39] [40] [20] [41 Chapter 5 [21]] Appendix B
[42] [43]
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[56]) [33] )
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[]@textrm You can tar-get spe-cific Sparc ar-chi-tec-tures for (slightly) highe
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[62] [63] Appendix D [64] [65] [66]
(Function and variable index) [67] (./R-admin.vrs) (Concept index) [68]
(./R-admin.cps) (Environment variable index) [69] (./R-admin.ens) [70] )
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[1] [2
[22] Chapter 1 [3]] [23]
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[24] [25] [4] [26 [5]] [27] [6] [28] [29 Chapter 2 [7]] [30] [8] [9 [31]] [10 [32]] [11 [33]] [12] [34
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
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columns to fac-tors un-less
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
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[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is
ap-plied to an ob-ject with class at-tribute
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[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 http : / /
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[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols.
They can be es-tab-lished us-ing
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[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
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[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[88 localization, [217]] [218] [219] [220] [89] formatting, and turning on texinfo input format.)
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [221] [90 [222)]] (./version.texi) [223])
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\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 '). Prox-ies can be spe
c-i-fied for HTTP and FTP \T1/pcr/m/n/10 url \T1/ptm/m/n/10 con-nec-tions: see
[92]}]
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[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
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\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
and web-pages gen-er-
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\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If it is re-quired (it is n
ot rec-om-mended) when writ-ing
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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
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\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
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[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[98) [246] Chapter 1] [247]
[248] Chapter 2 [1 [249] [99]] [250] [251] [252] [100] [2] [253] [101 [254]] [255])
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
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@textbf storage.mode|
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
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[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
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[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
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\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
but this can be changed by set-ting
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[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
a data frame by call-ing
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[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
is a generic func-tion, meth-ods can be
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[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
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[171 [114]]] [172] [173] [174] [10 [115]] [175] [176]
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\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz =
"UTC") \T1/ptm/m/n/10 will give
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[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10
reads the file byte-by-byte. This al-lows a
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issing"))
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[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
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[]\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(1+2, "y", {cat(" HO
! "); pi+2})[]
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[]\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so
urce \T1/ptm/m/n/10 at-tribute), use
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\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
make the re-sult parseable.
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[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
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[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
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[]\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[]
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[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
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\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
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[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / IEEE _ 754-[]198
5$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / en . wikipedia .
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\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 http : / / en . wikipedia . org / wiki / Double _
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[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
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[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[143
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
from the re-verse
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\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
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[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent
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[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
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[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
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Chapter 7
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live/fonts/type1/bluesky/cm/cmr7.pfb [252]></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmr8.pfb [156></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb [253]]> [254]</usr
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[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
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[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
and
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exlive/fonts/type1/bluesky/cm/cmtt12.pfb [131]> [132] Chapter 9</usr/share/texmf-texlive/fonts/type1/
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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[158
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[136]] [137] [43] [138] [159 Chapter 10 [139]] [44]
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[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
passed as an ar-gu-ment
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\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
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[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
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[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
found by
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[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
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\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
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Ok [158] [165 [48 [160]]] [161] [162] [166 [49 [163]] [164]] [165] [166] [167]
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[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
Underfull \hbox (badness 2221) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[167 [50 [168]] [169]] [170] (Function and Variable Index) [168 [51]
[171]] (./R-lang.vrs [172] [173] [169] [174] [175] [176]
[52 [170 [177]] [178] [179]] [180]) [181] (Concept Index) [171 [53]] [182 (./R-lang.cps]
[183]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11761--11761
[]\T1/pcr/m/n/9 A <- data.frame(x = 1:3, y = I(matrix(4:6)), z = I(matrix(lett
ers[1:9], 3, 3)))[]
[172 [184]] [185] [186] [187]) [173 [188])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exbraces.mf
Ok [94] Appendix A [126] [23] [40]] [41] [54 [60] [124] [62] [91] [93] [92] [123] [125]
[95] [127] [32]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/expunct.mf
Ok [14] [15] [19]] [174 [20] [13]] [18] [55 [33]] [39] [42] [43] )
(see the transcript file for additional information)</usr/share/texmf-texlive/f
onts/type1/bluesky/cm/cmb10.pfb [44] [46] [47] [58]
[59] [61]> [96] [189]</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmbx12.pfb [17] [45] [16] [21]> [175 [22])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exaccent.mf</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb
Ok [0]></usr/
share/texmf-texlive/fonts/type1/bluesky/cm/cmmi12.pfb] [1]> [2]</usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmmi9.pfb [3] [4]></usr/share/texmf-texlive/fonts/type1/bluesky
/cm/cmr10.pfb> [176</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb]></usr/s
hare/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb></usr/share/texmf-texlive/fo
nts/type1/bluesky/cm/cmsl10.pfb> [5]</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmsltt10.pfb [6] [7] [8] [9]>
Underfull \hbox (badness 2221) in paragraph at lines 12121--12127
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[177</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb [10] [11] [12])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exsign.mf></us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy9.pfb
Ok [24] [34] [35]]></usr/share/texmf-texliv
e/fonts/type1/bluesky/cm/cmti10.pfb [36]> [37]</usr/share/texmf-texlive/fonts/type1/blues
ky/cm/cmtt10.pfb [64] [191]> [159])</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrlig.mf
Ok [25] [26]> [178 [28]] [27]
Output written on R-lang.pdf (60 pages, 413992 bytes).
Transcript written on R-lang.log.
[29] [30] [179] [31])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exromp.mf
Ok [38] [63] [190])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrulett.mf
Ok [65] [66] [67] [180 [68]] [69] [70] [71] [72] [73
Underfull \hbox (badness 2253) in paragraph at lines 12350--12352
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
[181] [74]] [75] [76] [77] [78]
[79] [80]
Underfull \hbox (badness 10000) in paragraph at lines 12454--12456
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[182 [81]] [82] [83] [84] [85] [86] [183 [87]] [88] [89] [90])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrllett.mf
Ok [97] [98] [99] [100]
Underfull \hbox (badness 10000) in paragraph at lines 12602--12604
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[184 [101] [102]] [103] [104] [105] [106] [185 [107] [108]]
[109] [110] [111] [112] [113] [114] [115]
Underfull \hbox (badness 10000) in paragraph at lines 12700--12704
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (30.78088pt too wide) in paragraph at lines 12750--12750
[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")
[186 [116] [117]] [118] [119] [120] [187
[121] [122]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrdigit.mf
Ok [48]] [49] [50] [51] [52] [53] [54] [55] [56] [57])
Underfull \hbox (badness 10000) in paragraph at lines 12839--12842
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12849--12849
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive TRUE)[]
[188
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrligtb.mf
Ok) ) ) )
(some charht values had to be adjusted by as much as 0.07599pt)
Font metrics written on ecrm1095.tfm.
Output written on ecrm1095.603gf (256 characters, 55528 bytes).
Transcript written on ecrm1095.log.
]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12932--12932
[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE)
Underfull \hbox (badness 7238) in paragraph at lines 12950--12957
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 12950--12957
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 12950--12957
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
of fact, the in-ter-nal al-go-
Underfull \hbox (badness 3965) in paragraph at lines 12958--12962
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[189] [190]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13066--13066
[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13067--13067
[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
[191]
Underfull \hbox (badness 10000) in paragraph at lines 13148--13152
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
Underfull \hbox (badness 1389) in paragraph at lines 13148--13152
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[192]
Underfull \hbox (badness 1314) in paragraph at lines 13208--13210
[]\T1/ptm/m/n/10 In re-cent ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 most u
n-nec-es-sary copy-ing is avoided: on the other hand us-ing
[193] [194] [195]
Underfull \hbox (badness 1168) in paragraph at lines 13402--13406
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real
or com-plex vec-
Underfull \hbox (badness 2012) in paragraph at lines 13402--13406
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
[196]
Underfull \hbox (badness 6944) in paragraph at lines 13496--13499
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13521--13521
[]\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[]
[197] [198] [199]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13668--13668
[] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx
= NA,[]
Underfull \hbox (badness 2790) in paragraph at lines 13675--13678
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
Underfull \hbox (badness 4254) in paragraph at lines 13691--13699
[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 13706--13710
[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[200]
Underfull \hbox (badness 10000) in paragraph at lines 13761--13763
[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so
Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point,
Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
Underfull \hbox (badness 10000) in paragraph at lines 13772--13780
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
com-plex (or
[201]
Underfull \hbox (badness 1009) in paragraph at lines 13806--13809
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 is
not ap-pro-pri-ate for use within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/1
0 meth-ods: use
[202]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13869--13869
[]\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[]
[203] [204] [205]mktexpk: /usr/src/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1095.603pk: successfully generated.
[206] [207] [208] )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk> [209] [210</usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmmi7.pfb [211></usr/share/texmf-texlive/fonts/type1/bl
uesky/cm/cmr10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb></
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmr9.pfb [212>]</usr/share/texmf-texlive/fonts/type1/bluesk
y/cm/cmsl10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfb><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmss10.pfb [213></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmsy10.pfb]></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmsy7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy9.pfb>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb></usr/share/texmf-t
exlive/fonts/type1/bluesky/cm/cmti9.pfb [214></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmtt10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt12.pf
b></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb></usr/share/texmf-
texlive/fonts/type1/bluesky/latex-fonts/lcircle1.pfb
[215>]
Output written on R-exts.pdf (164 pages, 834304 bytes).
Transcript written on R-exts.log.
Underfull \hbox (badness 2418) in paragraph at lines 14776--14780
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
,
Underfull \hbox (badness 6510) in paragraph at lines 14783--14786
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
Underfull \hbox (badness 2326) in paragraph at lines 14811--14818
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[216] [217] [218] [219]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15057--15057
[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
Underfull \hbox (badness 1867) in paragraph at lines 15082--15089
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[220] [221] [222] [223]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15316--15316
[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 15343--15343
[]\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[]
Underfull \vbox (badness 10000) has occurred while \output is active [224]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
file:line:error style messages enabled.
%&-line parsing enabled.
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15387--15387
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
Underfull \hbox (badness 10000) in paragraph at lines 15393--15397
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
Underfull \hbox (badness 1028) in paragraph at lines 15393--15397
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[225]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts, [226] markup, glyphs,
page headings, tables, conditionals, indexing, [227 sectioning,] toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex [228
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,] [229] formatting, and turning on texinfo input format.) [230
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)]) (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [231]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15921--15921
[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[232] [233}]] [2] (./R-ints.toc [234]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
file:line:error style messages enabled.
%&-line parsing enabled.
[235]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi
[-1
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts,]
Underfull \hbox (badness 2435) in paragraph at lines 16174--16176
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
. unicode . org / reports / tr35 /
Underfull \hbox (badness 2285) in paragraph at lines 16227--16229
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16235--16235
[]\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[]
[236]) [-2] markup, (./R-ints.toc
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16245--16245
[] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16265--16265
[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[237) (./R-ints.toc glyphs,
page headings,] tables,) Chapter 1 conditionals, indexing, sectioning, toc, environments, [238
defuns, macros, cross references,] insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, [1 [239]] [240 formatting,] and turning on texinfo input format.) (./R-lang.aux
[2] [241] [242 [3]] [4] [243] [5
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[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[244]] [6]
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[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[245]
[7] [246] [8] [247] [9] [248] [10 [249]] [250] [11]
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[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the atomic types (\T1/pcr
/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[251] [12] [252] [13]
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[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[253] [14]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [254]) (./version.texi)
[1 [15{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map]
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[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[255] [16 [256]] [17 [257]] [258 [18}]] [2]] (./R-lang.toc [259]
[-1] [260] [19]
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\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
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\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is the same as
[261 [-2]] [20])
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[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
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\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
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\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
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\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[262 [-3] Chapter 2]
[21 (./R-lang.toc) (./R-lang.toc]) Chapter 1
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[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 17979--17986
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
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\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
with
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\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
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[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is equiv-a-lent to
[263 [22]] Chapter 2 [1]
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[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[264] [23] [2 [265]] [24] [266] [25 [267] Chapter 3 [26]] [268]
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@textbf storage.mode|
[3 [27]] Chapter 4 [28
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[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[269]] [29
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[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
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[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
[270]] Chapter 5
[30] [4 [271 Chapter 6 [31]]] [32
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[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[272]] [33 [273]] [34] [5
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[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use
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[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
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\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of
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\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
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\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion
3 of the li-cense can be dis-played by
[274 [35]]] [36] [275] [37] [276] [38]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[277] [39] [6
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[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
many more file han-dling func-tions and
[278] [40]]
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[] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments
as for lists[]
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[] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
pr = 0.2))),[]
[279] [41] [280
Chapter 7 [42]] [7
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[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
[281 [43]] Chapter 8 [44]]
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[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/pcr/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only \T1/pcr/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "LC
_CTYPE"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
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\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, OS X) or
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\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
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[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
[282] Chapter 3
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\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[283 [45]] [8] [284]
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@textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[46] [285] [47 [9]] [286] [10 [48]
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[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
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\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing names.
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\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[287]] [288 [49 [11]]] Chapter 9 [50] [12] [289] [51] Chapter 10 [52] [290 Chapter 11 [53]] [13
Chapter 12] [54] [291] [14] [55
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[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[292]] (Function and variable index) [56] [293] (./R-ints.vrs [15] [294] [16 [295]] [296 [57
[17]] [18 [297]
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[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
[298]] [19]])
(Concept index) [299 [58]] [20 [300]] Chapter 4 (./R-ints.cps [21 [301]]) [59] [302 )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
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/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb]> [305] [23</usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmmi12.pfb></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmmi9.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb [306]>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb
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\T1/pcr/m/n/10 www . bzip . org/$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http
: / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n
/10 http : / / tukaani .
[307] [24>]</usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmr9.pfb [308> Chapter 5]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb [25]></u
sr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfbThis is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
file:line:error style messages enabled.
%&-line parsing enabled.
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[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
space can-not ex-ceed
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\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
[309] [26]></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmti10.pfb [310> [27]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pf
b>]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts,
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[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
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-texlive/fonts/type1/bluesky/cm/cmtt9.pfb
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
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\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[312
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Transcript written on R-ints.log.
[313 markup,] glyphs, [29
page headings, tables, conditionals, indexing,] [314 sectioning,] toc, environments,
defuns, macros, [30 cross references, insertions, (./epsf.tex] [315
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, Chapter 6] [31] [32 [316] formatting, and turning on texinfo input format.)]
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi [317)
[1 [33{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map]] [34 [318]]
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[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[319]}] [2] [35 (./R-exts.toc]
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[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute
via the gen-eral rules:
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\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
[320]
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[323]] [-3 [38 [324]] Chapter 7
[39]] [325]) [-4] (./R-exts.toc) (./R-exts.toc [326]) (Acknowledgements)
Chapter 1 [327 [1]] Cross reference values unknown; you must run TeX again. Chapter 8 [40] [2 [328 [41]]] [329] Chapter 9 [42]
[3 [330]]
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[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
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\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
[331] [43] [4]
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[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the
pack-
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\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
[332 Chapter 10 [44]] [5]
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[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
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\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
[333] [6] [45 [334]] [7
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[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
found by
[46] [335]] [8 [47]]
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[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of
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[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
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\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[336] [9
Underfull \hbox (badness 4120) in paragraph at lines 22997--23004
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[337] [48]] [49 [10
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
(see `De-tails');
[338]]] [339] [50] [11] [340 (Function and Variable Index) [51]] (./R-lang.vrs [12
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[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[341]]
[52 [342] [13]]) (Concept Index) [53]
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\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",
"methods")\T1/ptm/m/n/10 .
[343 [14 (./R-lang.cps]] [15
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[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
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[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
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[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[344) Appendix A]] [54 [16] [345] [55]] )
(see the transcript file for additional information)</usr/share/texmf-texlive/f
onts/type1/bluesky/cm/cmb10.pfb [17>]</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmbx12.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb [346></usr/
share/texmf-texlive/fonts/type1/bluesky/cm/cmmi12.pfb] [18></usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmmi9.pfb>]</usr/share/texmf-texlive/fonts/type1/bluesky
/cm/cmr10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb></usr/s
hare/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb>
[19
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[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "http://www.bioconductor.org"\
T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T
1/ptm/m/n/10 '. Can be set by
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[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
and
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[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[347</usr/share/texmf-texlive/fo
nts/type1/bluesky/cm/cmsl10.pfb>]</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmsltt10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb></us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb [20></usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmtt10.pfb]></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmtt9.pfb
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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
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[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
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[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
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[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
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\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a
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\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
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\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
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[]\T1/ptm/m/n/10 a char-ac-ter string, the path of the com-mand used for un-zip
-ping help files, or
[348 [21>]] [349
Output written on R-lang.pdf (60 pages, 409837 bytes).
Transcript written on R-lang.log.
] [22 [350]] [23 [351]]
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[]@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[]
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[]@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[]
[24] [25
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[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
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\T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10
A[c(arrayindex.x, arrayindex.y)]
[353]] [26 [354]] [27] [355] [28] [356] [29]
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[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
[357] [30] [358] [31] [359] [360] [361] [32] [362] [33] [363] [34
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[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully,
[364]]
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[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
see
[365 [35]] [366] [36] [367] [37]
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[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[368] [38] [369]TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi
[39 [370]] [40 [371]] [41] [372This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
file:line:error style messages enabled.
%&-line parsing enabled.
] [373 [42]]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: [374] pdf, fonts, [43] [375] [44 markup, glyphs,
page headings,] tables, conditionals, indexing, [376 sectioning,] toc, environments,
defuns, macros, [45 cross references, insertions, (./epsf.tex]
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,
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\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[377] [46]
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[] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 =
rep(c(0,0,1),2))[]
[378] [47] formatting, [379 and turning on texinfo input format.) (./R-ints.aux
] [48] [380] [49] [381 [50]]
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[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
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[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
[382 [51]] [383] [52]
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[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[384] [385 [53]]
Chapter 2 [386] [54]
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[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[387] [55
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[388]] [56
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[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[389]] [57
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[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal:
for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and
[390]]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [58]
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\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[391) (./version.texi)]
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [392 [59]] [393] [60]}] [394 [2] [395] [61] (./R-ints.toc] [396]
[-1 [62]
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[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
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\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
mode:
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\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
"int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[397]]) [-2 [398]] (./R-ints.toc) (./R-ints.toc [63) Chapter 1] [399] [400] [1 [64]] [401] [2 [402]] [65] [403]
Underfull \hbox (badness 10000) in paragraph at lines 5752--5759
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[66 [404]] [3]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27743--27743
[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
[405] [4] [406 [67]] [5] [407]
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[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[68] [6 [408]] [69]
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
* + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '.
[409
[7]] [70 [8 [410]]] Chapter 3 [71] [9
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[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
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[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
[411] [72]] [73]
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[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
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[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[412] [10] [413 [74]] [414] [11] [75] [415] [76] [12 [77 [416]]] [78] [13 Chapter 4]
[79] [417] [14 [80]]
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[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[418] [81] [82 [15 [419]]] [83] [420] [16
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
e.g.
[84]] [421] [17] [85 [422]] [86 [18]] [423] [87 [424]] [19
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[]@textrm Some ver-sions have greatly in-creased com-pi-la-tion times on a few
files (e.g.
[88 [425]]] [426 [20]
Underfull \hbox (badness 10000) in paragraph at lines 7592--7594
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
[89]] [427 Chapter 2
[21]]
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[]@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[]
[90] [22 [91 [428]]] [23] [429] [92] [93] [24 Chapter 5 [94]]
Underfull \hbox (badness 10000) in paragraph at lines 29470--29473
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,
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\T1/pcr/m/n/10 save(list = ls(all = TRUE), file = ".RData")\T1/ptm/m/n/10 .
It is also what hap-
[430] [25] Chapter 3 [26] [431] [95] [27 [96] [432]] Chapter 4 [28]
Underfull \hbox (badness 2302) in paragraph at lines 29681--29688
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
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\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
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\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[433 [97]] [29] [98
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[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[434] Chapter 5
[30]] Chapter 6 [99 [31]]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
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[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[435] [32 [100]]
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[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
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\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
will give an empty
[436] [33 [101]] [34
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[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[437]] [35] [438
[102 [36]]] [103 [37 [439]]] [104 [440 [38]]] [39]
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[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2,
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
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[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less
[441 [105]] [40 [442]]
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[]@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[]
[106 [41] [443]]
Chapter 7 [42] [107 [444]] [108 [445]] [446 [43]] [109 Chapter 8 [44]] [447] [110] [448 [111] [45]] [449 [112]]
Underfull \hbox (badness 10000) in paragraph at lines 3848--3853
@textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[46] [450] [113] [451 [47] [114]] [452
Underfull \hbox (badness 10000) in paragraph at lines 9854--9856
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[115] [48]]
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\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
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[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
out-put from
[453] [116] [117 [454]] [49] Chapter 9 [50] [455 [118]] [119] [51 [120] [456 Chapter 10]] [52] Chapter 11 [121 [53]] [122 [457]
Chapter 12 [54]] [123] [458 [55 [124]]] (Function and variable index) [459 [56] [125] (./R-ints.vrs]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
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NilValue);[]
[127]
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[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[461 [57]entering extended mode
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[]\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[]
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[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
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[]\T1/ptm/m/n/10 Markus Kuhn, ``ASCII and Uni-code quo-ta-tion marks''. [][]$\T
1/pcr/m/n/10 http : / / www . cl . cam . ac . uk /
[472] [134}]] [2] [-1] (Preface)
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[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
[473]
Cross reference values unknown; you must run TeX again. Chapter 1 [1] [474] [135] [2 [475]]
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[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 '
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\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
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\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
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\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
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\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
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\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
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\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
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[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
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\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
first in architecture-specific di-rec-to-ries,
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\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
[476
[3]] [136]
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[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
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\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
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\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[477] [4] [478] [137] [479] [5] Chapter 2
[138 [6]] [480]
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@texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt
R_orderVector(indx, n,
[139
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[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[481]] [482 [7]] [140
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[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
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\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[483]] [8 [484]] [141] [485] [142
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[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
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[486]]
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tput.[]
[487 [9]] [143] [488] [144 [10]
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[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [145]] [489] [146] Chapter 8
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[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
[490 [11 [147]]]
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[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[491 Chapter 3 [12]] [148] [492] [149] [13 [493
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
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[150]]] [494
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
[151]] [14] [495
Chapter 4] [15] [152] [496 [153]] [16] [497 [154]] Chapter 5 [17]
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[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
signif[][][]() \T1/ptm/m/n/10 (for
[498] [155] [156]
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[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[499]
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@texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[157 [18]] [158 [19 [500]]]
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[]@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [159] (./R-exts.vrs [501] [20] [502] [160
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\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
is a match then that el-e-ment is eval-u-ated un-less
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eval-u-ated, so for ex-am-ple
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[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[503] [21]] [504] [505 [161] [22]]
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[]\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not.
[506] [23
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[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
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\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[507]]) (Concept index)
[162
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\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
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\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[508]] [24 (./R-exts.cps] [509
Chapter 6] [25] [163 [510] [26]])
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[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
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[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[511 [164]] )
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esky/cm/cmb10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb><
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[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
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[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[519] [33] <./i
mages/hist.pdf> [520 [34]] <./images/ecdf.pdf> <./images/QQ.pdf> [35] [521] [36] <./images/
ice.pdf> [522 [37]] [38] Chapter 9 [39] [523]
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[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies
[524] [40]
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[]\T1/pcr/m/n/10 table(..., exclude = if (useNA == "no") c(NA, NaN), useNA = c
("no",
[525 Chapter 10] [41]
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[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/pcr/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[526 [42]]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[527] [528 [43]] [529] [44]
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[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[530] [45]
[46
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[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$http : / / developer .
[531]] [47] [532]
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[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http : / /
[533 [48]] [49] Chapter 11
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[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http :
[534 [50]] [51 [535]] [52] [536] [537 [53]] [538] [54] [539]
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the Ol-son/IANA
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\T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion
in the file sys-tem varies,
[540] [55]
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[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Time _ zone$[][]
\T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / www . twinsun . com /
[541] [56] [542] [57 [543]] [58]
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[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[544] [545
[59]] [546 [60]] [547] [548] [61] [549] Chapter 12 [62]
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[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
, and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[550] [551 [63]]
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[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
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\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
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[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
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\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
some-thing like
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\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
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[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
and sup-press-ing the print-ing of er-ror mes-sages;
[552] [64]
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[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
"integer"\T1/ptm/m/n/10 ,
[553] [65] [554] [66] [555]
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[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[556 [67]] [557 [68]]
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[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[558 [69]] [70] [559] <./image
s/fig11.pdf> [71 [560]] <./images/fig12.pdf> [72] [73 [561]] [562 [74]] [75 [563]] Chapter 13 [76]
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[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
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\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[564] [565]
[77 [566]] Chapter 14 [78]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[567] [79] [568
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[]@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t
extrm and
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@texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they
may work in
[80]] Appendix A [81] [569] [82] [570 [83]]
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[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
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\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
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\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[571 Appendix B] [84]
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[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[572] [85] [573 [86]] [87 [574]] [88] [575] [576 [89]]
[90 [577] Appendix C] [91] [92
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[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
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\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
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\T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[578]] Appendix D [93] Appendix E [94] Appendix F
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[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[579 [95]]
[96] )
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[]\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[]
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[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[580])</usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb (./compiler-pkg.tex></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb><
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live/fonts/type1/bluesky/cm/cmcsc10.pfb
Chapter 2.
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luesky/cm/cmex10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pf
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sky/cm/cmsl10.pfb
Chapter 3.
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[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
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[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[590]
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[]\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[]
[591] [592] [593] [594] [595]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[596] [597]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[598] [599] [600] [601]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[602] [603] [604] [605] [606]
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[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[607] [608]
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[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[609]
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[]\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[610] [611]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[612]
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[]\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[]
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[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
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[] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
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[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[634] [635] [636] [637] [638] [639] [640]
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[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
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[]\T1/ptm/m/n/10 Files for all 182 dis-tricts in 1888 and other years have been
avail-able at [][]$\T1/pcr/m/n/10 http :
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\T1/pcr/m/n/10 / / opr . princeton . edu / archive / eufert / switz . html$[][]
\T1/ptm/m/n/10 or [][]$\T1/pcr/m/n/10 http : / / opr .
[642]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
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[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
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Chapter 4.
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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[][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
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[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
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[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[675 [13]]
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\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[676] [14
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
. com / Lab / Graphics / Colors /
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[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[677]] [15
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[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[678]]
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[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
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\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
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\T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
oth-er-wise a ma-trix of color names (for
[682] [20]) [21
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[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
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[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[683 (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)]])
(./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [684 [22]] [685
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[]@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[]
[23]]
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[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
pro-duce and print a postscript copy. This will not
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\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10
for how to set this up. Win-dows users may pre-fer to use
[686
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[]@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[]
[24}]]]
[2] (./R-intro.toc [25]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
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[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-
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\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[687 [26 [-1]]] [27 [688]] [-2] [28
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the
set-ting of
[689]] [29 [-3] [690]]) [-4] (./R-intro.toc) (./R-intro.toc
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
[691 [30])
(Preface)] Chapter 1 [1] [692 [31]]
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\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
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\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
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\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
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\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[693] [32 [2
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
[694]]] [695] [33 [3]] [696 [34]] [4] [697] [35] [698] [5
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[699 [36]] Chapter 2 [6]] [700] [37 [701]] [702 [7] [38]] [703
[39]] [8] [704 [40]]
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[]\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv",
scale.in = 255))[]
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[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
[705] [41
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[706] [9]] [707 [42]] [10 [43] [708]]
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[]\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1)
[709] [11 [44]
Chapter 3] [12 [710]] [45]
Underfull \hbox (badness 3525) in paragraph at lines 3409--3412
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[711 [13]] [46] [712 [47] [14]] [713 Chapter 4] [15] [48 [714]] [16] [49
Underfull \hbox (badness 5939) in paragraph at lines 3717--3722
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[715]] Chapter 5 [17 [50]] [716] [51 [717]] [18] [19] [52] [718] [719]
Chapter 2 [20 [53]] [720] [54] [721]
[21 [55]
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[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[722]] [56]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the
type of anti-aliasing (if any) to be
[723] [57 [22] [724]]
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[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
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[]\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024,
height = 768)[]
[725 [58]] [23]
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[726 [59]] [24
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[727] [60 Chapter 6] [25]]
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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East
Asian lan-guages -- see
[728] [26] [61 [729]]
Underfull \hbox (badness 7344) in paragraph at lines 4792--4794
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
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[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[730 [27] [62]] [731] [28] Chapter 7
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\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
[732 [29 [63]]] [30
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\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
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[]\T1/pcr/m/n/10 Baekmuk-Batang \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m/n
/10 ftp : / / ftp . mizi . com / pub / baekmuk/$[][]\T1/ptm/m/n/10 .
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\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m
/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /
Underfull \vbox (badness 10000) has occurred while \output is active [733]] [64
Underfull \hbox (badness 7344) in paragraph at lines 5003--5005
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
[734]] [31]
Chapter 8 [32 [735]]
Underfull \hbox (badness 10000) in paragraph at lines 5752--5759
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[65] [736] [33]
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[737 <./images/hist.pdf>] [34 [66]] <./images/ecdf.pdf>
Underfull \hbox (badness 10000) in paragraph at lines 5280--5282
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
for on-screen de-vices and to
[738 <./images/QQ.p
df> [35]]
Underfull \hbox (badness 10000) in paragraph at lines 5929--5935
[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[67] [36
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[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots
due to cor-rupted or du-pli-
[739]] <./images/ice.pdf> [37] [740 [38 [68]] Chapter 9 [39]] [741] [69] [742 Chapter 3] [40 [70]] Chapter 10
[41
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[]\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
sep = "."))[]
Underfull \hbox (badness 10000) in paragraph at lines 5623--5626
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[743]] [71] [744] [72] [42] [745] [73] [746] [43] [747 [74]] [44] [75 [748]] [76] [45] [77]
Underfull \hbox (badness 1189) in paragraph at lines 6019--6021
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[749 [46 Chapter 4]
[78]] [750] [79] [47
Underfull \hbox (badness 10000) in paragraph at lines 6117--6119
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK
lan-guages and
Underfull \hbox (badness 10000) in paragraph at lines 6156--6163
[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
Underfull \hbox (badness 1584) in paragraph at lines 6156--6163
\T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s
ys-tems which have the Wine
[751] [80]] [81]
Underfull \hbox (badness 3088) in paragraph at lines 6240--6244
[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[752] [82 [48]]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
e.g.
[83
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
Underfull \hbox (badness 10000) in paragraph at lines 6317--6320
[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[753 [49]]] Chapter 11 [50] [754] [84] [51
Underfull \hbox (badness 5637) in paragraph at lines 6408--6414
\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1721) in paragraph at lines 6441--6444
[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[755] [85] [756]] [86] [52 [757]]
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[]@textrm Some ver-sions have greatly in-creased com-pi-la-tion times on a few
files (e.g.
[87]
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\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
via
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[758]
Underfull \hbox (badness 10000) in paragraph at lines 7592--7594
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
[88] [53 [759]] [760]) (./graphics-pkg.tex
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[]@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[]
[89] [90]
Chapter 5.
Underfull \hbox (badness 10000) in paragraph at lines 16--18
[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use
[761]
[54] [762 [91]] [92] Chapter 5 [93] [763] [55 [764]] [94
Underfull \hbox (badness 1412) in paragraph at lines 286--291
[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[765]] [95 [56]] [766 [96] [57]] [97 [767 [58]]] [98
Underfull \hbox (badness 2726) in paragraph at lines 465--471
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
lo-ca-tions are com-puted in-ter-nally (the same way
[768] [59]] [99 [769]] [60] [100 [770]]
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[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or
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[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
Underfull \hbox (badness 2735) in paragraph at lines 683--690
[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[771] [101
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[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
[772]] [61
[102]] [773 Chapter 12] [103] [62]
Underfull \hbox (badness 1062) in paragraph at lines 849--852
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[774] [775] [104] [63 [776]]
Overfull \hbox (16.31242pt too wide) in paragraph at lines 9020--9020
[]@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[]
[105] [777] [64] [106 [778]] [779 [65] [107]] [780 [66]] [108]
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[] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names =
NULL,[]
Underfull \hbox (badness 1024) in paragraph at lines 1319--1327
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
[781
[67]] [109]
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\T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
Underfull \hbox (badness 6893) in paragraph at lines 1347--1353
\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and
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[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
Overfull \hbox (19.3703pt too wide) in paragraph at lines 1375--1379
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) +
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[782 [110]] [68
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1423--1423
[]\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1424--1424
[]\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi
s=..,main=..)")[]
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[]\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
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[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[783]] [111] [69 [784]] [112 [70] [785]] [113 <./images/fig11.pdf>] [71 [786]] <./images/fig12.pdf>
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[114 [72] [787]
[73]] [115]
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[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10
contourplot[][][] \T1/ptm/m/n/10 (and
[788 [74 [116]]]
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[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
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[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
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[789] [75] [117] [118
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[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[790 Chapter 13] [76]] [119] [791 [120]] [121]
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[]\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
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[792 [122 [77]]] Chapter 14 [78] [123] [793 [79]] [794
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[]@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t
extrm and
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@texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they
may work in
[80] [124]] Appendix A [81] [125 [795]] [82]
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[] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
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[126 [796] [83]] Chapter 6
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\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
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[797 Appendix B [127 [84]]] [798] [128 [85 [799]]] [800] [129] [86] [801] [87] [88
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[802]] [130 [89]] [803] [131
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
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/10 or
[804
[90]]] Appendix C [91] [132 [805]]
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
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[806 [133]] [92] [807 Appendix D] [93] (./R-intro.vrs [808] [94
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[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[809] [134]]
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raster im-ages are used when the
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
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[810] [95 [135 [811]]]) [812 Appendix E]
[96
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[813]] (./R-intro.cps [136]
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[814 [97]
[137]]) Appendix F [98] [815 [99]
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@texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt
R_orderVector(indx, n,
[138 )
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[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
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ol = "blue")[]
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[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
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[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
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[143
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[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a
mul-ti-ple of
[824]
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[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7] [144] [825] [145] Chapter 8 [146 [826]] [147 [827]] [148]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[828]
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[]
[149]
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\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10
oma \T1/ptm/m/n/10 when chang-ing
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are
to be used: see
[829]
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
[150
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[]\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel
= panel.cor)[]
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[] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
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[830]] [151]
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[]\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue") # hmm...[]
[831] [152]
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\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[832 [153]] [833 [154]] [155]
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@texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[156
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[834]] [157]
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[]@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [158
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[838]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[839 [160]
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[]\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9,
physicians = 9,[]
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[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
[840]]
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[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
[841]) (Concept index)
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[842
[161]] [843] (./R-exts.cps [844] [162 [845]]) [163] )
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[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing
or an er-ror; us-ing, e.g.,
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\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
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[852]
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[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[853] [854] [855] [856] [857]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[858] [859]
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[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
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[]\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
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[861]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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[] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[]
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[]\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[]
[864]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
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[865] [866] [867]
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[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
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[868]
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[]\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
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[869] [870] [871] [872] [873] [874]
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[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
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[875] [876] [877] [878] [879] [880]
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[]\T1/ptm/m/n/10 The Euro sym-bol was in-tro-duced rel-a-tively re-cently and m
ay not be avail-able in
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[892]
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[897]) (./grid-pkg.tex [898]
Chapter 6.
[899] [900] [901] [902] [903] [904]
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de-scrib-ing a cir-cle), but only
[919] [-3] [920 formatting,) and turning on texinfo input format.]) [-4 (./R-exts.aux
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[926] [4 [927]] [928] [5
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[929]] Chapter 2 [6]
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[930]
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[931] [932 [7]] [933] [8
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[934]] [935] [936 [9]]
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[937] [10] [938] [939 [11]]
Chapter 3 [12]
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[940] [941 [13]] [942] [14] [943 Chapter 4] [15]
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[944] [16] [945]) Chapter 5 [17 (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)] [946]) (./version.texi)
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[949]}] [2] (./R-exts.toc
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[950 [20]]
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[953]] [22 [954 [-3]]] [955]) [-4
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[956 [23]] (./R-exts.toc]) (./R-exts.toc) (Acknowledgements) [957
Chapter 1] [1] [24] [958 Chapter 6 [25]] [2] [959 [26]] [3 [960]] [961 [27 [4]]] [5 [962 [28]]] Chapter 7 [29 [963] [6]] [30 [964]] [7]
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[965] [31]
Chapter 8 [8 [32]] [966] [9 [967] [33]]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
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[968 <./images/hist.pdf>] [34] [10 <./images/ecdf.pdf>] <./images/QQ.p
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[969]] [36] [970 [11] <./images/ice.pdf>] [37] [38 [971] Chapter 9] [39] [12]
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[972] [973 [13] [40]] [974 Chapter 10]
[41] [14] [975] [42] [15 [976]] [977
[16] [43]] [17 [978]] [18 [44 [979]]] [45] [980] [19] [46] [47 [20]
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[981]] [21] [982 [48]] [49] [22 Chapter 11 [983 [50]]] [51
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[]@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
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[23 [984]]] [52]
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[24 [985]] [25] [986 [53]] [26] [987] [27 [988
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[991]] [30] [57 [992]] [31 [58]] [993] [59 [32 [994]]] [60] [995] [33]
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[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for
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[996] [34] [61
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[997]] [35 Chapter 12 [62]] [998]
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
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[999 [36] [63]] [1000] [37 [64 [1001]]]
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[1002]) (./methods-pkg.tex [65] [38
Chapter 7.
[1003]] [66
[39] [1004]] [40
[67] [1005]] [68 [41
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[1006]]] [69 [42 [1007]]] [70] [43 [1008]] <./images/fig11.pdf> [71] [1009] <./images/fig12.pdf> [72 [44]
[73]] [1010] [45 [1011]] [74]
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[]\T1/ptm/m/n/10 Note that the pre-ced-ing def-i-ni-tion means that the next me
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[1012] [46] [75] [1013 [47] Chapter 13 [76]] [48 [1014]] [1015 [49] [77]] Chapter 14 [78] [1016 [50]] [79] [1017 [51]
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extrm and
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@texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they
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[80]] Appendix A [81] [1018 [52]] [82] [1019 [83]]
Chapter 2 [53 Appendix B [84]] [1020] [54 [85] [1021]] [86 [55] [1022]] [87] [56]
[1023 [88]] [57 [89] [1024]]
[90 [1025] [58 Appendix C] [91]] [1026] [92 [59]
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[1027 Appendix D]] [93] (./R-intro.vrs [1028 [60]] [94
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an be an ob-ject of class
[1029]] [61 [1030]] [95 [1031] [62]] [1032]) Appendix E
[96 [63 [1033]] (./R-intro.cps]
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
[1034 [97] [64]) Appendix F [98] [1035]] [99] )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
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[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
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bluesky/cm/cmsy10.pfb [1040></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7.pf
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
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Output written on R-intro.pdf (105 pages, 673913 bytes).
Transcript written on R-intro.log.
Chapter 3 [1043 [70]] [1044 [71]] [72] [1045] [1046 [73]] [1047] [1048 [74]] [75 [1049]] [76] [77
Underfull \hbox (badness 10000) in paragraph at lines 3531--3535
[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1050]] Chapter 4
[78]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these
classes takes spe-cial ar-gu-ments
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[]
[1051 [79]] [80
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1052]] [81]
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\T1/ptm/m/n/10 If ar-gu-ment \T1/pcr/m/n/10 fullInfo \T1/ptm/m/n/10 is \T1/pcr/
m/n/10 TRUE\T1/ptm/m/n/10 , the call re-turns a named list of ob-jects of class
[1053 [82]]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
e.g.
[83 [1054]] [1055 [84]] [85
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[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
[1056]] [1057 [86]] [1058]
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[]@textrm Some ver-sions have greatly in-creased com-pi-la-tion times on a few
files (e.g.
[87]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method
ex-ists for
[1059]
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[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
[88
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\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is
to mod-ify a field ex-plic-itly by
[1060]]
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[]\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(),
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[] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[]
[1061]
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[]@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[]
[89] [90]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1062] [91] [92] Chapter 5 [93 [1063]] [1064] [1065 [94]] [95 [1066]] [96 [1067]] [97
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[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
[1068]] [98]
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[1070 [99]]
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
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[]\T1/pcr/m/n/9 stopifnot(identical(abs(y), 1:10)) # (version 2.9.0 or earlier
fails here)[]
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[]\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[]
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[1072]]
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\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
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[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1073] [101 [1074]]
[102 [1075]] [103 [1076]] [1077] [104]
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[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
Underfull \hbox (badness 10000) in paragraph at lines 5632--5636
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5632--5636
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1078]
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[]@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[]
[105
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5723--5727
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1079]] [1080 [106]]
Underfull \hbox (badness 10000) in paragraph at lines 5900--5916
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1081 [107]] [1082] [1083 [108]]
Underfull \hbox (badness 1248) in paragraph at lines 6186--6190
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
Underfull \hbox (badness 1960) in paragraph at lines 6186--6190
\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1084 [109]] [110]
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1085] [111]
Underfull \hbox (badness 1072) in paragraph at lines 6348--6355
[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1086] [1087 [112]] [1088] [113 [1089]] [1090
Underfull \hbox (badness 10000) in paragraph at lines 9854--9856
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[114]]pdfTeX warning (ext4): destination with the s
ame identifier (name{Rfn.S4}) has been already used, duplicate ignored
<to be read again>
\relax
l.6707 \aliasA{S4}{S3Part}{S4}
[1091] [115] [116 [1092]] [1093 [117]] [118]
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[]\T1/pcr/m/n/9 ## note the these classes can insert an S3 subclass of "lm" as
the S3 part:[]
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[]\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c
("mlm", "lm")[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex})
has been already used, duplicate ignored
<to be read again>
\relax
l.6983 \aliasA{Complex}{S4groupGeneric}{Complex}
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ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
ignored
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\relax
l.6985 \aliasA{Logic}{S4groupGeneric}{Logic}
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with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
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\relax
l.6986 \aliasA{Math}{S4groupGeneric}{Math}
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th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
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l.6988 \aliasA{Ops}{S4groupGeneric}{Ops}
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the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
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l.6989 \aliasA{Summary}{S4groupGeneric}{Summary}
[1094] [119] [120] [121]
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[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic
can be ob-tained by call-ing
Underfull \hbox (badness 6708) in paragraph at lines 7063--7075
[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3209) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1095] [122] [1096 [123]] [124
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[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
[1097]] [125]
Underfull \hbox (badness 10000) in paragraph at lines 7247--7250
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1098
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[] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[]
[126]] [1099] Chapter 6 [127 [1100]] [1101] [128] [1102] [1103] [129]
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[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),[]
[1104] [1105] [130
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[]\T1/ptm/m/n/10 Note that call-ing \T1/pcr/m/n/10 setGeneric() \T1/ptm/m/n/10
in this form is not strictly nec-es-sary be-fore call-ing
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[]\T1/ptm/m/n/10 If you \T1/ptm/m/it/10 don't \T1/ptm/m/n/10 want the ex-ist-in
g func-tion to be taken as de-fault, sup-ply the ar-gu-ment
[1106]]
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[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
\T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1107] [131] [1108] [132 [1109]] [1110] [133]
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[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
[1111]
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[]\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the
method. For
[1112]
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[]\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li
nk{setClass})[]
[1113] [134 [1114]] [1115] [135] [1116] [1117] [136
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[]\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date
= "POSIXt"))[]
[1118]]
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[]\T1/pcr/m/n/9 # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
s class, then calls the S3 print method.[]
[1119]
[137]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1120]
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@texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt
R_orderVector(indx, n,
[138] [1121] [1122] [139 [1123]] [1124 [140]] [1125] [141] [1126] [142 [1127]] [143 [1128]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12517
[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7] [144] [145
Underfull \hbox (badness 10000) in paragraph at lines 9634--9636
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
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[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
Underfull \hbox (badness 1681) in paragraph at lines 9642--9646
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1129]] Chapter 8 [146] [1130] [147] [1131] [148 [1132]]) (./parallel-pkg.tex
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[]
[149]
Chapter 8.
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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1133]
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
[150]
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[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1134] [151] [1135 [152]]
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[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1136] [153
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[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, OS X, FreeBSD, So-laris, I
rix and Win-dows.
[1137]] [154 [1138]] [155]
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@texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[156]
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[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1139] [157]
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[]@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [158 [1140]] (./R-exts.vrs [1141] [1142] [159
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[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class
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\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1143]] [1144] [160
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[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1145]] [1146] [1147)] (Concept index)
[161
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[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1148]] (./R-exts.cps
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[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if
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[]\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[]
[1149] [162 [1150])] [163] )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
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[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
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[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
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luesky/cm/cmmi7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi9.pfb [1153>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb]) (./splines-pkg.tex [1154>]</usr/share/texmf-te
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Chapter 9.
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[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
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] [1159] [1160] [1161]
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[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1162] [1163] [1164]
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[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1165] [1166] [1167]) (./stats-pkg.tex [1168]
Chapter 10.
[1169]
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[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of
\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
[1170] [1171] [1172] [1173] [1174]
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[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
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[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
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[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189]
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[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1190]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
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\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
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\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199]
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[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
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\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
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\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
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[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
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\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1200]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
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[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
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\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1205 pdf, fonts,]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1206] markup, glyphs,
page headings, tables, [1207 conditionals, indexing,] sectioning, toc, environments,
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[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1208
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) localization,] [1209] formatting, and turning on texinfo input format.) (./R-exts.aux
[1210] [1211]
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[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1212] [1213] [1214]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1215] [1216] [1217] [1218] [1219] [1220]
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[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1221] [1222] [1223] [1224]
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[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1225] [1226] [1227] [1228] [1229]
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[]\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
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[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1230] [1231] [1232]
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[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1233]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [1234)] (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [1235]
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[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1236]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1237}]] [2] (./R-exts.toc [1238]
[-1] [1239] [-2 [1240]] [1241] [-3
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[]\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[]
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[]\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
= c(-0.9,0.1))[]
[1242]]) [-4
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[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an
ar-gu-ment to all these con-trast func-tions, how-ever
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\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1243] (./R-exts.toc]) (./R-exts.toc) (Acknowledgements) [1244
Chapter 1 [1]] [2
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[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
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[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
[1245]]
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[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is
given by
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1246] [3] [1247] [4] [1248] [5]
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
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\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
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\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1249 [6]] [1250]
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[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1251] [7]
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[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1252 [8]] [1253] [9]
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[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1254] [10 [1255]] [1256] [11]
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[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
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[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When
[1260] [13] [1261] [14 [1262]] [15
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1263]]
[16]
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[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
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[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
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\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
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[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1264 [17]]
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[]\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE,
type = "tr")[]
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[]\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[]
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[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
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[1266] [19] [1267] [20 [1268]] [21]
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[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
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[]@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[]
[23]
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[]@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[]
[24 [1272]] [25] [1273] [26 [1274]] [27]
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\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1275] [28
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[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1276]] [29] [1277]
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[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tp : / / cran . r-[]project . org / web / views /
[1278 [30]] [1279] [31] [1280] [32 [1281]] [1282] [33] [1283] [34]
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[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1284] [35] [1285] [36]
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[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
= TRUE)\T1/ptm/m/n/10 .
[1286] [37] [1287] [38 [1288]]
[39]
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[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1289] [40] [1290] [41] [1291] [42] [1292] [43] [1293] [44] [1294] [45] [1295] [46
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[] \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[]
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[]\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link
= "log")) # fails[]
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[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
[1296]] [47] [1297] [48]
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[]\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
.90) # ~= 7e-9[]
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\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
i.e., if
[1298] [49 [1299]] [1300 [50]] [1301 [51]] [1302] [52]
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[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate
S", "VeryS")))[]
[1303]
Chapter 2 [53] [1304] [54] [1305] [55]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
homogeneity of variances"\T1/ptm/m/n/10 .
[1306] [56] [1307 [57]] [1308] [58] [1309] [59] [1310] [1311] [60] [1312]
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[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1313 [61]] [1314] [62] [1315]
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[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org /
wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1316 [63]] [1317] [64 [1318]] [1319]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[65]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1320]
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1321 [66]]
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[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
fitted.values \T1/ptm/m/n/10 and
[1322
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[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[67]] [1323] [68] [1324] [69
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[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1325]] Chapter 3 [70]
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[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1326] [71] [72
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[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
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\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1327]] [1328 [73]]
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\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1329] [74] [1330] [75] [76]
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[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
[1331 [77]] Chapter 4
[78]
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[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
den-dro-gram is re-ordered ac-cord-
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\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1332] [79]
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[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
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[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
[1333 [80]] [81
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[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1334]] [82] [1335]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
e.g.
[83] [1336] [84] [1337] [85] [1338]
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[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
been already used, duplicate ignored
<to be read again>
\relax
l.11349 \aliasA{hat}{influence.measures}{hat}
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[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
[1339 [86]]
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[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
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[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1340
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[]@textrm Some ver-sions have greatly in-creased com-pi-la-tion times on a few
files (e.g.
[87]] [1341]
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[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
[88]
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[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if
[1342] [1343
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[]@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[]
[89]] [90]
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[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
[1344] [91]
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[] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
= "tobacco",[]
[1345 [92]] Chapter 5 [93]
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[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1346] [94 [1347]] [95] [1348] [96
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[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
fit-ted to
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[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
[1349]] [97] [1350] [98]
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[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
/ / bugs . r-[]project . org / bugzilla3 /
[1351] [99] [1352] [100]
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\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
\T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1353]
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[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of
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[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
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\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1354] [101 [1355]]
[102 [1356]] [103 [1357]] [1358] [104] [1359]
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[]@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[]
[105 [1360]] [1361] [106] [1362] [107] [1363] [108 [1364]] [109]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1365 [110]] [111] [1366] [112] [1367] [113]
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[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
,
[1368]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[114] [1369] [115] [116]
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[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1370] [117] [118 [1371]] [119] [1372 [120]] [121] [122]
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\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1373] [123]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1374] [124] [1375 [125]]
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[] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[]
[126 [1376]]
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[]\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1377 Chapter 6] [127]
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[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
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\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1378] [128 [1379]] [1380] [129] [1381]
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[]\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1382] [130]
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[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
[1383] [1384 [131]] [132] [1385] [133 [1386]] [1387] [1388] [134 [1389]]
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[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1390] [135] [1391] [1392] [136] [1393] [1394
[137]] [1395]
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@texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt
R_orderVector(indx, n,
[138] [1396] [1397 [139]] [1398] [140] [1399] [1400 [141]]
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[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1401] [142] [1402] [143]
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[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [144] [1403 [145]] Chapter 8 [146]
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
sup-ply vari-ables with the same names as would
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\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1404] [147
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[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b
= "contr.poly"))[]
[1405]] [148] [1406
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[]
[149]] [1407
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
[150]] [1408] [151] [1409 [152]] [1410 [153]] [1411] [154] [155] [1412
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@texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[156]] [157]
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[]@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index)
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[]\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects
with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[]
[1413 [158]] (./R-exts.vrs [1414] [159 [1415]] [1416]
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[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
[1417] [160 [1418]] [1419]) (Concept index)
[161 [1420]] (./R-exts.cps [1421] [162 [1422]])
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[]\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate
s. When
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\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr
/m/n/10 start \T1/ptm/m/n/10 is tried (if
[1423 [163]] )
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[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
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uesky/cm/cmss10.pfb
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[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
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b
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[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
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Output written on R-exts.pdf (169 pages, 1007799 bytes).
Transcript written on R-exts.log.
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17373--17373
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1431]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
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[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
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\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
Underfull \hbox (badness 1478) in paragraph at lines 17978--17982
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and
[1440]
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[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1441]
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[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
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[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
[1443]
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1444]
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[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
[1445] [1446] [1447]
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[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1448]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1455]
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[] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
vs Leverage " * h[ii] / (1 - h[ii]))),[]
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[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
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[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
Underfull \hbox (badness 1194) in paragraph at lines 19323--19326
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1461]
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[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1462]
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[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
[1463]
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[]\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty =
1, y.intersp = 1)[]
Underfull \hbox (badness 10000) in paragraph at lines 19492--19495
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
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\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1464]
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[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1465] [1466]
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[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1467]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
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Underfull \hbox (badness 6859) in paragraph at lines 20681--20688
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 20692--20698
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
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[1493] [1494] [1495] [1496] [1497] [1498]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21684--21684
[] \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) ==
"Pr(",[]
[1499] [1500] [1501] [1502] [1503]
Underfull \hbox (badness 1337) in paragraph at lines 22007--22013
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1514] [1515]
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 5091) in paragraph at lines 22800--22803
\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
ef-fi-ciency if
[1516] [1517] [1518]
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[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1519] [1520] [1521]
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[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1522] [1523]
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[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1524]
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[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
end point rule and is called by de-fault from
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[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1525] [1526] [1527] [1528]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-je
ct which is co-ercible to one by
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[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][
][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/
ptm/m/n/10 mod-els (with ex-am-
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1538] [1539]
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[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
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[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
Underfull \hbox (badness 2435) in paragraph at lines 24443--24448
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1540] [1541]
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[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) /
tol) ))[]
[1542] [1543] [1544]
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[]\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
sep = " = "),[]
[1545]
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[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
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[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
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[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of
an
[1552] [1553]
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[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[]
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[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1555]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Underfull \hbox (badness 3240) in paragraph at lines 25533--25537
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
[1556]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1557]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1558]
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[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25677--25677
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
[1559] [1560]
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[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
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[]\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response
and gradient[]
[1561]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1562]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Underfull \hbox (badness 2922) in paragraph at lines 25965--25970
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1563]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1564]
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[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1565]
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[]\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
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[]\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
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Underfull \hbox (badness 10000) in paragraph at lines 26611--26614
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
Underfull \hbox (badness 10000) in paragraph at lines 26611--26614
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
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Underfull \hbox (badness 3396) in paragraph at lines 27040--27042
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
, usu-ally, a re-sult of a call to
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Underfull \hbox (badness 2237) in paragraph at lines 27217--27219
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
, usu-ally the re-sult of a call to
[1585]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
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Underfull \hbox (badness 3407) in paragraph at lines 27606--27610
[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low)
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1591] [1592]
Underfull \hbox (badness 10000) in paragraph at lines 27856--27859
[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
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[]\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200,
main = t.tit,[]
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[] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[]
[1595]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
resid-u-als, when
[1596]
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[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
[1597]
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[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
TRUE,[]
[1598]
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
is re-turned. The ob-ject it-self is the re-ordered (un-less
[1599]
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[]\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv
en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
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[]\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)
[1608]
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[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1609] [1610]
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[]\T1/ptm/m/n/10 In \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.2 and ear-lier the re-
sults were \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 for fits with \T1/pcr/m/n/10 na.act
ion \T1/ptm/m/n/10 meth-ods such as
[1611] [1612]
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[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
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[] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[]
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[] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
= 0)[]
[1613] [1614]
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[]\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[]
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[]\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[]
[1615] [1616] [1617] [1618]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1627]
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
ar-gu-ment
[1628] [1629] [1630] [1631] [1632]
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
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[] \T1/pcr/m/n/10 na.action, exclude = c(NA, NaN), drop.unused.levels = F
ALSE)[]
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[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1633] [1634]
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[] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[]
[1635]) (./stats4-pkg.tex [1636]
Chapter 11.
[1637] [1638] [1639]
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[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
[1640] [1641] [1642]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again>
\relax
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
[1643]
Underfull \hbox (badness 10000) in paragraph at lines 440--443
[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1644] [1645]) (./tcltk-pkg.tex [1646]
Chapter 12.
[1647] [1648] [1649] [1650]
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
ref in here[]
[1651] [1652] [1653]
Underfull \vbox (badness 10000) has occurred while \output is active [1654]
Underfull \hbox (badness 1292) in paragraph at lines 649--656
[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
any Tk or Tcl com-mand by sim-ply run-ning
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665]
Underfull \hbox (badness 1490) in paragraph at lines 1390--1393
[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept
on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1666]) (./tools-pkg.tex
Chapter 13.
[1667]
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
[1668]
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[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
which will be eval-u-ated via
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[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1669]
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
[1670]
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[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1671]
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[]\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine
to use. Over-rides any
[1672] [1673] [1674]
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[][][]$\T1/pcr/m/n/10 http : / / partners . adobe . com / public / developer /
en / opentype / glyphlist .
[1675] [1676] [1677] [1678] [1679] [1680]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 900--900
[]\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[]
[1681]
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[]\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[]
[1682]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1683]
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[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:
Underfull \hbox (badness 3724) in paragraph at lines 1117--1125
\T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen
-den-cies (de-fault:
[1684]
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[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
[1685] [1686]
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[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and
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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1687] [1688] [1689]
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[] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
sub-set of
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1690] [1691] [1692]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again>
\relax
l.1666 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
[1693] [1694]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if
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\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
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\T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R
\T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
[1699] [1700]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
sub-set of
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1701]
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[] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[]
[1702] [1703] [1704] [1705] [1706] [1707] [1708]
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to
r of links, as re-turned by
[1709] [1710] [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718]
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[] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1719] [1720] [1721] [1722] [1723]
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[]\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright,
bugs)
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[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
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[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1724]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-
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\T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie
d (for in-stance if there was
[1725] [1726]
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[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
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\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
[1727]
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[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for
R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 3623) in paragraph at lines 3989--3992
[]\T1/ptm/m/n/10 Invisibly re-turns the num-ber of pack-ages de-scribed in the
re-sult-ing `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ' and
[1728] [1729] [1730]) (./utils-pkg.tex
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1731] [1732] [1733]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 by de-
[1734]
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[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1735] [1736] [1737]
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[]\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"),
[1738]
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[]\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
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[]\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
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[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
, \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4416) in paragraph at lines 536--542
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1739] [1740]
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\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1741]
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\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
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\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1742]
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[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1743] [1744] [1745]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1746] [1747] [1748] [1749] [1750]
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[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1751] [1752]
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[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1753] [1754]
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[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
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[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL)
[1755]
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[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL)
[1756] [1757]
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
[1758]
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[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1759]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1760]
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[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
[1761]
Underfull \hbox (badness 1057) in paragraph at lines 2146--2153
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1762]
Underfull \hbox (badness 10000) in paragraph at lines 2158--2160
[]\T1/ptm/m/n/10 Factors \T1/pcr/m/n/10 x \T1/ptm/m/n/10 are ac-cepted from \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.0 (al-though co-in-ci-den-tally they worked fo
r
[1763] [1764] [1765]
Underfull \hbox (badness 10000) in paragraph at lines 2336--2338
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1766] [1767] [1768]
Underfull \hbox (badness 10000) in paragraph at lines 2568--2571
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
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[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";")\T1/ptm/m/n/10 ,
[1769]
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[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set
[1770]
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[]\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[]
[1771]
Underfull \hbox (badness 2452) in paragraph at lines 2769--2772
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1772] [1773] [1774] [1775] [1776]
Underfull \hbox (badness 1077) in paragraph at lines 3116--3118
[]\T1/ptm/m/n/10 character vec-tor of ad-di-tional command-line ar-gu-ments for
the \T1/pcr/m/n/10 "wget"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
Underfull \hbox (badness 1377) in paragraph at lines 3155--3161
\T1/pcr/m/n/10 internet.info \T1/ptm/m/n/10 op-tion. The de-tails de-pend on th
e plat-form and scheme, but set-ting
[1777]
Underfull \hbox (badness 1057) in paragraph at lines 3180--3194
[]\T1/ptm/m/n/10 Proxies can be spec-i-fied via en-vi-ron-ment vari-ables. Set-
ting \T1/pcr/m/n/10 "no_proxy" \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "*" \T1/ptm/m/n
/10 stops
Underfull \hbox (badness 1742) in paragraph at lines 3180--3194
\T1/ptm/m/n/10 fail-ing that, the all upper-case ver-sion) is con-sulted and if
non-empty used as a proxy
Underfull \hbox (badness 1360) in paragraph at lines 3180--3194
\T1/ptm/m/n/10 site. For FTP trans-fers, the user-name and pass-word on the pro
xy can be spec-i-fied by
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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers
via en-vi-ron-ment vari-able
[1778]
Underfull \hbox (badness 4660) in paragraph at lines 3266--3269
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
[1779] [1780] [1781]
Underfull \hbox (badness 1565) in paragraph at lines 3472--3476
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
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[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1782]
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[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
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\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 .
[1783] [1784] [1785] [1786] [1787]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3896--3896
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1788]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.3967 ...mat Unordered and Ordered Lists}{format}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.3967 ...mat Unordered and Ordered Lists}{format}
[1789] [1790] [1791]
[1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802]
[1803]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4871--4871
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[1804]
Underfull \hbox (badness 10000) in paragraph at lines 4955--4957
[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 http : / / www . r-[]p
roject . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1805]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
Underfull \hbox (badness 2103) in paragraph at lines 5004--5009
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[1806] [1807]
Underfull \hbox (badness 10000) in paragraph at lines 5166--5175
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
Underfull \hbox (badness 10000) in paragraph at lines 5166--5175
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10
', which can be re-made by
[1808] [1809]
Underfull \hbox (badness 3118) in paragraph at lines 5283--5285
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
sub-architecture used by
[1810] [1811]
Underfull \hbox (badness 1348) in paragraph at lines 5434--5439
[]\T1/ptm/m/n/10 logical in-di-cat-ing to also in-stall unin-stalled pack-ages
which these pack-
Underfull \hbox (badness 3884) in paragraph at lines 5434--5439
\T1/ptm/m/n/10 ages de-pend on/link to/import/suggest (and so on re-cur-sively)
. Not
Underfull \hbox (badness 1776) in paragraph at lines 5434--5439
\T1/ptm/m/n/10 used if \T1/pcr/m/n/10 repos = NULL\T1/ptm/m/n/10 . Can also be
a char-ac-ter vec-tor, a sub-set of
Overfull \hbox (44.55087pt too wide) in paragraph at lines 5434--5439
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
Overfull \hbox (48.30977pt too wide) in paragraph at lines 5447--5454
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
Underfull \hbox (badness 10000) in paragraph at lines 5460--5464
[]\T1/ptm/m/n/10 Possible val-ues are (cur-rently) \T1/pcr/m/n/10 "source"\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2073) in paragraph at lines 5460--5464
\T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "win.bi
nary"\T1/ptm/m/n/10 : the bi-nary types
[1812]
Underfull \hbox (badness 10000) in paragraph at lines 5518--5521
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed
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\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1813]
Underfull \hbox (badness 1314) in paragraph at lines 5628--5635
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
[1814]
Underfull \hbox (badness 10000) in paragraph at lines 5649--5654
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5670--5670
[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
Underfull \hbox (badness 5133) in paragraph at lines 5706--5710
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
pack-age's
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[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1815]
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[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[1816]
Underfull \hbox (badness 4132) in paragraph at lines 5796--5798
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[1817] [1818]
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[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[1819] [1820] [1821]
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[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
[1822] [1823] [1824]
Underfull \hbox (badness 10000) in paragraph at lines 6270--6272
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
[1825] [1826] [1827] [1828]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 6537--6537
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[1829] [1830] [1831] [1832]
Underfull \hbox (badness 10000) in paragraph at lines 6810--6812
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut,
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 6815--6820
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
given pack-age is found and can suc-cess-fully be read,
[1833] [1834]
Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1835] [1836]
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[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
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[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[1837] [1838] [1839] [1840]
Underfull \hbox (badness 1789) in paragraph at lines 7353--7355
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
more dis-cus-sion of the
[1841]
Underfull \hbox (badness 10000) in paragraph at lines 7411--7415
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1842]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7524--7528
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1843] [1844]
Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1845] [1846] [1847] [1848]
Underfull \hbox (badness 5203) in paragraph at lines 7914--7917
[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
ex-trac-tor are de-ter-mined by the generic func-tion
[1849] [1850] [1851]
Underfull \hbox (badness 1776) in paragraph at lines 8136--8143
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8160--8160
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[1852] [1853]
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[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[1854] [1855] [1856]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8491--8491
[]\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23
456 98 76 54[]
[1857]
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[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
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[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
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[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[1858]
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[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[1859] [1860] [1861] [1862] [1863] [1864]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9094--9094
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[1865] [1866]
Underfull \hbox (badness 10000) in paragraph at lines 9181--9183
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1867] [1868]
Underfull \hbox (badness 10000) in paragraph at lines 9313--9317
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1869] [1870]
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[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[1871] [1872] [1873] [1874]
Underfull \hbox (badness 6725) in paragraph at lines 9694--9703
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
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\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
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\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 9694--9703
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[1875] [1876]
Underfull \hbox (badness 10000) in paragraph at lines 9820--9822
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Ctags$[][]\T1/pt
m/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / www . gnu . org / software /
[1877] [1878] [1879]
Underfull \hbox (badness 10000) in paragraph at lines 9998--10002
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 10029--10035
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1880]
Underfull \hbox (badness 2012) in paragraph at lines 10124--10130
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
for fig-ures should be auto-generated. Use
Underfull \hbox (badness 2096) in paragraph at lines 10137--10139
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
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[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1527) in paragraph at lines 10147--10150
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
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[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
[1881]
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[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
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[]\T1/ptm/m/n/10 A re-place-ment for [][]\T1/pcr/m/n/10 dev.off[][][] \T1/ptm/m
/n/10 can be pro-vided as a func-tion with suf-fix \T1/pcr/m/n/10 .off\T1/ptm/m
/n/10 ,
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[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[1882] [1883]
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\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1884] [1885]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form. For re-cent v
er-
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\T1/ptm/m/n/10 sions where sub-architectures are in use this is of the form
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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1886]
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\T1/ptm/m/n/10 That file can be edited for a site, or a user can have a per-son
al copy in
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[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
[1887] [1888]
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[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[1889] [1890] [1891]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10865--10865
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
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[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
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[]\T1/ptm/m/n/10 string in-di-cat-ing if the \T1/pcr/m/n/10 width \T1/ptm/m/n/1
0 ar-gu-ment's spec-i-fi-ca-tion should be fol-
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\T1/ptm/m/n/10 to the \T1/pcr/m/n/10 strict.width \T1/ptm/m/n/10 com-po-nent of
op-tion \T1/pcr/m/n/10 "str" \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][
][]\T1/ptm/m/n/10 )
Underfull \hbox (badness 1859) in paragraph at lines 10904--10913
\T1/ptm/m/n/10 which de-faults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back c
om-pat-i-bil-ity rea-sons; \T1/pcr/m/n/10 "wrap" \T1/ptm/m/n/10 uses
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[][]\T1/pcr/m/n/10 strwrap[][][](*, width = width) \T1/ptm/m/n/10 whereas \T1/p
cr/m/n/10 "cut" \T1/ptm/m/n/10 cuts di-rectly to
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\T1/pcr/m/n/10 width\T1/ptm/m/n/10 . Note that a small \T1/pcr/m/n/10 vec.lengt
h \T1/ptm/m/n/10 may be bet-ter than set-ting
[1892]
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[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
[1893] [1894]
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[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
[1895] [1896]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
then the avail-able syn-tax ob-jects are con-sulted in
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\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 2452) in paragraph at lines 11226--11233
\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
[1897] [1898] [1899]
Underfull \hbox (badness 2020) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[1900]
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[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Tar _ (file _ fo
rmat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[1901] [1902] [1903] [1904] [1905] [1906] [1907]
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\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Overfull \hbox (36.87935pt too wide) in paragraph at lines 11987--11991
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be passed to
Underfull \hbox (badness 1052) in paragraph at lines 11996--11998
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
[1908]
Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with
Underfull \hbox (badness 10000) in paragraph at lines 12055--12058
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[1909] [1910] [1911] [1912] [1913]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12331--12331
[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
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[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
ex-am-ple,
[1914]
Underfull \hbox (badness 1715) in paragraph at lines 12383--12386
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 12428--12430
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
Underfull \hbox (badness 3271) in paragraph at lines 12440--12444
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
\T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[1915] [1916] [1917]) [1918] [1919] [1920] (./KernSmooth-pkg.tex
Chapter 15.
[1921]
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[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[1922] [1923] [1924] [1925] [1926]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[1927] [1928] [1929] [1930]) (./MASS-pkg.tex
Chapter 16.
[1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772
[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
[1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952]
[1953]
Underfull \hbox (badness 7256) in paragraph at lines 1601--1603
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962] [1963] [1964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2409--2409
[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
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[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
[1965] [1966] [1967] [1968]
Underfull \hbox (badness 6559) in paragraph at lines 2691--2694
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
graph-i-cal pa-ram-e-ters. Note that
[1969] [1970] [1971]
Underfull \hbox (badness 7362) in paragraph at lines 2861--2866
\T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "lognormal"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
Underfull \hbox (badness 3118) in paragraph at lines 2897--2905
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
\T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[1972] [1973]
Underfull \hbox (badness 4686) in paragraph at lines 3029--3031
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
Underfull \hbox (badness 1515) in paragraph at lines 3043--3047
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[1974] [1975] [1976]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3224--3224
[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
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[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[1977]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3354--3354
[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
[1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988]
[1989]
Underfull \hbox (badness 1845) in paragraph at lines 4160--4162
[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[1990] [1991] [1992] [1993] [1994] [1995] [1996]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4656--4656
[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
[1997] [1998]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[1999]
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[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2000] [2001] [2002] [2003] [2004]
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[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
Underfull \hbox (badness 5022) in paragraph at lines 5290--5293
[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2005]
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[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
the case of
[2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5925--5925
[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2014]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5987--5987
[]\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log")
[2015] [2016]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6129 ...sical N, P, K Factorial Experiment}{npk}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again>
\relax
l.6129 ...sical N, P, K Factorial Experiment}{npk}
[2017]
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[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space.
That is
[2018] [2019] [2020] [2021]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 6545--6545
[] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[]
[2023]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6633--6633
[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2024] [2025] [2026] [2027] [2028] [2029]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7072--7072
[]\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[]
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[] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2030]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
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[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2031]
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2032] [2033]
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\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2034] [2035]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7476--7476
[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2036]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2037] [2038] [2039] [2040] [2041] [2042]
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
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[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2043] [2044]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8098--8098
[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
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[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055]
[2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9501--9501
[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2065]
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[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
"Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2066]
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[]\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25)
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[]\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[]
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[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
[2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077]
[2078] [2079]) (./Matrix-pkg.tex [2080]
Chapter 17.
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[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2081]
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[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2082]
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[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
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\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2083]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
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[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2084] [2085]
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[]\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE)
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[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal
mean-ing as in
[2086]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
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[]\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[]
[2087] [2088]
Underfull \hbox (badness 3189) in paragraph at lines 681--685
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2089]
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[]\T1/ptm/m/n/10 In some ver-sions of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 eigen[][][](CAex) \T1/ptm/m/n/10 fell into an in-fi-nite loop (where
as
[2090] [2091]
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[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2092]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
Underfull \hbox (badness 10000) in paragraph at lines 971--976
[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of
the lower tri-
Underfull \hbox (badness 10000) in paragraph at lines 971--976
\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
de-com-po-si-tion. This method is equiv-a-lent to
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\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in
the above de-scrip-tion of
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical")
[2093]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again>
\relax
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again>
\relax
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
[2094pdfTeX warning (ext4):
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1082 \end{Description}
pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate i
gnored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1082 \end{Description}
pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate i
gnored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1082 \end{Description}
] [2095]
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[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2096]
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[]\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
0, ...)
[2097]
Underfull \hbox (badness 2277) in paragraph at lines 1314--1317
[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
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[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2098]
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[]\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[]
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[]\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[]
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[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
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[]\T1/pcr/m/n/9 ## each has a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n
/9 matrix %% FIXME !! --- "check" them __unfinished__[]
[2099]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky", ...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3861) in paragraph at lines 1457--1464
\T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1492--1496
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
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\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2100]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again>
\relax
l.1549 ... Row and Column Sums and Means}{colSums}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again>
\relax
l.1549 ... Row and Column Sums and Means}{colSums}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.1550 \aliasA{colMeans}{colSums}{colMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again>
\relax
l.1571 \aliasA{rowMeans}{colSums}{rowMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again>
\relax
l.1582 \aliasA{rowSums}{colSums}{rowSums}
[2101] [2102]
Underfull \hbox (badness 3547) in paragraph at lines 1757--1760
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
, the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2103] [2104] [2105] [2106]
Underfull \hbox (badness 10000) in paragraph at lines 1994--1996
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2107]
Underfull \hbox (badness 10000) in paragraph at lines 2116--2118
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
Underfull \hbox (badness 3068) in paragraph at lines 2177--2181
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
or sim-i-lar. Of-ten how-ever, more eas-ily via
[2108]
Underfull \hbox (badness 4713) in paragraph at lines 2212--2214
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2109]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10
or
[2110] [2111]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix", ...)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
Underfull \hbox (badness 2707) in paragraph at lines 2486--2490
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
[2112]
Underfull \hbox (badness 2689) in paragraph at lines 2546--2548
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
If miss-ing,
[2113]
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[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
[2114]
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[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
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[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
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[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
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[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2115]
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[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 :
the re-sult is from class
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[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
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[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2116] [2117]
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[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
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[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2118]
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[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
, via
[2119] [2120]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix", ...) \T1/ptm/m/n/10 or
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[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 .
[2121]
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[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2122] [2123]
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[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
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\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
triv-ial
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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
if
[2124]
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[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
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[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
[2125]
Underfull \hbox (badness 6364) in paragraph at lines 3700--3703
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2126]
Underfull \hbox (badness 4060) in paragraph at lines 3817--3820
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse
tri-an-gu-lar solve (aka
[2127]
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[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
Underfull \hbox (badness 3635) in paragraph at lines 3923--3927
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
Underfull \hbox (badness 10000) in paragraph at lines 3932--3935
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
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\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
[2128]
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[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2129] [2130] [2131] [2132]
Underfull \hbox (badness 10000) in paragraph at lines 4225--4230
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite
Tay-lor se-ries
[2133] [2134]
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[] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[]
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[] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[]
[2135] [2136] [2137] [2138]
Underfull \hbox (badness 10000) in paragraph at lines 4670--4675
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2139]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4751--4751
[]\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons"
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[] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2,
dimnames=dns))[]
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[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
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[] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[]
[2140] [2141]
Underfull \hbox (badness 4120) in paragraph at lines 4892--4895
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4921--4921
[]\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[]
[2142]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4926--4926
[]\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4933--4933
[]\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[]
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[] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[]
[2143]
Underfull \hbox (badness 1817) in paragraph at lines 5024--5033
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
the
Underfull \hbox (badness 5637) in paragraph at lines 5065--5067
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2144]
Underfull \hbox (badness 3138) in paragraph at lines 5091--5093
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2145]
Underfull \hbox (badness 1603) in paragraph at lines 5175--5177
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2146] [2147] [2148]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5411--5411
[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[]
[2149]
Underfull \hbox (badness 10000) in paragraph at lines 5487--5490
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5498--5498
[]\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[]
[2150]
Underfull \hbox (badness 1622) in paragraph at lines 5535--5540
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
\T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
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\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2151] [2152]
Underfull \hbox (badness 1062) in paragraph at lines 5720--5723
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2153]
Underfull \hbox (badness 2809) in paragraph at lines 5749--5752
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2154]
Underfull \hbox (badness 2635) in paragraph at lines 5861--5866
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 5861--5866
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 5869--5872
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2155]
Underfull \hbox (badness 1184) in paragraph at lines 6042--6045
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2156] [2157]
Underfull \hbox (badness 10000) in paragraph at lines 6140--6143
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2158]
Underfull \hbox (badness 10000) in paragraph at lines 6215--6218
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6231--6231
[]\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
Underfull \hbox (badness 2443) in paragraph at lines 6269--6275
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
Underfull \hbox (badness 1776) in paragraph at lines 6269--6275
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
sin-gu-lar,
[2159]
Underfull \hbox (badness 1675) in paragraph at lines 6286--6289
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6344--6344
[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2160] [2161]
Underfull \hbox (badness 6268) in paragraph at lines 6480--6483
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2162]
Underfull \hbox (badness 5036) in paragraph at lines 6504--6508
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
. How-ever,
Underfull \hbox (badness 10000) in paragraph at lines 6504--6508
\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2163]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again>
\relax
l.6596 \aliasA{det}{Matrix-class}{det}
Underfull \hbox (badness 1348) in paragraph at lines 6670--6673
[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
Underfull \hbox (badness 10000) in paragraph at lines 6675--6678
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
Underfull \hbox (badness 10000) in paragraph at lines 6692--6695
[2164] [2165]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn..Rpcent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again>
\relax
l.6761 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again>
\relax
l.6851 ...A{crossprod}{matrix-products}{crossprod}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again>
\relax
l.6933 ...tcrossprod}{matrix-products}{tcrossprod}
Underfull \hbox (badness 1881) in paragraph at lines 7015--7021
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
Underfull \hbox (badness 10000) in paragraph at lines 7068--7071
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 7068--7071
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 5637) in paragraph at lines 7071--7076
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2166pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7076 \item[crossprod]
\code{signature(x = "dgeMatrix", y = "dgeMatrix")}:pdfT
eX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rd
ash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7076 \item[crossprod]
\code{signature(x = "dgeMatrix", y = "dgeMatrix")}:]
Underfull \hbox (badness 10000) in paragraph at lines 7080--7082
[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
Underfull \hbox (badness 10000) in paragraph at lines 7082--7084
[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10
and
[2167]
Underfull \hbox (badness 1062) in paragraph at lines 7203--7206
[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2168]
Underfull \hbox (badness 2809) in paragraph at lines 7237--7240
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 10000) in paragraph at lines 7289--7291
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2169]
Underfull \hbox (badness 1406) in paragraph at lines 7329--7333
[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
Underfull \hbox (badness 1019) in paragraph at lines 7329--7333
\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2170] [2171]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7427--7427
[]\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[]
Underfull \hbox (badness 2635) in paragraph at lines 7492--7497
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 7492--7497
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 7500--7503
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2172] [2173]
Underfull \hbox (badness 10000) in paragraph at lines 7686--7688
[]\T1/ptm/m/n/10 fast
[2174]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again>
\relax
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again>
\relax
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
[2175] [2176]
Underfull \hbox (badness 1184) in paragraph at lines 7971--7974
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2177]
Underfull \hbox (badness 10000) in paragraph at lines 8061--8064
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2178]
Underfull \hbox (badness 10000) in paragraph at lines 8137--8140
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8153--8153
[]\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
[2179] [2180]
Underfull \hbox (badness 10000) in paragraph at lines 8263--8265
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
Underfull \hbox (badness 1596) in paragraph at lines 8279--8281
[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 :
co-er-cion to sparse
Underfull \hbox (badness 1721) in paragraph at lines 8285--8289
\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2181]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8369--8369
[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8374--8374
[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
[2182]
Underfull \hbox (badness 3989) in paragraph at lines 8396--8406
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
Underfull \hbox (badness 10000) in paragraph at lines 8396--8406
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2183]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}
) has been already used, duplicate ignored
<to be read again>
\relax
l.8488 \aliasA{qr}{qr-methods}{qr}
[2184]
Underfull \hbox (badness 5119) in paragraph at lines 8530--8533
[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
Overfull \hbox (36.7804pt too wide) in paragraph at lines 8550--8550
[] \T1/pcr/m/n/9 c1=rep(c(1,0,0), 2), c2=rep(c(0,1,0), 2), c3
=rep(c(0,0,1),2)),[]
[2185]
Underfull \hbox (badness 10000) in paragraph at lines 8599--8605
[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
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[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2186]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 8687--8687
[]\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
free"[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8708--8708
[]\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # wa
rning + ~1.5 sec[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8709--8709
[]\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.8723 ... the Reciprocal Condition Number}{rcond}
[2187] [2188]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2189] [2190] [2191]
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[]\T1/ptm/m/n/10 the ran-dom num-ber gen-er-a-tor for the \T1/pcr/m/n/10 x \T1/
ptm/m/n/10 slot, a [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 such that
Underfull \hbox (badness 10000) in paragraph at lines 9019--9021
[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
[2192] [2193]
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[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2194]
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[] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[]
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[]\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[]
[2195]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again>
\relax
l.9292 \aliasA{solve}{solve-methods}{solve}
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[] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9394--9394
[] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[]
[2196]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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[]\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2197]
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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[]\T1/ptm/m/n/10 works via
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via
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[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9561--9561
[]\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][]
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[] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
[FIXME ??] only[]
[2198]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
er-ca-ble to)
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\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
[2199]
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[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
[2200]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
== c(3, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2201]
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[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2202]
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[] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij =
FALSE)[]
[2203]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2204]
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[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
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[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
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[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
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[]\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x =
1:6, dimnames = dn)[]
[2205]
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[]\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[]
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[] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
X@dimension)[]
[2206]
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[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject
of S3 class
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[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
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[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or
[2207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again>
\relax
l.10284 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2208]
Underfull \hbox (badness 1430) in paragraph at lines 10394--10396
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
[2209]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10420--10420
[] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[]
[2210]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.toe
plitz}) has been already used, duplicate ignored
<to be read again>
\relax
l.10559 ...toeplitz}{sparseVector-class}{toeplitz}
Underfull \hbox (badness 2970) in paragraph at lines 10571--10577
[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-
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\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
[2211]
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[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
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[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or
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[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2212] [2213]
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[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
[2214]
Underfull \hbox (badness 2591) in paragraph at lines 10868--10873
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2215]
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[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2216]
Underfull \hbox (badness 6641) in paragraph at lines 10999--11002
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
vir-tual class of all sparse ma-tri-ces coded in
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\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2217] [2218] [2219]
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[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
sparse ma-trix (i.e., of sub-class of
[2220]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
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[]\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x =
1:6, dimnames = dn)[]
[2221] [2222]
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2223] [2224]) (./boot-pkg.tex
Chapter 18.
[2225] [2226] [2227] [2228] [2229] [2230] [2231]
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[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2232]
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[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
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\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2233]
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[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2234]
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\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2235]
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[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
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[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2236]
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[]\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt,
data = nuke)[]
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[2238]
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[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
[2239]
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[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
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\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
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\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2240] [2241] [2242] [2243] [2244]
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[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2245] [2246] [2247] [2248]
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[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2249] [2250] [2251] [2252]
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[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
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[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2254] [2255] [2256] [2257]
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
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\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
[2258]
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2437--2438
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2259]
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[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
sam-ple
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\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
is used. This is mul-ti-plied by
[2260] [2261] [2262] [2263] [2264]
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[]\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,
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[]\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,[]
[2265] [2266] [2267]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2268]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2269] [2270] [2271]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
[2272] [2273] [2274] [2275] [2276] [2277] [2278]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2279] [2280]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2281] [2282] [2283]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault
is
[2284]
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[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2285] [2286]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
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\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294] [2295]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2296] [2297] [2298] [2299]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2300]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2301] [2302] [2303] [2304] [2305] [2306] [2307] [2308]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5861--5861
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2309]
Underfull \hbox (badness 1127) in paragraph at lines 5983--6001
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2310]
Underfull \hbox (badness 2837) in paragraph at lines 6016--6019
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2311] [2312] [2313] [2314]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6301--6301
[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2315] [2316]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6490--6490
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6492--6492
[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
[2317] [2318] [2319]
Underfull \hbox (badness 1596) in paragraph at lines 6737--6741
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2320] [2321]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6897--6897
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2322] [2323] [2324] [2325] [2326] [2327] [2328] [2329]) (./class-pkg.tex
[2330]
Chapter 19.
[2331] [2332] [2333] [2334] [2335] [2336] [2337] [2338]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2339] [2340] [2341] [2342] [2343] [2344] [2345] [2346]) (./cluster-pkg.tex
Chapter 20.
[2347]
Underfull \hbox (badness 10000) in paragraph at lines 133--140
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when
us-ing \T1/pcr/m/n/10 method = "flexible"
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 par-tic-u-larly for the case when \T1/pcr/m/n/10 par.method \T1/
ptm/m/n/10 is spec-i-fied of longer length
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 than one. The \T1/ptm/m/it/10 weighted av-er-age \T1/ptm/m/n/10
(\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n/10 . Fur-ther, \T
1/pcr/m/n/10 method= "single" \T1/ptm/m/n/10 is
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c
(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 .
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 165--167
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2349]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 250--250
[] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC]) ,[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 251--251
[] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, -.5))[iC]),[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 252--252
[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
[2350] [2351]
Underfull \vbox (badness 7685) has occurred while \output is active [2352]
[2353]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 516--516
[] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
= axes,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 520--520
[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2354]
Underfull \hbox (badness 5374) in paragraph at lines 537--539
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2355] [2356]
Underfull \hbox (badness 3078) in paragraph at lines 680--683
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2357]
Underfull \hbox (badness 2941) in paragraph at lines 761--764
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10
,
[2358]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 799--799
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
[2359]
Underfull \hbox (badness 10000) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
Overfull \hbox (12.78088pt too wide) in paragraph at lines 893--893
[]\T1/pcr/m/n/10 clusGap(x, FUNcluster, K.max, B = 100, verbose = interactive(
), ...)
[2360]
Underfull \hbox (badness 4872) in paragraph at lines 934--936
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
[2361]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1036--1036
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
[2362] [2363]
Underfull \hbox (badness 4144) in paragraph at lines 1112--1116
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
e.g., for
[2364]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1188--1188
[] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
cex.txt = cex,[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1194--1194
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2365] [2366]
Underfull \hbox (badness 10000) in paragraph at lines 1394--1398
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
[2367]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1412--1412
[]\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1421--1421
[] \T1/pcr/m/n/9 axes=FALSE,ann=FALSE, sub="", col.p=NA, col.txt="dark
green", labels=3)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1429--1429
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2368]
Underfull \hbox (badness 5741) in paragraph at lines 1469--1472
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2369] [2370]
Underfull \hbox (badness 5008) in paragraph at lines 1645--1653
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1736--1736
[]\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1755--1755
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2372] [2373] [2374] [2375] [2376]
Underfull \hbox (badness 10000) in paragraph at lines 2057--2059
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
Underfull \hbox (badness 3179) in paragraph at lines 2081--2087
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2377] [2378]
Underfull \hbox (badness 10000) in paragraph at lines 2239--2242
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2379]
Underfull \hbox (badness 1292) in paragraph at lines 2307--2310
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
[2380]
Underfull \hbox (badness 6675) in paragraph at lines 2316--2318
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2339--2342
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
Overfull \vbox (12.60576pt too high) has occurred while \output is active
[2381] [2382] [2383]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2546--2546
[]\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[]
[2384] [2385] [2386]
Underfull \hbox (badness 1067) in paragraph at lines 2734--2739
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
\T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2387] [2388]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2889--2889
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2389] [2390] [2391]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3085--3085
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3086--3086
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2392]
Underfull \hbox (badness 10000) in paragraph at lines 3153--3156
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2393]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3203--3203
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3204--3204
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2394] [2395] [2396]
Underfull \hbox (badness 10000) in paragraph at lines 3389--3392
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
Underfull \hbox (badness 3471) in paragraph at lines 3389--3392
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2397]
Underfull \hbox (badness 10000) in paragraph at lines 3452--3457
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2398]
Underfull \hbox (badness 1735) in paragraph at lines 3521--3523
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "twins"\T1/ptm/m/n/10 , typ
-i-cally cre-ated by ei-ther [][]\T1/pcr/m/n/10 agnes[][][]() \T1/ptm/m/n/10 or
Underfull \hbox (badness 4621) in paragraph at lines 3538--3543
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1990) in paragraph at lines 3538--3543
\T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1
/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider
Underfull \hbox (badness 6268) in paragraph at lines 3550--3553
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2399]
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[]\T1/ptm/m/n/10 currently [][]$\T1/pcr/m/n/10 http : / / www . agoras . ua . a
c . be / datasets / clusplot-[]examples . tar .
[2400] [2401]
Underfull \hbox (badness 10000) in paragraph at lines 3733--3736
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2402]
Underfull \hbox (badness 10000) in paragraph at lines 3764--3767
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2403]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3817--3817
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
Underfull \hbox (badness 2035) in paragraph at lines 3828--3830
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2404] [2405] [2406]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4021--4021
[] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[]
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[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2407]
Underfull \hbox (badness 1946) in paragraph at lines 4052--4057
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
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[]\T1/ptm/m/n/10 numeric (rank 1) ar-ray of clus-ter-wise \T1/ptm/m/it/10 means
\T1/ptm/m/n/10 of sil-hou-ette widths where
[2408]
Underfull \hbox (badness 10000) in paragraph at lines 4118--4126
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4160--4160
[]\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4169--4169
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4171--4171
[] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4174--4174
[]\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4176--4176
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE,[]
[2409]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4190--4190
[] \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t
olerance = 0))[]
[2410] [2411] [2412] [2413] [2414] [2415] [2416]) (./codetools-pkg.tex
Chapter 21.
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
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[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
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[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2417]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2418]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2419] [2420] [2421]) (./foreign-pkg.tex [2422]
Chapter 22.
[2423]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2424] [2425]
Underfull \hbox (badness 3601) in paragraph at lines 234--242
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2426]
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[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2427] [2428] [2429]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 459--459
[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame)[]
[2430]
Underfull \hbox (badness 10000) in paragraph at lines 515--523
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
[2431]
Underfull \hbox (badness 7613) in paragraph at lines 533--539
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2432] [2433] [2434]
Underfull \hbox (badness 10000) in paragraph at lines 730--731
Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2435]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 816--816
[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2436]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 879--879
[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
Underfull \hbox (badness 6708) in paragraph at lines 905--908
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2437] [2438]
Underfull \hbox (badness 10000) in paragraph at lines 989--990
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1025--1025
[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2439]
Underfull \hbox (badness 1286) in paragraph at lines 1110--1114
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates =
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2440]
Underfull \hbox (badness 10000) in paragraph at lines 1183--1189
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2441] [2442]) (./lattice-pkg.tex
Chapter 23.
[2443] [2444] [2445]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 287--287
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 291--291
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[]
[2446]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 299--299
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 306--306
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 314--314
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 335--335
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 339--339
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[]
[2447]
Underfull \hbox (badness 4060) in paragraph at lines 358--370
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
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\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 398--413
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
both
Underfull \hbox (badness 10000) in paragraph at lines 414--416
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
one can ei-ther set
[2448]
Underfull \hbox (badness 7631) in paragraph at lines 480--485
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2449] [2450]
Underfull \hbox (badness 1221) in paragraph at lines 651--659
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
ar-gu-ments to
[2451] [2452] [2453] [2454]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of
fac-tors will be
Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a
use-ful lay-out.
[2455]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2456] [2457]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
Underfull \hbox (badness 1917) in paragraph at lines 1239--1240
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2458] [2459] [2460]
Underfull \hbox (badness 1540) in paragraph at lines 1479--1485
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2461]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2462]
Underfull \vbox (badness 10000) has occurred while \output is active [2463]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671
[] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[]
Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2464]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
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[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10
, etc; see
[2465]
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
An-drews
[2466] [2467] [2468]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2469]
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2470] [2471] [2472]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2347--2347
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2351--2351
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[]
Underfull \hbox (badness 4441) in paragraph at lines 2364--2368
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2473] [2474] [2475]
Underfull \hbox (badness 4441) in paragraph at lines 2549--2556
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2476] [2477]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2691--2691
[] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[]
[2478]
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[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2479]
Underfull \hbox (badness 2913) in paragraph at lines 2793--2798
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2793--2798
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
Underfull \hbox (badness 6758) in paragraph at lines 2879--2883
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
Underfull \hbox (badness 7576) in paragraph at lines 2879--2883
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2885--2887
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2480]
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
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\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
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\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2961--2965
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for
the de-fault panel func-tion
[2481] [2482]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
[] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3063--3063
[] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3064--3064
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3075--3075
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3087--3087
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
[2483]
Underfull \hbox (badness 10000) in paragraph at lines 3112--3120
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
Underfull \hbox (badness 2913) in paragraph at lines 3145--3152
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3145--3152
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2484] [2485] [2486] [2487]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3433 \aliasA{parallel}{B\_08\_splom}{parallel}
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3475--3475
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
[2488]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3498--3498
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2489] [2490] [2491] [2492] [2493]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3834--3834
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2494]
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\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
Underfull \hbox (badness 2435) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2495] [2496]
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[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
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[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
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[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
Underfull \hbox (badness 1728) in paragraph at lines 4107--4111
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2497]
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[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4172--4176
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2498] [2499]
Underfull \hbox (badness 1067) in paragraph at lines 4286--4296
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1735) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4286--4296
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
Underfull \hbox (badness 1701) in paragraph at lines 4311--4314
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4314--4316
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2500] [2501] [2502] [2503] [2504] [2505]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4718--4718
[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2506] [2507]
Underfull \hbox (badness 10000) in paragraph at lines 4905--4908
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2508] [2509]
Underfull \hbox (badness 1442) in paragraph at lines 5037--5040
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2510] [2511] [2512] [2513] [2514] [2515]
Underfull \hbox (badness 3646) in paragraph at lines 5369--5372
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 ,
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5399--5399
[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5400--5400
[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2516]
Underfull \hbox (badness 10000) in paragraph at lines 5488--5491
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
Underfull \hbox (badness 2103) in paragraph at lines 5488--5491
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
Underfull \hbox (badness 6412) in paragraph at lines 5505--5511
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
though this can be
[2517]
Underfull \hbox (badness 1635) in paragraph at lines 5514--5519
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2518]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5663--5663
[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
[2519]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5677--5677
[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5678--5678
[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5681--5681
[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5684--5684
[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5686--5686
[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5694--5694
[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5695--5695
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5696--5696
[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
Underfull \hbox (badness 10000) in paragraph at lines 5712--5714
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
[2520]
Underfull \hbox (badness 2376) in paragraph at lines 5723--5725
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2521]
Underfull \hbox (badness 2538) in paragraph at lines 5848--5852
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5859--5866
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5859--5866
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
used (in com-bi-na-tion with
[2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 6012--6016
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2524] [2525]
Underfull \hbox (badness 4242) in paragraph at lines 6159--6164
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2526] [2527]
Underfull \hbox (badness 3601) in paragraph at lines 6275--6280
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6275--6280
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2528] [2529]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6362--6362
[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2530]
Underfull \hbox (badness 1888) in paragraph at lines 6494--6501
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2531]
Underfull \hbox (badness 10000) in paragraph at lines 6551--6554
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
Underfull \hbox (badness 1558) in paragraph at lines 6551--6554
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2532]
Underfull \hbox (badness 1005) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
Underfull \hbox (badness 1571) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2533] [2534] [2535] [2536] [2537]
Underfull \hbox (badness 1320) in paragraph at lines 6957--6964
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 6957--6964
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
ef-fi-cient. When us-ing
[2538]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7027--7027
[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
[2539]
Underfull \hbox (badness 10000) in paragraph at lines 7057--7060
[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
to
Underfull \hbox (badness 1584) in paragraph at lines 7057--7060
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2540]
Underfull \hbox (badness 10000) in paragraph at lines 7161--7164
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2541] [2542]
Underfull \hbox (badness 2012) in paragraph at lines 7327--7330
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2543]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7373--7373
[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2544] [2545]
Underfull \hbox (badness 2644) in paragraph at lines 7514--7518
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on
to
Underfull \hbox (badness 2772) in paragraph at lines 7527--7530
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a
list of ar-gu-ments to be sup-plied to
Underfull \hbox (badness 4242) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
Underfull \hbox (badness 1147) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
co-erced to a list. This al-lows ar-
Underfull \hbox (badness 2351) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
Underfull \hbox (badness 1675) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1
/ptm/m/n/10 , which adds the
Underfull \hbox (badness 1769) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
e.g.,
[2546]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7597--7597
[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7607--7607
[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2547]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7668--7668
[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7673--7673
[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2548] [2549] [2550]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7854--7854
[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2551]
Underfull \hbox (badness 1436) in paragraph at lines 7909--7915
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
Underfull \hbox (badness 1231) in paragraph at lines 7909--7915
\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2552] [2553] [2554] [2555] [2556] [2557] [2558] [2559]
Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2560] [2561]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8642--8642
[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8643--8643
[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8655--8655
[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
[2562]
Underfull \hbox (badness 3118) in paragraph at lines 8674--8677
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2563]
Underfull \hbox (badness 1515) in paragraph at lines 8750--8754
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2564]
Underfull \hbox (badness 6316) in paragraph at lines 8856--8861
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2565] [2566]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8963--8963
[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2567] [2568]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9102--9102
[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2569]
Overfull \hbox (84.94879pt too wide) in paragraph at lines 9161--9165
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left, right, left.name, right.name, condition
Overfull \hbox (104.63074pt too wide) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left, right.x, right.y, left.name
, right.x.name, right.y.name, condition
[2570] [2571] [2572] [2573] [2574] [2575] [2576]
Underfull \hbox (badness 4205) in paragraph at lines 9619--9623
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4518) in paragraph at lines 9619--9623
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 6300) in paragraph at lines 9624--9627
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2577] [2578] [2579]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9850 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2580] [2581] [2582] [2583])
(./mgcv-pkg.tex [2584]
Chapter 24.
Underfull \hbox (badness 1052) in paragraph at lines 40--42
[]\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term
p-values. See
[2585] [2586]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147
[]\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,
Overfull \hbox (6.78088pt too wide) in paragraph at lines 150--150
[] \T1/pcr/m/n/10 chunk.size=10000,rho=0,AR.start=NULL,sparse=FALSE,cluster
=NULL,[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 151--151
[] \T1/pcr/m/n/10 gc.level=1,use.chol=FALSE,samfrac=1,drop.unused.levels=TR
UE,...)[]
[2587]
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
Underfull \hbox (badness 1043) in paragraph at lines 193--198
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2588]
Underfull \hbox (badness 2626) in paragraph at lines 248--251
[]\T1/ptm/m/n/10 If all smooths are P-splines and all ten-sor prod-ucts are of
the form
[2589] [2590]
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2591] [2592] [2593]
Underfull \hbox (badness 2922) in paragraph at lines 521--522
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
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[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[]
[2601] [2602] [2603] [2604] [2605] [2606] [2607]
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[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2608] [2609] [2610] [2611] [2612] [2613]
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\T1/ptm/m/n/10 de-grees of free-dom (mix-tures of the two are per-mit-ted). Mul
ti-dimensional smooths are
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[]\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[]
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[] \T1/pcr/m/n/10 fit=TRUE,paraPen=NULL,G=NULL,in.out,drop.unused.levels=TR
UE,...)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2614]
Underfull \hbox (badness 1043) in paragraph at lines 1806--1811
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2615] [2616]
Underfull \hbox (badness 1043) in paragraph at lines 1966--1972
\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2619]
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[2623] [2624] [2625] [2626] [2627] [2628]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2720--2720
[] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
[] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[]
[2629] [2630] [2631] [2632] [2633]
Underfull \hbox (badness 5189) in paragraph at lines 3038--3042
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2634] [2635]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3155--3155
[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[2637] [2638] [2639] [2640] [2641] [2642] [2643] [2644]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3709--3709
[] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[]
[2645] [2646]
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[]\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[]
Underfull \hbox (badness 1142) in paragraph at lines 3855--3859
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2647] [2648] [2649]
Underfull \hbox (badness 5970) in paragraph at lines 4035--4041
[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
[2650]
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[2652] [2653]
Underfull \hbox (badness 1577) in paragraph at lines 4280--4283
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
Underfull \hbox (badness 2181) in paragraph at lines 4287--4288
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
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[2665]
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[2667] [2668]
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[]\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
to rule the world.",[]
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[] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[]
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[2695]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2696]
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[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 3108) in paragraph at lines 6979--6982
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
be
[2697] [2698] [2699]
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[]\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s
cale=-1,[]
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[] \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla
b=NULL,[]
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[] \T1/pcr/m/n/10 shift=0,trans=I,seWithMean=FALSE,unconditional=FALSE
,by.resids=FALSE,[]
[2700] [2701] [2702]
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\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
some-times to clone the
[2703] [2704] [2705]
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[] \T1/pcr/m/n/10 block.size=50000,newdata.guaranteed=FALSE,na.action=n
a.pass,cluster=NULL,...)[]
[2706] [2707]
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[] \T1/pcr/m/n/10 block.size=NULL,newdata.guaranteed=FALSE,na.action=na
.pass,[]
[2708] [2709] [2710]
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[] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[]
[2712]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2713]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
[2714]
Underfull \hbox (badness 10000) in paragraph at lines 8142--8145
[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2715] [2716]
Underfull \hbox (badness 1253) in paragraph at lines 8272--8274
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion
cri-te-rion re-ported is one of GCV,
[2717] [2718] [2719] [2720]
Underfull \hbox (badness 1946) in paragraph at lines 8450--8457
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
Underfull \hbox (badness 2221) in paragraph at lines 8450--8457
\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
Underfull \hbox (badness 2042) in paragraph at lines 8450--8457
\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee
Underfull \hbox (badness 2846) in paragraph at lines 8458--8461
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
Underfull \hbox (badness 5862) in paragraph at lines 8458--8461
\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2721]
Underfull \hbox (badness 10000) in paragraph at lines 8537--8540
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
"deviance"\T1/ptm/m/n/10 ,
[2722] [2723] [2724] [2725] [2726] [2727] [2728] [2729]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9044--9044
[] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[]
Underfull \hbox (badness 1975) in paragraph at lines 9055--9060
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2730] [2731]
Underfull \hbox (badness 1803) in paragraph at lines 9132--9136
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 9144--9156
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
Underfull \hbox (badness 2401) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able.
Plot meth-ods can be
Underfull \hbox (badness 2970) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2732] [2733] [2734]
Underfull \hbox (badness 6876) in paragraph at lines 9354--9360
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one
or two vari-ables, spec-i-fied via terms like
[2735]
Underfull \hbox (badness 10000) in paragraph at lines 9395--9396
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2736] [2737]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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\T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs",
...) \T1/ptm/m/n/10 or
[2738] [2739]
Underfull \hbox (badness 10000) in paragraph at lines 9652--9653
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2740] [2741]
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[]\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first
deriv penalty[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9734--9734
[]\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[]
Underfull \hbox (badness 7613) in paragraph at lines 9772--9775
\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2742] [2743] [2744] [2745]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9985--9985
[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[2746]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2747] [2748]
Underfull \hbox (badness 10000) in paragraph at lines 10138--10141
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method
a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 10138--10141
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 10138--10141
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[2749]
Underfull \hbox (badness 10000) in paragraph at lines 10237--10243
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
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\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[2750] [2751] [2752]
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[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
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[] \T1/pcr/m/n/9 te(v,w,t,bs=c("sf","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))+[]
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[] \T1/pcr/m/n/9 te(v,w,t,bs=c("sw","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))[]
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[]\T1/pcr/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax)
),knots=knots,method="REML")[]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 10541--10541
[] \T1/pcr/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax))
,knots=knots,method="REML")[]
[2755]
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[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the
sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 10581--10582
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2756] [2757]
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[]\T1/pcr/m/n/9 bk <- gam(y~s(la,lo,bs="sos",k=60),knots=list(la=dat$la[ind],l
o=dat$lo[ind]),data=dat)[]
[2758] [2759]
Underfull \hbox (badness 3396) in paragraph at lines 10841--10846
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any
num-ber of vari-ables, spec-i-fied via terms like
[2760]
Underfull \hbox (badness 10000) in paragraph at lines 10886--10888
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2761] [2762] [2763] [2764]
Underfull \hbox (badness 10000) in paragraph at lines 11074--11077
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
Underfull \hbox (badness 3068) in paragraph at lines 11074--11077
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
Underfull \hbox (badness 10000) in paragraph at lines 11107--11111
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 5652) in paragraph at lines 11107--11111
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , code[][]soap[][][], code[][]Spheri
cal.Spline[][][], [][]\T1/pcr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 ,
[2765] [2766]
Underfull \hbox (badness 2158) in paragraph at lines 11259--11259
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2767] [2768]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 11334--11334
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[2769] [2770]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11468--11468
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[2771] [2772]
Underfull \hbox (badness 4846) in paragraph at lines 11604--11607
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or
es-ti-ma-tors if
[2773] [2774] [2775] [2776] [2777] [2778] [2779] [2780] [2781] [2782] [2783]
[2784] [2785] [2786] [2787]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 12501--12501
[]\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[]
[2788] [2789] [2790] [2791] [2792] [2793] [2794]) (./nlme-pkg.tex
Chapter 25.
[2795]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2796]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2797] [2798] [2799] [2800] [2801]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
[] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[2802] [2803] [2804] [2805] [2806] [2807] [2808] [2809] [2810] [2811]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1094--1094
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[]
[2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819]
Underfull \hbox (badness 10000) in paragraph at lines 1633--1636
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[2820]
Underfull \hbox (badness 3780) in paragraph at lines 1650--1652
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[2821] [2822] [2823] [2824] [2825]
Underfull \hbox (badness 2042) in paragraph at lines 1997--2003
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[2826]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2059--2059
[]\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla
pse = "Dog")[]
[2827]
Underfull \hbox (badness 1132) in paragraph at lines 2147--2149
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[2828] [2829]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[2830]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[2831] [2832] [2833] [2834] [2835] [2836] [2837] [2838]
Underfull \hbox (badness 10000) in paragraph at lines 2846--2850
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849]
[2850]
Underfull \hbox (badness 6493) in paragraph at lines 3582--3590
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[2851] [2852] [2853] [2854] [2855] [2856] [2857] [2858] [2859] [2860] [2861]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 4348--4348
[]\T1/pcr/m/n/10 fdHess(pars, fun, ..., .relStep=(.Machine$double.eps)^(1/3),
minAbsPar=0)
[2862] [2863] [2864] [2865] [2866] [2867] [2868] [2869] [2870] [2871] [2872]
[2873] [2874]
Underfull \hbox (badness 10000) in paragraph at lines 5158--5162
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[2875] [2876] [2877] [2878] [2879]
Underfull \hbox (badness 10000) in paragraph at lines 5475--5479
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
Underfull \hbox (badness 2671) in paragraph at lines 5475--5479
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[2880] [2881]
Underfull \hbox (badness 10000) in paragraph at lines 5590--5593
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890]
Underfull \hbox (badness 2799) in paragraph at lines 6096--6102
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[2891]
Underfull \hbox (badness 7133) in paragraph at lines 6157--6161
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2892]
Underfull \hbox (badness 2057) in paragraph at lines 6241--6252
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[2893]
Underfull \hbox (badness 10000) in paragraph at lines 6305--6307
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6334--6334
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2894] [2895] [2896] [2897]
Underfull \hbox (badness 7133) in paragraph at lines 6553--6557
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2898]
Underfull \hbox (badness 10000) in paragraph at lines 6652--6658
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
[2899]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6718
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2900]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6743--6743
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2901] [2902] [2903]
Underfull \hbox (badness 10000) in paragraph at lines 6986--6993
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7003--7003
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7011--7011
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
[2904]
Underfull \hbox (badness 2875) in paragraph at lines 7033--7035
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[2905] [2906] [2907]
Underfull \hbox (badness 10000) in paragraph at lines 7248--7253
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[2908] [2909]
Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 1817) in paragraph at lines 7400--7408
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that
20 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7423--7426
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[2910] [2911] [2912] [2913]
Underfull \hbox (badness 3354) in paragraph at lines 7638--7640
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
which \T1/ptm/m/n/10 is not equal to
[2914] [2915] [2916] [2917] [2918] [2919]
Underfull \hbox (badness 1642) in paragraph at lines 8030--8052
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2920] [2921]
Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8193--8193
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
Underfull \hbox (badness 1642) in paragraph at lines 8202--8224
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2922] [2923] [2924] [2925] [2926]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8466--8466
[]\T1/pcr/m/n/10 lmeControl(maxIter, msMaxIter, tolerance, niterEM, msMaxEval,
msTol,
Underfull \hbox (badness 10000) in paragraph at lines 8509--8511
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2927]
Underfull \hbox (badness 1320) in paragraph at lines 8522--8526
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][] \T1/ptm/m/n/10 (those from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8544--8544
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2928] [2929] [2930]
Underfull \hbox (badness 10000) in paragraph at lines 8707--8719
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[2931] [2932] [2933] [2934] [2935] [2936] [2937] [2938] [2939]
Underfull \hbox (badness 10000) in paragraph at lines 9297--9304
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9308--9308
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[2940]
Underfull \hbox (badness 6300) in paragraph at lines 9390--9393
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[2941] [2942] [2943] [2944]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[2945]
Underfull \hbox (badness 10000) in paragraph at lines 9679--9682
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
[2946]
Underfull \hbox (badness 3108) in paragraph at lines 9727--9730
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
Underfull \hbox (badness 2521) in paragraph at lines 9727--9730
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[2947] [2948]
Underfull \hbox (badness 2435) in paragraph at lines 9900--9905
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[2949] [2950] [2951] [2952] [2953]
Underfull \hbox (badness 7291) in paragraph at lines 10190--10192
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[2954] [2955] [2956]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10406--10406
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[2957]
Underfull \hbox (badness 1596) in paragraph at lines 10435--10461
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[2958] [2959] [2960]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10611--10611
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[2961] [2962] [2963]
Underfull \hbox (badness 10000) in paragraph at lines 10808--10810
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Underfull \hbox (badness 1092) in paragraph at lines 10818--10821
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10840--10840
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2964] [2965] [2966]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10996--10996
[]\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool)
[2967]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11091--11091
[]\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool)[]
[2968] [2969] [2970] [2971] [2972] [2973] [2974] [2975] [2976] [2977] [2978]
Underfull \hbox (badness 6268) in paragraph at lines 11852--11862
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[2979] [2980] [2981] [2982]
Underfull \hbox (badness 10000) in paragraph at lines 12113--12119
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[2983] [2984] [2985] [2986] [2987] [2988] [2989]
Underfull \hbox (badness 2452) in paragraph at lines 12576--12583
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[2990]
Underfull \hbox (badness 10000) in paragraph at lines 12641--12647
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001]
[3002] [3003] [3004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13593--13593
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3005]
Underfull \hbox (badness 10000) in paragraph at lines 13620--13623
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 6016) in paragraph at lines 13648--13651
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13648--13651
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13655--13658
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13663--13670
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13663--13670
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
[3006]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13720--13720
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
Underfull \hbox (badness 10000) in paragraph at lines 13727--13730
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13727--13730
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
[3007]
Underfull \hbox (badness 4582) in paragraph at lines 13755--13758
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13755--13758
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,
"labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13759--13762
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3008]
Underfull \hbox (badness 10000) in paragraph at lines 13835--13838
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 1472) in paragraph at lines 13860--13867
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3009]
Underfull \hbox (badness 10000) in paragraph at lines 13929--13931
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3010] [3011] [3012] [3013]
Underfull \hbox (badness 1540) in paragraph at lines 14144--14149
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
Underfull \hbox (badness 1215) in paragraph at lines 14191--14193
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
De-faults to
[3014] [3015] [3016] [3017] [3018]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14434--14434
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been
already used, duplicate ignored
<to be read again>
\relax
l.15072 ...Extract Random Effects}{random.effects}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again>
\relax
l.15072 ...Extract Random Effects}{random.effects}
[3028] [3029] [3030]
[3031] [3032] [3033] [3034] [3035] [3036] [3037]
Underfull \hbox (badness 1009) in paragraph at lines 15729--15738
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3038] [3039] [3040]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15876--15876
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3041] [3042] [3043] [3044]
Underfull \hbox (badness 10000) in paragraph at lines 16154--16172
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16154--16172
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3045]
Underfull \hbox (badness 10000) in paragraph at lines 16211--16217
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 1728) in paragraph at lines 16731--16734
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3054] [3055] [3056] [3057] [3058]
Underfull \hbox (badness 1867) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal"
Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3059]
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 ,
[3060] [3061] [3062] [3063]
Underfull \hbox (badness 10000) in paragraph at lines 17375--17382
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3064] [3065] [3066] [3067] [3068] [3069] [3070]
Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3071]
Underfull \hbox (badness 3579) in paragraph at lines 17942--17947
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3072]
Underfull \hbox (badness 3579) in paragraph at lines 18006--18011
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3073]
Underfull \hbox (badness 3579) in paragraph at lines 18069--18074
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3074]
Underfull \hbox (badness 1577) in paragraph at lines 18130--18132
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
Underfull \hbox (badness 3579) in paragraph at lines 18132--18137
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3075]
Underfull \hbox (badness 3579) in paragraph at lines 18195--18200
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3076]
Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3579) in paragraph at lines 18267--18272
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3077] [3078]
Underfull \hbox (badness 1009) in paragraph at lines 18416--18425
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3079] [3080] [3081]
Underfull \hbox (badness 1009) in paragraph at lines 18550--18559
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089]) (./nnet-pkg.tex
[3090]
Chapter 26.
[3091]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3092] [3093] [3094] [3095]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 383--383
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 440--440
[]\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 443--443
[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3096]
Underfull \hbox (badness 4013) in paragraph at lines 488--491
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if
the net was gen-er-ated by
[3097]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 523--523
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3098]) (./rpart-pkg.tex
Chapter 27.
[3099] [3100] [3101] [3102]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324
[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3103]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3104] [3105] [3106]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
at the hor-i-zon-tal plot co-or-di-nates of
[3107] [3108]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
[3109]
Underfull \hbox (badness 2941) in paragraph at lines 785--787
[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
if
[3110]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902
[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
[3111]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921
[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[]
[3112] [3113] [3114]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
[]\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164
[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
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\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3115]
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[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3116]
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[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
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[]\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01,
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[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
[3117] [3118] [3119] [3120] [3121] [3122]
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[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3123] [3124]
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[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3125] [3126] [3127]) (./spatial-pkg.tex [3128]
Chapter 28.
[3129] [3130] [3131] [3132] [3133] [3134]
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[3135] [3136] [3137] [3138] [3139] [3140] [3141] [3142] [3143] [3144] [3145]
[3146] [3147]) (./survival-pkg.tex [3148]
Chapter 29.
[3149] [3150]
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[]\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
= lung, nmin = 1[]
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[]\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t
he last point[]
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[]\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a
nd Grambsch.[]
[3151]
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[]\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)
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[]\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
been already used, duplicate ignored
<to be read again>
\relax
l.267 ... Myelogenous Leukemia survival data}{aml}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again>
\relax
l.267 ... Myelogenous Leukemia survival data}{aml}
[3152] [3153]
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[]\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian)
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[]\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[]
[3154]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3155] [3156]
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[]\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size,
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[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3158] [3159]
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[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3160] [3161]
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[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3162]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again>
\relax
l.957 ...herapy for Stage B/C colon cancer}{colon}
[3163] [3164] [3165]
[3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173]
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[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
[3174] [3175]
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[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3176] [3177] [3178] [3179]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
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[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
[3180] [3181]
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[]\T1/pcr/m/n/9 lines(fit[1], lwd=2, xscale=365.24) #darken the first curve
and add marks[]
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[]\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[]
[3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191]
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[] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[]
[3192] [3193]
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[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3194] [3195]
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[]\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[]
[3196]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3197] [3198]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3199] [3200]
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[]\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod,
[3201] [3202]
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[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3203]
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[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
[3204]
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[]\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age
+ sex, mgus,[]
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[]\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[]
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[]\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[]
[3205] [3206]
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[]\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[]
[3207] [3208] [3209] [3210] [3211]
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[]\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[]
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[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3212] [3213]
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[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[]
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[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[]
[3214] [3215] [3216] [3217] [3218] [3219] [3220]
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[] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[]
[3221] [3222] [3223]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
form
[3224] [3225]
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[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
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[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3226]
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[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3227]
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[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3228] [3229]
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[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[]
[3230] [3231] [3232]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3233]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3234] [3235]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3236] [3237]
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[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3238]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3239] [3240]
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\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3241]
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[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3242] [3243] [3244]
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[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3245] [3246]
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[] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[]
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[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3247] [3248] [3249] [3250]
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[3252])
No file fullrefman.ind.
(./fullrefman.aux) )
(see the transcript file for additional information)pdfTeX warning (dest): name
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(/usr/share/texmf-texlive/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5]
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36]
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Chapter 1.
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[3]
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[]\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one
char-ac-ter vec-tors. The first en-try is al-ways
[4]
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
x \T1/ptm/m/n/10 such that
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\T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base
^ ulp.digits \T1/ptm/m/n/10 if ei-
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\T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m
/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise,
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\T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt
m/m/n/10 . Nor-mally
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[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1
/ptm/m/n/10 if
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\T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin
g \T1/ptm/m/n/10 is 0; oth-er-wise, it is
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\T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma
lly
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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-
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\T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) *
[5] [6]
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\T1/ptm/m/n/10 ues \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.
binary"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 an
d
[7]
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[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
[8]
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[]\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[9] [10]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11] [12] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pcr.fd) [13] [14]
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[]\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE)
[15] [16] [17] [18] [19]
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[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[20] [21] [22]
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[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[23] [24] [25] [26] [27]
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[]\T1/ptm/m/n/10 A char-ac-ter string. If not spec-i-fied, it will try \T1/pcr/
m/n/10 "%Y-%m-%d" \T1/ptm/m/n/10 then
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[]\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by
[28] [29]
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[]\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[]
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[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x, parent = emptyenv())
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[]\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[30] [31]
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[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[32] [33]
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[]\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[]
[34] [35]
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[36] [37] [38] [39] [40]
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[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-
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\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[54] [55] [56] [57] [58] [59] [60]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an
ob-ject
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\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[61]
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[]\T1/ptm/m/n/10 Are the \T1/pcr/m/n/10 R.app \T1/ptm/m/n/10 GUI com-po-nents a
nd the [][]\T1/pcr/m/n/10 quartz[][][] \T1/ptm/m/n/10 func-tion op-er-a-
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\T1/ptm/m/n/10 tional? Only on some OS X builds. Note that this is dis-tinct fr
om
[62] [63] [64]
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[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
[65]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for
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[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-
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\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
columns to fac-tors un-less
[66]
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
[67] [68] [69] [70]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[71] [72] [73] [74] [75]
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[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is
ap-plied to an ob-ject with class at-tribute
[76] [77] [78] [79] [80] [81] [82] [83]
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[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 http : / /
[84] [85] [86] [87]
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[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols.
They can be es-tab-lished us-ing
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[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
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[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[88] [89] [90] [91]
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\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 '). Prox-ies can be spe
c-i-fied for HTTP and FTP \T1/pcr/m/n/10 url \T1/ptm/m/n/10 con-nec-tions: see
[92]
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[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[93] [94]
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
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\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
and web-pages gen-er-
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\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If it is re-quired (it is n
ot rec-om-mended) when writ-ing
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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[95]
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\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[96]
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[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[98] [99] [100] [101] [102]
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[105] [106] [107]
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[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
[108]
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[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
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\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
but this can be changed by set-ting
[109]
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[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
a data frame by call-ing
Underfull \hbox (badness 1062) in paragraph at lines 7258--7269
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
is a generic func-tion, meth-ods can be
Overfull \hbox (4.63962pt too wide) in paragraph at lines 7291--7295
[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[110] [111] [112] [113] [114] [115]
Underfull \hbox (badness 10000) in paragraph at lines 7733--7745
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 7733--7745
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz =
"UTC") \T1/ptm/m/n/10 will give
[116] [117]
Underfull \hbox (badness 5802) in paragraph at lines 7938--7942
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10
reads the file byte-by-byte. This al-lows a
[118] [119]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8053--8057
\T1/pcr/m/n/10 trace("plot", browser, exit = browser, signature = c("track", "m
issing"))
[120]
Underfull \hbox (badness 10000) in paragraph at lines 8106--8110
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[121]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8187--8187
[]\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(1+2, "y", {cat(" HO
! "); pi+2})[]
[122] [123]
Underfull \hbox (badness 4254) in paragraph at lines 8340--8344
[]\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so
urce \T1/ptm/m/n/10 at-tribute), use
[124]
Underfull \hbox (badness 1132) in paragraph at lines 8383--8390
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
make the re-sult parseable.
[125]
Underfull \hbox (badness 1603) in paragraph at lines 8492--8495
[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
[126] [127] [128] [129] [130] [131] [132] [133] [134]
Underfull \hbox (badness 1917) in paragraph at lines 9077--9080
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
Overfull \hbox (36.7804pt too wide) in paragraph at lines 9130--9130
[]\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9131--9131
[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
[135] [136]
Underfull \hbox (badness 1168) in paragraph at lines 9231--9236
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[137] [138]
Underfull \hbox (badness 10000) in paragraph at lines 9369--9373
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / IEEE _ 754-[]198
5$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / en . wikipedia .
Underfull \hbox (badness 10000) in paragraph at lines 9369--9373
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 http : / / en . wikipedia . org / wiki / Double _
[139] [140] [141]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9588--9588
[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
[142]
Underfull \hbox (badness 1629) in paragraph at lines 9661--9665
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[143] [144]
Underfull \hbox (badness 2150) in paragraph at lines 9760--9763
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
from the re-verse
Underfull \hbox (badness 3690) in paragraph at lines 9774--9782
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
Underfull \hbox (badness 10000) in paragraph at lines 9783--9785
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent
to but faster than
[145]
Underfull \hbox (badness 3735) in paragraph at lines 9815--9822
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[146] [147]
Underfull \hbox (badness 10000) in paragraph at lines 10010--10013
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[148] [149] [150] [151] [152] [153] [154] [155] [156]
Underfull \hbox (badness 5288) in paragraph at lines 10669--10671
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
Underfull \hbox (badness 3039) in paragraph at lines 10679--10684
[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
and
[157]
Underfull \hbox (badness 10000) in paragraph at lines 10737--10739
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[158] [159]
Underfull \hbox (badness 4569) in paragraph at lines 10854--10858
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
passed as an ar-gu-ment
Underfull \hbox (badness 2401) in paragraph at lines 10854--10858
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[160]
Underfull \hbox (badness 10000) in paragraph at lines 10965--10967
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[161] [162] [163]
Underfull \hbox (badness 4048) in paragraph at lines 11151--11161
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
Underfull \hbox (badness 3657) in paragraph at lines 11151--11161
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[164] [165] [166]
Underfull \hbox (badness 5460) in paragraph at lines 11398--11407
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
Underfull \hbox (badness 2221) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[167] [168] [169] [170] [171]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11761--11761
[]\T1/pcr/m/n/9 A <- data.frame(x = 1:3, y = I(matrix(4:6)), z = I(matrix(lett
ers[1:9], 3, 3)))[]
[172] [173] [174] [175] [176]
Underfull \hbox (badness 2221) in paragraph at lines 12121--12127
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[177] [178] [179] [180]
Underfull \hbox (badness 2253) in paragraph at lines 12350--12352
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
[181]
Underfull \hbox (badness 10000) in paragraph at lines 12454--12456
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[182] [183]
Underfull \hbox (badness 10000) in paragraph at lines 12602--12604
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[184] [185]
Underfull \hbox (badness 10000) in paragraph at lines 12700--12704
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (30.78088pt too wide) in paragraph at lines 12750--12750
[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")
[186] [187]
Underfull \hbox (badness 10000) in paragraph at lines 12839--12842
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12849--12849
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive TRUE)[]
[188]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12932--12932
[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE)
Underfull \hbox (badness 7238) in paragraph at lines 12950--12957
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 12950--12957
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 12950--12957
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
of fact, the in-ter-nal al-go-
Underfull \hbox (badness 3965) in paragraph at lines 12958--12962
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[189] [190]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13066--13066
[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13067--13067
[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
[191]
Underfull \hbox (badness 10000) in paragraph at lines 13148--13152
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
Underfull \hbox (badness 1389) in paragraph at lines 13148--13152
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[192]
Underfull \hbox (badness 1314) in paragraph at lines 13208--13210
[]\T1/ptm/m/n/10 In re-cent ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 most u
n-nec-es-sary copy-ing is avoided: on the other hand us-ing
[193] [194] [195]
Underfull \hbox (badness 1168) in paragraph at lines 13402--13406
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real
or com-plex vec-
Underfull \hbox (badness 2012) in paragraph at lines 13402--13406
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
[196]
Underfull \hbox (badness 6944) in paragraph at lines 13496--13499
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13521--13521
[]\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[]
[197] [198] [199]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13668--13668
[] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx
= NA,[]
Underfull \hbox (badness 2790) in paragraph at lines 13675--13678
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
Underfull \hbox (badness 4254) in paragraph at lines 13691--13699
[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 13706--13710
[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[200]
Underfull \hbox (badness 10000) in paragraph at lines 13761--13763
[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so
Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point,
Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
Underfull \hbox (badness 10000) in paragraph at lines 13772--13780
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
com-plex (or
[201]
Underfull \hbox (badness 1009) in paragraph at lines 13806--13809
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 is
not ap-pro-pri-ate for use within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/1
0 meth-ods: use
[202]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13869--13869
[]\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[]
[203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214]
[215]
Underfull \hbox (badness 2418) in paragraph at lines 14776--14780
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
,
Underfull \hbox (badness 6510) in paragraph at lines 14783--14786
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
Underfull \hbox (badness 2326) in paragraph at lines 14811--14818
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[216] [217] [218] [219]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15057--15057
[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
Underfull \hbox (badness 1867) in paragraph at lines 15082--15089
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[220] [221] [222] [223]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15316--15316
[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 15343--15343
[]\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[]
Underfull \vbox (badness 10000) has occurred while \output is active [224]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15387--15387
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
Underfull \hbox (badness 10000) in paragraph at lines 15393--15397
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
Underfull \hbox (badness 1028) in paragraph at lines 15393--15397
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[225] [226] [227] [228] [229] [230] [231]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15921--15921
[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[232] [233] [234] [235]
Underfull \hbox (badness 2435) in paragraph at lines 16174--16176
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
. unicode . org / reports / tr35 /
Underfull \hbox (badness 2285) in paragraph at lines 16227--16229
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16235--16235
[]\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[]
[236]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16245--16245
[] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16265--16265
[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[237] [238] [239] [240] [241] [242] [243]
Underfull \hbox (badness 10000) in paragraph at lines 16701--16703
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[244]
Underfull \hbox (badness 4217) in paragraph at lines 16785--16794
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2057) in paragraph at lines 16800--16816
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[245] [246] [247] [248] [249] [250]
Underfull \hbox (badness 4699) in paragraph at lines 17207--17210
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the atomic types (\T1/pcr
/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[251] [252]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17329--17329
[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[253] [254]
Underfull \hbox (badness 4739) in paragraph at lines 17460--17462
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[255] [256] [257] [258] [259] [260]
Underfull \hbox (badness 1430) in paragraph at lines 17858--17863
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 17858--17863
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is the same as
[261]
Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
Underfull \hbox (badness 5008) in paragraph at lines 17919--17924
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[262]
Underfull \hbox (badness 10000) in paragraph at lines 17979--17986
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 17979--17986
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
Underfull \hbox (badness 5064) in paragraph at lines 17979--17986
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
with
Underfull \hbox (badness 5908) in paragraph at lines 17979--17986
\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
Underfull \hbox (badness 10000) in paragraph at lines 17995--17997
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is equiv-a-lent to
[263]
Underfull \hbox (badness 1975) in paragraph at lines 18067--18070
[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[264] [265] [266] [267] [268]
Underfull \hbox (badness 10000) in paragraph at lines 18364--18368
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[269]
Underfull \hbox (badness 10000) in paragraph at lines 18494--18498
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
Underfull \hbox (badness 1454) in paragraph at lines 18494--18498
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
[270] [271]
Underfull \hbox (badness 10000) in paragraph at lines 18589--18596
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[272] [273]
Underfull \hbox (badness 10000) in paragraph at lines 18710--18714
[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use
Underfull \hbox (badness 5161) in paragraph at lines 18765--18770
[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
Underfull \hbox (badness 6592) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of
Underfull \hbox (badness 5133) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion
3 of the li-cense can be dis-played by
[274] [275] [276]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 18927--18927
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 18931--18931
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[277]
Underfull \hbox (badness 3343) in paragraph at lines 18987--18991
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
many more file han-dling func-tions and
[278]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19073--19073
[] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments
as for lists[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19084--19084
[] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
pr = 0.2))),[]
[279] [280]
Underfull \hbox (badness 6380) in paragraph at lines 19229--19234
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
[281]
Underfull \hbox (badness 10000) in paragraph at lines 19258--19261
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/pcr/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only \T1/pcr/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "LC
_CTYPE"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1337) in paragraph at lines 19287--19294
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
Underfull \hbox (badness 2229) in paragraph at lines 19287--19294
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, OS X) or
Underfull \hbox (badness 1043) in paragraph at lines 19287--19294
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
Underfull \hbox (badness 2564) in paragraph at lines 19306--19309
[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
[282]
Underfull \hbox (badness 1205) in paragraph at lines 19359--19364
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[283] [284] [285] [286]
Underfull \hbox (badness 2469) in paragraph at lines 19668--19674
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 1939) in paragraph at lines 19668--19674
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing names.
Underfull \hbox (badness 10000) in paragraph at lines 19668--19674
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[287] [288] [289] [290] [291]
Underfull \hbox (badness 10000) in paragraph at lines 19977--19979
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[292] [293] [294] [295] [296] [297]
Underfull \hbox (badness 1655) in paragraph at lines 20374--20378
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
[298] [299] [300] [301] [302] [303] [304] [305] [306]
Underfull \hbox (badness 4366) in paragraph at lines 20965--20971
\T1/pcr/m/n/10 www . bzip . org/$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http
: / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n
/10 http : / / tukaani .
[307] [308]
Underfull \hbox (badness 10000) in paragraph at lines 21094--21100
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
space can-not ex-ceed
Underfull \hbox (badness 6316) in paragraph at lines 21094--21100
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
[309] [310]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 21203--21203
[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
[311]
Underfull \hbox (badness 10000) in paragraph at lines 21254--21258
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
Underfull \hbox (badness 10000) in paragraph at lines 21254--21258
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[312] [313] [314] [315] [316] [317] [318]
Underfull \hbox (badness 3849) in paragraph at lines 21797--21802
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[319]
Underfull \hbox (badness 10000) in paragraph at lines 21877--21880
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute
via the gen-eral rules:
Underfull \hbox (badness 10000) in paragraph at lines 21877--21880
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
[320] [321] [322]
Underfull \hbox (badness 10000) in paragraph at lines 22025--22027
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[323] [324] [325] [326] [327] [328] [329] [330]
Underfull \hbox (badness 2197) in paragraph at lines 22624--22628
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
Underfull \hbox (badness 4048) in paragraph at lines 22624--22628
\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
[331]
Underfull \hbox (badness 2846) in paragraph at lines 22638--22642
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the
pack-
Underfull \hbox (badness 1990) in paragraph at lines 22638--22642
\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
[332]
Underfull \hbox (badness 10000) in paragraph at lines 22722--22728
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
Underfull \hbox (badness 1168) in paragraph at lines 22722--22728
\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
[333] [334] [335]
Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of
Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[336]
Underfull \hbox (badness 4120) in paragraph at lines 22997--23004
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[337]
Underfull \hbox (badness 1694) in paragraph at lines 23107--23110
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
(see `De-tails');
[338] [339] [340]
Underfull \hbox (badness 1603) in paragraph at lines 23346--23348
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[341] [342]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 23464--23473
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",
"methods")\T1/ptm/m/n/10 .
[343]
Underfull \hbox (badness 5475) in paragraph at lines 23559--23569
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 3271) in paragraph at lines 23578--23581
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
Underfull \hbox (badness 10000) in paragraph at lines 23593--23595
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[344] [345] [346]
Underfull \hbox (badness 3138) in paragraph at lines 23833--23839
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4132) in paragraph at lines 23833--23839
\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "http://www.bioconductor.org"\
T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror
Underfull \hbox (badness 4001) in paragraph at lines 23833--23839
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T
1/ptm/m/n/10 '. Can be set by
Underfull \hbox (badness 1194) in paragraph at lines 23845--23848
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
and
Underfull \hbox (badness 1389) in paragraph at lines 23869--23871
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[347]
Underfull \hbox (badness 10000) in paragraph at lines 23886--23892
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
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[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 23907--23914
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
Underfull \hbox (badness 10000) in paragraph at lines 23916--23923
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 10000) in paragraph at lines 23916--23923
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a
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\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
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\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
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[]\T1/ptm/m/n/10 a char-ac-ter string, the path of the com-mand used for un-zip
-ping help files, or
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[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
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\T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10
A[c(arrayindex.x, arrayindex.y)]
[353] [354] [355] [356]
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[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
[357] [358] [359] [360] [361] [362] [363]
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[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully,
[364]
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[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
see
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[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[368] [369] [370] [371] [372] [373] [374] [375] [376]
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\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[377]
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[] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 =
rep(c(0,0,1),2))[]
[378] [379] [380] [381]
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[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
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[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
[382] [383]
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[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[384] [385] [386]
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[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[387]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[388]
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[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[389]
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[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal:
for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and
[390]
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\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[391] [392] [393] [394] [395] [396]
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[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
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\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
mode:
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\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
"int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[397] [398] [399] [400] [401] [402] [403] [404]
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[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
[405] [406] [407] [408]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 28025--28027
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
* + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '.
[409] [410]
Underfull \hbox (badness 7558) in paragraph at lines 28234--28238
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 5417) in paragraph at lines 28250--28253
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
[411]
Underfull \hbox (badness 10000) in paragraph at lines 28254--28256
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 28257--28259
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[412] [413] [414] [415] [416] [417]
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[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[418] [419] [420] [421] [422] [423] [424] [425] [426] [427] [428] [429]
Underfull \hbox (badness 10000) in paragraph at lines 29470--29473
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,
Underfull \hbox (badness 1430) in paragraph at lines 29470--29473
\T1/pcr/m/n/10 save(list = ls(all = TRUE), file = ".RData")\T1/ptm/m/n/10 .
It is also what hap-
[430] [431] [432]
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[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
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\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
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\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[433]
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[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[434]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
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[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[435]
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[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
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\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
will give an empty
[436]
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[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[437] [438] [439] [440]
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[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2,
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
Underfull \hbox (badness 7759) in paragraph at lines 30289--30292
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less
[441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452]
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\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
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[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
out-put from
[453] [454] [455] [456] [457] [458] [459] [460]
Underfull \hbox (badness 2512) in paragraph at lines 31636--31638
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[461] [462] [463] [464]
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[466]
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[]\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[]
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[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
[467] [468] [469] [470] [471]
Underfull \hbox (badness 1087) in paragraph at lines 32416--32418
[]\T1/ptm/m/n/10 Markus Kuhn, ``ASCII and Uni-code quo-ta-tion marks''. [][]$\T
1/pcr/m/n/10 http : / / www . cl . cam . ac . uk /
[472]
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[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
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[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
[473] [474] [475]
Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
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\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
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\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
Underfull \hbox (badness 6542) in paragraph at lines 32696--32706
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
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\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
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\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 32740--32746
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
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\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
first in architecture-specific di-rec-to-ries,
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\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
[476]
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[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 32753--32760
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
Underfull \hbox (badness 2573) in paragraph at lines 32753--32760
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[477] [478] [479] [480]
Underfull \hbox (badness 10000) in paragraph at lines 33049--33055
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[481] [482]
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[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
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\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[483] [484] [485]
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[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
[486]
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[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
[487] [488] [489]
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[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
[490]
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[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[491] [492] [493] [494] [495] [496] [497]
Underfull \hbox (badness 10000) in paragraph at lines 34212--34215
[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
signif[][][]() \T1/ptm/m/n/10 (for
[498]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34259--34259
[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[499] [500] [501] [502]
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\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
is a match then that el-e-ment is eval-u-ated un-less
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\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is
eval-u-ated, so for ex-am-ple
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[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[503] [504] [505]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34688--34688
[]\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not.
[506]
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[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
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\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[507]
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\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
Underfull \hbox (badness 10000) in paragraph at lines 34864--34867
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[508] [509] [510]
Underfull \hbox (badness 10000) in paragraph at lines 35040--35044
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
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[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[511] [512] [513]
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[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used
[514] [515]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[516] [517] [518]
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[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[519] [520] [521] [522] [523]
Underfull \hbox (badness 1515) in paragraph at lines 35904--35907
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies
[524]
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[]\T1/pcr/m/n/10 table(..., exclude = if (useNA == "no") c(NA, NaN), useNA = c
("no",
[525]
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[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/pcr/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[526]
Underfull \hbox (badness 4096) in paragraph at lines 36123--36126
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[527] [528] [529]
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[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[530]
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[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$http : / / developer .
[531] [532]
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[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http : / /
[533]
Underfull \hbox (badness 10000) in paragraph at lines 36626--36630
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http :
[534] [535] [536] [537] [538] [539]
Underfull \hbox (badness 5637) in paragraph at lines 37038--37047
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the Ol-son/IANA
Underfull \hbox (badness 1629) in paragraph at lines 37038--37047
\T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion
in the file sys-tem varies,
[540]
Underfull \hbox (badness 3460) in paragraph at lines 37092--37094
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Time _ zone$[][]
\T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / www . twinsun . com /
[541] [542] [543]
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[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[544] [545] [546] [547] [548] [549]
Underfull \hbox (badness 6542) in paragraph at lines 37718--37720
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
, and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[550] [551]
Underfull \hbox (badness 1708) in paragraph at lines 37841--37849
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 37841--37849
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
Underfull \hbox (badness 10000) in paragraph at lines 37850--37854
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
Underfull \hbox (badness 10000) in paragraph at lines 37850--37854
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
some-thing like
Underfull \hbox (badness 3281) in paragraph at lines 37850--37854
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
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[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
and sup-press-ing the print-ing of er-ror mes-sages;
[552]
Underfull \hbox (badness 3895) in paragraph at lines 37926--37938
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in
Underfull \hbox (badness 1303) in paragraph at lines 37926--37938
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
"integer"\T1/ptm/m/n/10 ,
[553] [554] [555]
Underfull \hbox (badness 1515) in paragraph at lines 38113--38118
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[556] [557]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 38252--38252
[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[558] [559] [560] [561] [562] [563]
Underfull \hbox (badness 1803) in paragraph at lines 38707--38710
[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
Underfull \hbox (badness 2334) in paragraph at lines 38711--38718
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 4726) in paragraph at lines 38737--38741
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
Underfull \hbox (badness 1122) in paragraph at lines 38737--38741
\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[564] [565] [566]
Underfull \hbox (badness 3668) in paragraph at lines 38915--38917
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[567] [568] [569] [570]
Underfull \hbox (badness 6220) in paragraph at lines 39189--39194
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
Underfull \hbox (badness 3098) in paragraph at lines 39189--39194
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
Underfull \hbox (badness 1533) in paragraph at lines 39189--39194
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[571]
Underfull \hbox (badness 1603) in paragraph at lines 39224--39228
[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[572] [573] [574] [575] [576] [577]
Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
\T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[578]
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[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[579]
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[]\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[]
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[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[580]) (./compiler-pkg.tex
Chapter 2.
[581] [582] [583]) (./datasets-pkg.tex [584]
Chapter 3.
Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[585] [586] [587] [588] [589]
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[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[590]
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[]\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[]
[591] [592] [593] [594] [595]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[596] [597]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[598] [599] [600] [601]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 1131--1134
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[602] [603] [604] [605] [606]
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[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[607] [608]
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[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[609]
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[]\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[610] [611]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[612]
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[]\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[]
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[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
[613] [614]
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[] \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[]
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[] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[]
[615] [616] [617] [618]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2127--2130
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[619] [620] [621] [622] [623] [624] [625] [626]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2666--2669
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[627]
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[628]
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[630]
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[631] [632]
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[633]
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[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[634] [635] [636] [637] [638] [639] [640]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3540--3540
[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[641]
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[]\T1/ptm/m/n/10 Files for all 182 dis-tricts in 1888 and other years have been
avail-able at [][]$\T1/pcr/m/n/10 http :
Underfull \hbox (badness 10000) in paragraph at lines 3639--3642
\T1/pcr/m/n/10 / / opr . princeton . edu / archive / eufert / switz . html$[][]
\T1/ptm/m/n/10 or [][]$\T1/pcr/m/n/10 http : / / opr .
[642]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[643]
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[644]
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[645]
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[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
[646] [647] [648] [649] [650] [651] [652] [653] [654] [655]
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[657] [658]) (./grDevices-pkg.tex
Chapter 4.
[659] [660] [661] [662] [663]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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[][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[664] [665]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462
[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[666] [667] [668] [669] [670] [671] [672] [673] [674]
Underfull \hbox (badness 5175) in paragraph at lines 1058--1060
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[675]
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\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[676]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
. com / Lab / Graphics / Colors /
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[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[677]
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[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[678] [679] [680]
Underfull \hbox (badness 10000) in paragraph at lines 1470--1474
[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
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\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
Underfull \hbox (badness 10000) in paragraph at lines 1470--1474
\T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
,
[681]
Underfull \hbox (badness 2221) in paragraph at lines 1515--1518
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
oth-er-wise a ma-trix of color names (for
[682]
Underfull \hbox (badness 10000) in paragraph at lines 1584--1588
[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
Underfull \hbox (badness 10000) in paragraph at lines 1584--1588
[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[683] [684] [685]
Underfull \hbox (badness 1565) in paragraph at lines 1743--1748
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1743--1748
\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10
for how to set this up. Win-dows users may pre-fer to use
[686]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1826--1826
[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
Underfull \hbox (badness 1184) in paragraph at lines 1867--1877
[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-
Underfull \hbox (badness 2057) in paragraph at lines 1867--1877
\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[687] [688]
Underfull \hbox (badness 10000) in paragraph at lines 1972--1974
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the
set-ting of
[689] [690]
Underfull \hbox (badness 6758) in paragraph at lines 2133--2136
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
[691] [692]
Underfull \hbox (badness 2326) in paragraph at lines 2240--2250
\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
Underfull \hbox (badness 2318) in paragraph at lines 2240--2250
\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
Underfull \hbox (badness 2460) in paragraph at lines 2240--2250
\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
Underfull \hbox (badness 1221) in paragraph at lines 2240--2250
\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[693]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2324--2324
[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
[694] [695] [696] [697] [698]
Underfull \hbox (badness 10000) in paragraph at lines 2650--2651
[699] [700] [701] [702] [703] [704]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3056--3056
[]\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv",
scale.in = 255))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3057--3057
[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
[705]
Underfull \hbox (badness 1210) in paragraph at lines 3088--3090
[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[706] [707] [708]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3302--3302
[]\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1)
[709] [710]
Underfull \hbox (badness 3525) in paragraph at lines 3409--3412
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
Underfull \hbox (badness 1968) in paragraph at lines 3423--3425
[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[711] [712] [713] [714]
Underfull \hbox (badness 5939) in paragraph at lines 3717--3722
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[715] [716] [717] [718] [719] [720] [721]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4200--4200
[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[722]
Underfull \hbox (badness 1502) in paragraph at lines 4247--4252
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the
type of anti-aliasing (if any) to be
[723] [724]
Underfull \hbox (badness 4765) in paragraph at lines 4407--4409
[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4421--4421
[]\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024,
height = 768)[]
[725]
Underfull \hbox (badness 5077) in paragraph at lines 4461--4467
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
Underfull \hbox (badness 1342) in paragraph at lines 4477--4479
[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[726]
Underfull \hbox (badness 1874) in paragraph at lines 4554--4562
\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[727]
Underfull \hbox (badness 1755) in paragraph at lines 4621--4623
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East
Asian lan-guages -- see
[728] [729]
Underfull \hbox (badness 7344) in paragraph at lines 4792--4794
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
Underfull \hbox (badness 7397) in paragraph at lines 4803--4807
[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[730] [731]
Underfull \hbox (badness 1552) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
[732]
Underfull \hbox (badness 4686) in paragraph at lines 4959--4965
\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 4984--4992
[]\T1/pcr/m/n/10 Baekmuk-Batang \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m/n
/10 ftp : / / ftp . mizi . com / pub / baekmuk/$[][]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 4984--4992
\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m
/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /
Underfull \vbox (badness 10000) has occurred while \output is active [733]
Underfull \hbox (badness 7344) in paragraph at lines 5003--5005
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
[734] [735] [736]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5194--5194
[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
Underfull \hbox (badness 1648) in paragraph at lines 5200--5204
[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[737]
Underfull \hbox (badness 10000) in paragraph at lines 5280--5282
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
for on-screen de-vices and to
[738]
Underfull \hbox (badness 1072) in paragraph at lines 5316--5322
[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots
due to cor-rupted or du-pli-
[739] [740] [741] [742]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5610--5610
[]\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
sep = "."))[]
Underfull \hbox (badness 10000) in paragraph at lines 5623--5626
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[743] [744] [745] [746] [747] [748]
Underfull \hbox (badness 1189) in paragraph at lines 6019--6021
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[749] [750]
Underfull \hbox (badness 10000) in paragraph at lines 6117--6119
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK
lan-guages and
Underfull \hbox (badness 10000) in paragraph at lines 6156--6163
[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
Underfull \hbox (badness 1584) in paragraph at lines 6156--6163
\T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s
ys-tems which have the Wine
[751]
Underfull \hbox (badness 3088) in paragraph at lines 6240--6244
[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[752]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6285--6285
[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
Underfull \hbox (badness 10000) in paragraph at lines 6317--6320
[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[753] [754]
Underfull \hbox (badness 5637) in paragraph at lines 6408--6414
\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1721) in paragraph at lines 6441--6444
[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[755] [756] [757]
Underfull \hbox (badness 6157) in paragraph at lines 6593--6596
\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
via
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[758] [759] [760]) (./graphics-pkg.tex
Chapter 5.
Underfull \hbox (badness 10000) in paragraph at lines 16--18
[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use
[761] [762] [763] [764]
Underfull \hbox (badness 1412) in paragraph at lines 286--291
[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[765] [766] [767]
Underfull \hbox (badness 2726) in paragraph at lines 465--471
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
lo-ca-tions are com-puted in-ter-nally (the same way
[768] [769] [770]
Underfull \hbox (badness 10000) in paragraph at lines 655--659
[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or
Underfull \hbox (badness 3250) in paragraph at lines 655--659
[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
Underfull \hbox (badness 2735) in paragraph at lines 683--690
[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[771]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740
[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
[772] [773]
Underfull \hbox (badness 1062) in paragraph at lines 849--852
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[774] [775] [776] [777] [778] [779] [780]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1274--1274
[] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names =
NULL,[]
Underfull \hbox (badness 1024) in paragraph at lines 1319--1327
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
[781]
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\T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
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\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and
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[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
Overfull \hbox (19.3703pt too wide) in paragraph at lines 1375--1379
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) +
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[782]
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[]\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1424--1424
[]\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi
s=..,main=..)")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1430--1430
[]\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
= "grey40",[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1431--1431
[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[783] [784] [785] [786] [787]
Underfull \hbox (badness 10000) in paragraph at lines 1731--1737
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10
contourplot[][][] \T1/ptm/m/n/10 (and
[788]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1768--1768
[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
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[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
[789]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1860--1860
[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[790] [791]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1989--1989
[]\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1994--1994
[]\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[]
[792] [793] [794] [795] [796]
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\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
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[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
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[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[809]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
raster im-ages are used when the
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the
grid is reg-u-lar and ei-ther
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
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[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
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[] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col =
par("fg"),[]
[813]
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[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[814] [815]
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[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
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[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
[816]
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[] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
= c(0, 0.3))[]
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[]\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[]
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[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
[818]
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[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for
[819] [820]
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[821] [822] [823]
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[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a
mul-ti-ple of
[824] [825] [826] [827]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[828]
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\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10
oma \T1/ptm/m/n/10 when chang-ing
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are
to be used: see
[829]
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[]\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel
= panel.cor)[]
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[] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[]
[830]
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[]\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue") # hmm...[]
[831]
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\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[832] [833]
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[834]
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</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf, id=27858, 28
9.08pt x 289.08pt>
<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf> [835 </u
sr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf>]
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</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf, id=27871, 25
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<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf>
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[837 </usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf>]
[838]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[839]
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[]\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9,
physicians = 9,[]
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[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
[840]
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[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
[841]
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[842] [843] [844] [845]
Underfull \hbox (badness 10000) in paragraph at lines 5580--5584
[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing
or an er-ror; us-ing, e.g.,
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\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[846] [847] [848] [849]
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[]\T1/pcr/m/n/9 axis(2, at = at.y, labels = formatC(at.y, format = "fg"), col.
axis = "red")[]
[850] [851]
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[]\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v
ector ~ factor[]
[852]
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[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[853] [854] [855] [856] [857]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[858] [859]
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[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of
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[][]
[860 </usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/pch.pdf>]
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[]\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[]
[861]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
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[863]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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[] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[]
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[]\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[]
[864]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[865] [866] [867]
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[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[868]
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[]\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[]
[869] [870] [871] [872] [873] [874]
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[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE))[]
[875] [876] [877] [878] [879] [880]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc = 0:1,[]
[881] [882] [883]
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[]\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)
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[]\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)[]
[884] [885]
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[]\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
...,[]
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[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[886]
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[]\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[]
[887]
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[]\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100,
lambda = 2),[]
[888] [889]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
[890]
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[]\T1/ptm/m/n/10 The Euro sym-bol was in-tro-duced rel-a-tively re-cently and m
ay not be avail-able in
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\T1/ptm/m/n/10 older fonts. In re-cent ver-sions of Adobe sym-bol fonts it is c
har-ac-ter 160, so
[891]
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[] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile:
Règles, Liberté, Egalité, Fraternité...")[]
[892]
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[]\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex-
pan-sion)
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[]\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[893]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again>
\relax
l.8643 \HeaderA{units}{Graphical Units}{units}
[894]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[895] [896]
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[]\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code =
2, length = 0.1)[]
[897]) (./grid-pkg.tex [898]
Chapter 6.
[899] [900] [901] [902] [903] [904]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
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\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
[905] [906] [907] [908] [909] [910] [911] [912] [913] [914]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[916] [917] [918]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject
de-scrib-ing a cir-cle), but only
[919] [920] [921] [922] [923] [924] [925]
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
[926] [927] [928]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[]
[929]
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[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 ,
[930]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
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[]\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10
to al-low a grob to per-form cus-tom ac-tions and
[931] [932] [933]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
[934] [935] [936]
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[]\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global =
FALSE)[]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[937] [938] [939]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2582--2582
[] \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[]
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[] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
NULL)[]
[940] [941] [942] [943]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
[944] [945] [946] [947] [948]
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[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
[949]
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[]\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
"bottom")))[]
[950]
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[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[951]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
[952]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
[953] [954] [955]
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[] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[]
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[] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other
anti-clockwise")[]
[956] [957] [958] [959] [960] [961] [962] [963] [964]
Underfull \hbox (badness 1430) in paragraph at lines 4159--4164
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[965] [966] [967]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[968]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[969] [970] [971]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[972] [973] [974] [975] [976] [977] [978] [979] [980]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
[981] [982] [983] [984] [985] [986] [987] [988] [989] [990]
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\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
"npc") - unit(1, "inches")\T1/ptm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 5856--5862
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[991] [992] [993] [994] [995]
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[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for
use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or
[996]
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[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[997] [998]
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
do-ing some-thing like
[999] [1000] [1001]
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[]\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[]
[1002]) (./methods-pkg.tex
Chapter 7.
[1003] [1004] [1005]
Underfull \hbox (badness 10000) in paragraph at lines 278--285
[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
\T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-
Underfull \hbox (badness 7704) in paragraph at lines 278--285
\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the
Underfull \hbox (badness 10000) in paragraph at lines 278--285
\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about
it, you'll prob-a-bly agree that you wouldn't
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\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,
Overfull \hbox (0.78088pt too wide) in paragraph at lines 278--285
\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1006] [1007] [1008] [1009] [1010] [1011]
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[]\T1/ptm/m/n/10 Note that the pre-ced-ing def-i-ni-tion means that the next me
thod is de-fined uniquely when
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[1023] [1024] [1025] [1026]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1841--1841
[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[]
Underfull \hbox (badness 10000) in paragraph at lines 1885--1887
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1027] [1028]
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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class
[1029] [1030] [1031] [1032] [1033]
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
[1034] [1035] [1036]
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1037]
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[]\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10
(a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
[1038] [1039] [1040]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
[1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049]
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1050]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these
classes takes spe-cial ar-gu-ments
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[]
[1051]
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1052]
Underfull \hbox (badness 1394) in paragraph at lines 3805--3810
\T1/ptm/m/n/10 If ar-gu-ment \T1/pcr/m/n/10 fullInfo \T1/ptm/m/n/10 is \T1/pcr/
m/n/10 TRUE\T1/ptm/m/n/10 , the call re-turns a named list of ob-jects of class
[1053] [1054] [1055]
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[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
[1056] [1057] [1058]
Underfull \hbox (badness 10000) in paragraph at lines 4252--4254
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method
ex-ists for
[1059]
Underfull \hbox (badness 1629) in paragraph at lines 4354--4363
\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is
to mod-ify a field ex-plic-itly by
[1060]
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[]\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(),
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[] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[]
[1061]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1062] [1063] [1064] [1065] [1066] [1067]
Underfull \hbox (badness 10000) in paragraph at lines 4945--4954
[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
[1068]
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[1070]
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
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[]\T1/pcr/m/n/9 stopifnot(identical(abs(y), 1:10)) # (version 2.9.0 or earlier
fails here)[]
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[]\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[]
Underfull \vbox (badness 10000) has occurred while \output is active [1071]
[1072]
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\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
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[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1073] [1074] [1075] [1076] [1077]
Underfull \hbox (badness 1087) in paragraph at lines 5619--5624
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5632--5636
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1078]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5723--5727
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1079] [1080]
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[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1081] [1082] [1083]
Underfull \hbox (badness 1248) in paragraph at lines 6186--6190
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
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\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1084]
Underfull \hbox (badness 4647) in paragraph at lines 6274--6276
[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1085]
Underfull \hbox (badness 1072) in paragraph at lines 6348--6355
[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1086] [1087] [1088] [1089] [1090]pdfTeX warning (ext4): destination with the s
ame identifier (name{Rfn.S4}) has been already used, duplicate ignored
<to be read again>
\relax
l.6707 \aliasA{S4}{S3Part}{S4}
[1091] [1092] [1093]
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[]\T1/pcr/m/n/9 ## note the these classes can insert an S3 subclass of "lm" as
the S3 part:[]
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[]\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c
("mlm", "lm")[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex})
has been already used, duplicate ignored
<to be read again>
\relax
l.6983 \aliasA{Complex}{S4groupGeneric}{Complex}
pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
ignored
<to be read again>
\relax
l.6985 \aliasA{Logic}{S4groupGeneric}{Logic}
pdfTeX warning (ext4): destination
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again>
\relax
l.6986 \aliasA{Math}{S4groupGeneric}{Math}
pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again>
\relax
l.6988 \aliasA{Ops}{S4groupGeneric}{Ops}
pdfTeX warning (ext4): destination with
the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again>
\relax
l.6989 \aliasA{Summary}{S4groupGeneric}{Summary}
[1094]
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[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic
can be ob-tained by call-ing
Underfull \hbox (badness 6708) in paragraph at lines 7063--7075
[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3209) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1095] [1096]
Underfull \hbox (badness 1694) in paragraph at lines 7223--7225
[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
[1097]
Underfull \hbox (badness 10000) in paragraph at lines 7247--7250
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1098] [1099] [1100] [1101] [1102] [1103]
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[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),[]
[1104] [1105]
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[]\T1/ptm/m/n/10 Note that call-ing \T1/pcr/m/n/10 setGeneric() \T1/ptm/m/n/10
in this form is not strictly nec-es-sary be-fore call-ing
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[]\T1/ptm/m/n/10 If you \T1/ptm/m/it/10 don't \T1/ptm/m/n/10 want the ex-ist-in
g func-tion to be taken as de-fault, sup-ply the ar-gu-ment
[1106]
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[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
\T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1107] [1108] [1109] [1110]
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[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
[1111]
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[]\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the
method. For
[1112]
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[]\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li
nk{setClass})[]
[1113] [1114] [1115] [1116] [1117]
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[]\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date
= "POSIXt"))[]
[1118]
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[]\T1/pcr/m/n/9 # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
s class, then calls the S3 print method.[]
[1119]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128]
Underfull \hbox (badness 10000) in paragraph at lines 9634--9636
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
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[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
Underfull \hbox (badness 1681) in paragraph at lines 9642--9646
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1129] [1130] [1131] [1132]) (./parallel-pkg.tex
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 15--17
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1133]
Underfull \hbox (badness 4242) in paragraph at lines 94--96
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1134] [1135]
Underfull \hbox (badness 1024) in paragraph at lines 194--197
[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1136]
Underfull \hbox (badness 5077) in paragraph at lines 281--284
[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, OS X, FreeBSD, So-laris, I
rix and Win-dows.
[1137] [1138]
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1139] [1140] [1141] [1142]
Underfull \hbox (badness 1917) in paragraph at lines 702--711
[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class
Underfull \hbox (badness 1178) in paragraph at lines 702--711
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1143] [1144]
Underfull \hbox (badness 10000) in paragraph at lines 839--842
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1145] [1146] [1147]
Underfull \hbox (badness 5388) in paragraph at lines 1028--1033
[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1148]
Underfull \hbox (badness 10000) in paragraph at lines 1052--1060
[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1088--1088
[]\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[]
[1149] [1150]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1203--1203
[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
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[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
Underfull \hbox (badness 1577) in paragraph at lines 1246--1249
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1151]
Underfull \hbox (badness 3375) in paragraph at lines 1292--1294
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
[1152] [1153]) (./splines-pkg.tex [1154]
Chapter 9.
Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1155] [1156] [1157] [1158] [1159] [1160] [1161]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 467--467
[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1162] [1163] [1164]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 678--678
[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1165] [1166] [1167]) (./stats-pkg.tex [1168]
Chapter 10.
[1169]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of
\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
[1170] [1171] [1172] [1173] [1174]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 416--416
[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 437--437
[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
[1175] [1176] [1177] [1178] [1179] [1180]
Underfull \hbox (badness 1024) in paragraph at lines 843--845
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189]
Underfull \hbox (badness 10000) in paragraph at lines 1387--1389
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1190]
Underfull \hbox (badness 10000) in paragraph at lines 1503--1507
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1503--1507
\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
Underfull \hbox (badness 1490) in paragraph at lines 1503--1507
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199]
Underfull \hbox (badness 10000) in paragraph at lines 2076--2081
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
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\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
Underfull \hbox (badness 1371) in paragraph at lines 2076--2081
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
Underfull \hbox (badness 1221) in paragraph at lines 2082--2088
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2082--2088
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1200]
Underfull \hbox (badness 3965) in paragraph at lines 2163--2165
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1201] [1202] [1203] [1204]
Underfull \hbox (badness 1221) in paragraph at lines 2418--2423
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2418--2423
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1205]
Underfull \hbox (badness 3965) in paragraph at lines 2495--2497
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1206] [1207]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2630--2630
[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1208] [1209] [1210] [1211]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2866--2866
[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1212] [1213] [1214]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3059--3061
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 .
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3106--3106
[]\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3107--3107
[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1215] [1216] [1217] [1218] [1219] [1220]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3485--3485
[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1221] [1222] [1223] [1224]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3755--3755
[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1225] [1226] [1227] [1228] [1229]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4040--4040
[]\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4041--4041
[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1230] [1231] [1232]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4276--4276
[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1233] [1234] [1235]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4439--4439
[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1236]
Underfull \hbox (badness 3989) in paragraph at lines 4528--4535
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1237] [1238] [1239] [1240] [1241]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4876--4876
[]\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4878--4878
[]\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
= c(-0.9,0.1))[]
[1242]
Underfull \hbox (badness 7397) in paragraph at lines 4965--4969
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an
ar-gu-ment to all these con-trast func-tions, how-ever
Underfull \hbox (badness 7326) in paragraph at lines 4965--4969
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1243] [1244]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5099--5099
[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5117--5117
[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
[1245]
Underfull \hbox (badness 2680) in paragraph at lines 5144--5146
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is
given by
Underfull \hbox (badness 10000) in paragraph at lines 5149--5151
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1246] [1247] [1248]
Underfull \hbox (badness 1436) in paragraph at lines 5327--5332
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
Underfull \hbox (badness 1377) in paragraph at lines 5327--5332
\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
Underfull \hbox (badness 1448) in paragraph at lines 5327--5332
\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1249] [1250]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5513--5513
[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1251]
Underfull \hbox (badness 1168) in paragraph at lines 5585--5590
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1252] [1253]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5679--5679
[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1254] [1255] [1256]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5864--5864
[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
[1257] [1258] [1259]
Underfull \hbox (badness 10000) in paragraph at lines 6027--6032
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When
[1260] [1261] [1262]
Underfull \hbox (badness 5954) in paragraph at lines 6215--6217
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1263]
Underfull \hbox (badness 2503) in paragraph at lines 6297--6300
[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
Underfull \hbox (badness 5563) in paragraph at lines 6301--6303
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6304--6309
\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
Underfull \hbox (badness 7238) in paragraph at lines 6339--6342
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1264]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6374--6374
[]\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE,
type = "tr")[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6389--6389
[]\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6404--6404
[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
Underfull \vbox (badness 10000) has occurred while \output is active [1265]
[1266] [1267] [1268]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6645--6645
[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
[1269] [1270] [1271] [1272] [1273] [1274]
Underfull \hbox (badness 10000) in paragraph at lines 7012--7016
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1275]
Underfull \hbox (badness 6493) in paragraph at lines 7109--7112
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1276] [1277]
Underfull \hbox (badness 1430) in paragraph at lines 7246--7249
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tp : / / cran . r-[]project . org / web / views /
[1278] [1279] [1280] [1281] [1282] [1283]
Underfull \hbox (badness 10000) in paragraph at lines 7656--7661
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1284] [1285]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7794--7796
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
= TRUE)\T1/ptm/m/n/10 .
[1286] [1287] [1288]
Underfull \hbox (badness 1210) in paragraph at lines 8011--8013
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1289] [1290] [1291] [1292] [1293] [1294] [1295]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8455--8455
[] \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8477--8477
[]\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link
= "log")) # fails[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8480--8480
[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
[1296] [1297]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8618--8618
[]\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
.90) # ~= 7e-9[]
Underfull \hbox (badness 1859) in paragraph at lines 8655--8660
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
i.e., if
[1298] [1299] [1300] [1301] [1302]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8987--8987
[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate
S", "VeryS")))[]
[1303] [1304] [1305]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9155--9157
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
homogeneity of variances"\T1/ptm/m/n/10 .
[1306] [1307] [1308] [1309] [1310] [1311] [1312]
Underfull \hbox (badness 2443) in paragraph at lines 9607--9613
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1313] [1314] [1315]
Underfull \hbox (badness 10000) in paragraph at lines 9821--9824
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org /
wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1316] [1317] [1318] [1319]
Underfull \hbox (badness 4518) in paragraph at lines 10081--10086
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1320]
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1321]
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[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
fitted.values \T1/ptm/m/n/10 and
[1322] [1323] [1324]
Underfull \hbox (badness 2142) in paragraph at lines 10423--10426
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1325]
Underfull \hbox (badness 1708) in paragraph at lines 10504--10507
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1326]
Underfull \hbox (badness 10000) in paragraph at lines 10545--10551
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 10583--10588
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1327] [1328]
Underfull \hbox (badness 2635) in paragraph at lines 10716--10719
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1329] [1330]
Underfull \hbox (badness 1694) in paragraph at lines 10883--10886
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
[1331]
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[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
den-dro-gram is re-ordered ac-cord-
Underfull \hbox (badness 3049) in paragraph at lines 10902--10911
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1332]
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[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11017--11017
[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
[1333]
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[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1334] [1335] [1336] [1337] [1338]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11334--11334
[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
been already used, duplicate ignored
<to be read again>
\relax
l.11349 \aliasA{hat}{influence.measures}{hat}
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[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
[1339]
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[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
Underfull \hbox (badness 1062) in paragraph at lines 11460--11465
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11471--11473
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1340] [1341]
Underfull \hbox (badness 3623) in paragraph at lines 11600--11602
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if
[1342] [1343]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11688--11688
[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
[1344]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11781--11781
[] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
= "tobacco",[]
[1345]
Underfull \hbox (badness 10000) in paragraph at lines 11829--11832
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1346] [1347] [1348]
Underfull \hbox (badness 4441) in paragraph at lines 12024--12026
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
fit-ted to
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[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
[1349] [1350]
Underfull \hbox (badness 2753) in paragraph at lines 12121--12123
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
/ / bugs . r-[]project . org / bugzilla3 /
[1351] [1352]
Underfull \hbox (badness 1292) in paragraph at lines 12246--12250
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
\T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1353]
Underfull \hbox (badness 10000) in paragraph at lines 12359--12361
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of
Underfull \hbox (badness 2894) in paragraph at lines 12365--12369
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
Underfull \hbox (badness 1038) in paragraph at lines 12365--12369
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364]
Underfull \hbox (badness 4518) in paragraph at lines 13059--13064
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1365] [1366] [1367]
Underfull \hbox (badness 10000) in paragraph at lines 13253--13257
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
,
[1368] [1369]
Underfull \hbox (badness 6995) in paragraph at lines 13438--13440
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1370] [1371] [1372]
Underfull \hbox (badness 1163) in paragraph at lines 13586--13594
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1373]
Underfull \hbox (badness 4518) in paragraph at lines 13706--13711
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1374] [1375] [1376]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13884--13884
[]\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13885--13885
[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1377]
Underfull \hbox (badness 10000) in paragraph at lines 13940--13943
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
Underfull \hbox (badness 1715) in paragraph at lines 13940--13943
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1378] [1379] [1380] [1381]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14226--14226
[]\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14227--14227
[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1382]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14277--14279
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 .
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14320--14320
[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
[1383] [1384] [1385] [1386] [1387] [1388] [1389]
Underfull \hbox (badness 2726) in paragraph at lines 14722--14725
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15436--15436
[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1401] [1402] [1403]
Underfull \hbox (badness 1648) in paragraph at lines 15627--15629
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
Underfull \hbox (badness 2591) in paragraph at lines 15641--15650
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
sup-ply vari-ables with the same names as would
Underfull \hbox (badness 3930) in paragraph at lines 15641--15650
\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1404]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15705--15705
[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b
= "contr.poly"))[]
[1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16258--16258
[]\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects
with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[]
[1413] [1414] [1415] [1416]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16486--16486
[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
[1417] [1418] [1419] [1420] [1421] [1422]
Underfull \hbox (badness 2772) in paragraph at lines 16922--16925
[]\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate
s. When
Underfull \hbox (badness 10000) in paragraph at lines 16922--16925
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr
/m/n/10 start \T1/ptm/m/n/10 is tried (if
[1423] [1424]
Underfull \hbox (badness 2359) in paragraph at lines 17041--17043
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1425]
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 17213--17213
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
[1428]
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[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1429] [1430]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17373--17373
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1431]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439]
Underfull \hbox (badness 1248) in paragraph at lines 17957--17960
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
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\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
Underfull \hbox (badness 1478) in paragraph at lines 17978--17982
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and
[1440]
Underfull \hbox (badness 2042) in paragraph at lines 18031--18033
[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1441]
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[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
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[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
[1443]
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 18240--18251
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1444]
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[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
[1445] [1446] [1447]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18518--18518
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1448]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1449] [1450] [1451] [1452] [1453] [1454]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18910--18910
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1455]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 18997--18997
[] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
vs Leverage " * h[ii] / (1 - h[ii]))),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19000--19000
[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1456] [1457] [1458] [1459] [1460]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19313--19313
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
Underfull \hbox (badness 1194) in paragraph at lines 19323--19326
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1461]
Underfull \hbox (badness 1107) in paragraph at lines 19381--19383
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1462]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19436--19436
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
[1463]
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[]\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty =
1, y.intersp = 1)[]
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[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
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\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1464]
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[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1465] [1466]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19658--19658
[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1467]
Underfull \hbox (badness 10000) in paragraph at lines 19716--19718
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
[1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478]
[1479] [1480] [1481]
Underfull \hbox (badness 6859) in paragraph at lines 20681--20688
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 20692--20698
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492]
[1493] [1494] [1495] [1496] [1497] [1498]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21684--21684
[] \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) ==
"Pr(",[]
[1499] [1500] [1501] [1502] [1503]
Underfull \hbox (badness 1337) in paragraph at lines 22007--22013
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Underfull \hbox (badness 1028) in paragraph at lines 22690--22693
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1514] [1515]
Underfull \hbox (badness 10000) in paragraph at lines 22800--22803
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 5091) in paragraph at lines 22800--22803
\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
ef-fi-ciency if
[1516] [1517] [1518]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23011--23011
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1519] [1520] [1521]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23230--23230
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1522] [1523]
Underfull \hbox (badness 10000) in paragraph at lines 23375--23378
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1524]
Underfull \hbox (badness 2134) in paragraph at lines 23426--23430
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
end point rule and is called by de-fault from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23439--23439
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1525] [1526] [1527] [1528]
Underfull \hbox (badness 7667) in paragraph at lines 23692--23694
[]\T1/ptm/m/n/10 a nu-meric vec-tor or an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-je
ct which is co-ercible to one by
[1529] [1530] [1531]
Underfull \hbox (badness 2591) in paragraph at lines 23895--23901
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][
][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/
ptm/m/n/10 mod-els (with ex-am-
[1532] [1533] [1534] [1535] [1536] [1537]
Underfull \hbox (badness 1412) in paragraph at lines 24301--24303
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1538] [1539]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 24388--24388
[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
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[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
Underfull \hbox (badness 2435) in paragraph at lines 24443--24448
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1540] [1541]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 24600--24600
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) /
tol) ))[]
[1542] [1543] [1544]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24770--24770
[]\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
sep = " = "),[]
[1545]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24837--24837
[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1546] [1547] [1548] [1549] [1550] [1551]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 25213--25213
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
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[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of
an
[1552] [1553]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 25392--25392
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 25393--25393
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
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Underfull \hbox (badness 2922) in paragraph at lines 25459--25464
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1555]
Underfull \hbox (badness 2922) in paragraph at lines 25521--25526
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Underfull \hbox (badness 3240) in paragraph at lines 25533--25537
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
[1556]
Underfull \hbox (badness 2922) in paragraph at lines 25578--25583
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1557]
Underfull \hbox (badness 2922) in paragraph at lines 25639--25645
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1558]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25661--25661
[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25677--25677
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
[1559] [1560]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 25791--25791
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25814--25814
[]\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response
and gradient[]
[1561]
Underfull \hbox (badness 2922) in paragraph at lines 25852--25857
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1562]
Underfull \hbox (badness 2922) in paragraph at lines 25908--25913
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Underfull \hbox (badness 2922) in paragraph at lines 25965--25970
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1563]
Underfull \hbox (badness 2922) in paragraph at lines 26020--26025
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1564]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26041--26041
[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
Underfull \hbox (badness 6493) in paragraph at lines 26089--26094
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1565]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26115--26115
[]\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26117--26117
[]\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
[1566] [1567] [1568] [1569] [1570] [1571] [1572]
Underfull \hbox (badness 10000) in paragraph at lines 26611--26614
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
Underfull \hbox (badness 10000) in paragraph at lines 26611--26614
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1573] [1574] [1575] [1576] [1577] [1578] [1579]
Underfull \hbox (badness 3396) in paragraph at lines 27040--27042
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
, usu-ally, a re-sult of a call to
[1580] [1581] [1582]
Underfull \hbox (badness 2237) in paragraph at lines 27217--27219
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1583] [1584]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
, usu-ally the re-sult of a call to
[1585]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1586] [1587] [1588]
Underfull \hbox (badness 3407) in paragraph at lines 27606--27610
[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low)
[1589] [1590]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1591] [1592]
Underfull \hbox (badness 10000) in paragraph at lines 27856--27859
[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1593] [1594]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27985--27985
[]\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200,
main = t.tit,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 28013--28013
[] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[]
[1595]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
resid-u-als, when
[1596]
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[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
[1597]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 28195--28195
[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
TRUE,[]
[1598]
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
is re-turned. The ob-ject it-self is the re-ordered (un-less
[1599]
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[]\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv
en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
[1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 28875--28875
[]\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)
[1608]
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[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1609] [1610]
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[]\T1/ptm/m/n/10 In \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.2 and ear-lier the re-
sults were \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 for fits with \T1/pcr/m/n/10 na.act
ion \T1/ptm/m/n/10 meth-ods such as
[1611] [1612]
Underfull \hbox (badness 10000) in paragraph at lines 29161--29165
[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
Underfull \hbox (badness 1596) in paragraph at lines 29161--29165
\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
Overfull \hbox (30.78088pt too wide) in paragraph at lines 29172--29172
[] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[]
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[] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
= 0)[]
[1613] [1614]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 29299--29299
[]\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 29308--29308
[]\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[]
[1615] [1616] [1617] [1618]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626]
Underfull \hbox (badness 1337) in paragraph at lines 30008--30012
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1627]
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
ar-gu-ment
[1628] [1629] [1630] [1631] [1632]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30426--30426
[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30427--30427
[] \T1/pcr/m/n/10 na.action, exclude = c(NA, NaN), drop.unused.levels = F
ALSE)[]
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[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1633] [1634]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30531--30531
[] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[]
[1635]) (./stats4-pkg.tex [1636]
Chapter 11.
[1637] [1638] [1639]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192
[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
[1640] [1641] [1642]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again>
\relax
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
[1643]
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[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1644] [1645]) (./tcltk-pkg.tex [1646]
Chapter 12.
[1647] [1648] [1649] [1650]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 342--342
[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
ref in here[]
[1651] [1652] [1653]
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[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
any Tk or Tcl com-mand by sim-ply run-ning
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665]
Underfull \hbox (badness 1490) in paragraph at lines 1390--1393
[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept
on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1666]) (./tools-pkg.tex
Chapter 13.
[1667]
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
[1668]
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[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
which will be eval-u-ated via
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[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1669]
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
[1670]
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[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1671]
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[]\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine
to use. Over-rides any
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[][][]$\T1/pcr/m/n/10 http : / / partners . adobe . com / public / developer /
en / opentype / glyphlist .
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[]\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[]
[1681]
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[]\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[]
[1682]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1683]
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[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:
Underfull \hbox (badness 3724) in paragraph at lines 1117--1125
\T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen
-den-cies (de-fault:
[1684]
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[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
[1685] [1686]
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[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and
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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1687] [1688] [1689]
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[] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
sub-set of
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1690] [1691] [1692]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again>
\relax
l.1666 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
[1693] [1694]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if
Underfull \hbox (badness 10000) in paragraph at lines 1792--1797
\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
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\T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R
\T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
[1699] [1700]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
sub-set of
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1701]
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[] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[]
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to
r of links, as re-turned by
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[] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1719] [1720] [1721] [1722] [1723]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3671--3671
[]\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright,
bugs)
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[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
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[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1724]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-
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\T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie
d (for in-stance if there was
[1725] [1726]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3916--3916
[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
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\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
[1727]
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[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for
R pack-ages, ex-tracts in-for-ma-tion from
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[]\T1/ptm/m/n/10 Invisibly re-turns the num-ber of pack-ages de-scribed in the
re-sult-ing `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ' and
[1728] [1729] [1730]) (./utils-pkg.tex
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1731] [1732] [1733]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 by de-
[1734]
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[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1735] [1736] [1737]
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[]\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"),
[1738]
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[]\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
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[]\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
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[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
, \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4416) in paragraph at lines 536--542
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1739] [1740]
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\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1741]
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\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
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\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1742]
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[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1743] [1744] [1745]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1746] [1747] [1748] [1749] [1750]
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[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1751] [1752]
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[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1753] [1754]
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[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
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[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL)
[1755]
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[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL)
[1756] [1757]
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
[1758]
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[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1759]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1760]
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[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
[1761]
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\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1762]
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[]\T1/ptm/m/n/10 Factors \T1/pcr/m/n/10 x \T1/ptm/m/n/10 are ac-cepted from \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.0 (al-though co-in-ci-den-tally they worked fo
r
[1763] [1764] [1765]
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[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1766] [1767] [1768]
Underfull \hbox (badness 10000) in paragraph at lines 2568--2571
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
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[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";")\T1/ptm/m/n/10 ,
[1769]
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[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set
[1770]
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[]\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[]
[1771]
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[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1772] [1773] [1774] [1775] [1776]
Underfull \hbox (badness 1077) in paragraph at lines 3116--3118
[]\T1/ptm/m/n/10 character vec-tor of ad-di-tional command-line ar-gu-ments for
the \T1/pcr/m/n/10 "wget"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
Underfull \hbox (badness 1377) in paragraph at lines 3155--3161
\T1/pcr/m/n/10 internet.info \T1/ptm/m/n/10 op-tion. The de-tails de-pend on th
e plat-form and scheme, but set-ting
[1777]
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[]\T1/ptm/m/n/10 Proxies can be spec-i-fied via en-vi-ron-ment vari-ables. Set-
ting \T1/pcr/m/n/10 "no_proxy" \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "*" \T1/ptm/m/n
/10 stops
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\T1/ptm/m/n/10 fail-ing that, the all upper-case ver-sion) is con-sulted and if
non-empty used as a proxy
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\T1/ptm/m/n/10 site. For FTP trans-fers, the user-name and pass-word on the pro
xy can be spec-i-fied by
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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers
via en-vi-ron-ment vari-able
[1778]
Underfull \hbox (badness 4660) in paragraph at lines 3266--3269
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
[1779] [1780] [1781]
Underfull \hbox (badness 1565) in paragraph at lines 3472--3476
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
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[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1782]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3555--3555
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
Overfull \hbox (2.55087pt too wide) in paragraph at lines 3583--3590
\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 .
[1783] [1784] [1785] [1786] [1787]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3896--3896
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1788]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.3967 ...mat Unordered and Ordered Lists}{format}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.3967 ...mat Unordered and Ordered Lists}{format}
[1789] [1790] [1791]
[1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802]
[1803]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4871--4871
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[1804]
Underfull \hbox (badness 10000) in paragraph at lines 4955--4957
[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 http : / / www . r-[]p
roject . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1805]
Underfull \hbox (badness 1502) in paragraph at lines 5004--5009
[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
Underfull \hbox (badness 2103) in paragraph at lines 5004--5009
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[1806] [1807]
Underfull \hbox (badness 10000) in paragraph at lines 5166--5175
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
Underfull \hbox (badness 10000) in paragraph at lines 5166--5175
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10
', which can be re-made by
[1808] [1809]
Underfull \hbox (badness 3118) in paragraph at lines 5283--5285
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
sub-architecture used by
[1810] [1811]
Underfull \hbox (badness 1348) in paragraph at lines 5434--5439
[]\T1/ptm/m/n/10 logical in-di-cat-ing to also in-stall unin-stalled pack-ages
which these pack-
Underfull \hbox (badness 3884) in paragraph at lines 5434--5439
\T1/ptm/m/n/10 ages de-pend on/link to/import/suggest (and so on re-cur-sively)
. Not
Underfull \hbox (badness 1776) in paragraph at lines 5434--5439
\T1/ptm/m/n/10 used if \T1/pcr/m/n/10 repos = NULL\T1/ptm/m/n/10 . Can also be
a char-ac-ter vec-tor, a sub-set of
Overfull \hbox (44.55087pt too wide) in paragraph at lines 5434--5439
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
Overfull \hbox (48.30977pt too wide) in paragraph at lines 5447--5454
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
Underfull \hbox (badness 10000) in paragraph at lines 5460--5464
[]\T1/ptm/m/n/10 Possible val-ues are (cur-rently) \T1/pcr/m/n/10 "source"\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2073) in paragraph at lines 5460--5464
\T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "win.bi
nary"\T1/ptm/m/n/10 : the bi-nary types
[1812]
Underfull \hbox (badness 10000) in paragraph at lines 5518--5521
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed
Underfull \hbox (badness 10000) in paragraph at lines 5518--5521
\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1813]
Underfull \hbox (badness 1314) in paragraph at lines 5628--5635
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
[1814]
Underfull \hbox (badness 10000) in paragraph at lines 5649--5654
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5670--5670
[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
Underfull \hbox (badness 5133) in paragraph at lines 5706--5710
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
pack-age's
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[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1815]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5765--5765
[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[1816]
Underfull \hbox (badness 4132) in paragraph at lines 5796--5798
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[1817] [1818]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5954--5954
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[1819] [1820] [1821]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6097--6097
[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
[1822] [1823] [1824]
Underfull \hbox (badness 10000) in paragraph at lines 6270--6272
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
[1825] [1826] [1827] [1828]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 6537--6537
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[1829] [1830] [1831] [1832]
Underfull \hbox (badness 10000) in paragraph at lines 6810--6812
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut,
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 6815--6820
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
given pack-age is found and can suc-cess-fully be read,
[1833] [1834]
Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1835] [1836]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7088--7088
[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7089--7089
[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[1837] [1838] [1839] [1840]
Underfull \hbox (badness 1789) in paragraph at lines 7353--7355
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
more dis-cus-sion of the
[1841]
Underfull \hbox (badness 10000) in paragraph at lines 7411--7415
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7411--7415
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1842]
Underfull \hbox (badness 10000) in paragraph at lines 7524--7528
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7524--7528
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1843] [1844]
Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1845] [1846] [1847] [1848]
Underfull \hbox (badness 5203) in paragraph at lines 7914--7917
[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
ex-trac-tor are de-ter-mined by the generic func-tion
[1849] [1850] [1851]
Underfull \hbox (badness 1776) in paragraph at lines 8136--8143
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8160--8160
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[1852] [1853]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8316--8316
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[1854] [1855] [1856]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8491--8491
[]\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23
456 98 76 54[]
[1857]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8577--8577
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8580--8580
[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 8585--8585
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[1858]
Underfull \hbox (badness 1077) in paragraph at lines 8656--8659
[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[1859] [1860] [1861] [1862] [1863] [1864]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9094--9094
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[1865] [1866]
Underfull \hbox (badness 10000) in paragraph at lines 9181--9183
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1867] [1868]
Underfull \hbox (badness 10000) in paragraph at lines 9313--9317
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1869] [1870]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9454--9454
[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[1871] [1872] [1873] [1874]
Underfull \hbox (badness 6725) in paragraph at lines 9694--9703
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
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\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
Underfull \hbox (badness 10000) in paragraph at lines 9694--9703
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 9694--9703
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[1875] [1876]
Underfull \hbox (badness 10000) in paragraph at lines 9820--9822
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Ctags$[][]\T1/pt
m/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / www . gnu . org / software /
[1877] [1878] [1879]
Underfull \hbox (badness 10000) in paragraph at lines 9998--10002
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 10029--10035
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1880]
Underfull \hbox (badness 2012) in paragraph at lines 10124--10130
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
for fig-ures should be auto-generated. Use
Underfull \hbox (badness 2096) in paragraph at lines 10137--10139
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 2698) in paragraph at lines 10140--10142
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1527) in paragraph at lines 10147--10150
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1067) in paragraph at lines 10151--10154
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
[1881]
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[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
Underfull \hbox (badness 10000) in paragraph at lines 10212--10214
[]\T1/ptm/m/n/10 A re-place-ment for [][]\T1/pcr/m/n/10 dev.off[][][] \T1/ptm/m
/n/10 can be pro-vided as a func-tion with suf-fix \T1/pcr/m/n/10 .off\T1/ptm/m
/n/10 ,
Underfull \hbox (badness 1009) in paragraph at lines 10217--10228
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[1882] [1883]
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\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1884] [1885]
Underfull \hbox (badness 10000) in paragraph at lines 10443--10446
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form. For re-cent v
er-
Underfull \hbox (badness 10000) in paragraph at lines 10443--10446
\T1/ptm/m/n/10 sions where sub-architectures are in use this is of the form
Underfull \hbox (badness 10000) in paragraph at lines 10451--10454
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1886]
Underfull \hbox (badness 10000) in paragraph at lines 10504--10508
\T1/ptm/m/n/10 That file can be edited for a site, or a user can have a per-son
al copy in
Underfull \hbox (badness 2158) in paragraph at lines 10524--10527
[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
[1887] [1888]
Underfull \hbox (badness 3333) in paragraph at lines 10704--10706
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[1889] [1890] [1891]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10865--10865
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
Underfull \hbox (badness 5970) in paragraph at lines 10893--10896
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
Underfull \hbox (badness 2600) in paragraph at lines 10893--10896
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
Underfull \hbox (badness 2401) in paragraph at lines 10904--10913
[]\T1/ptm/m/n/10 string in-di-cat-ing if the \T1/pcr/m/n/10 width \T1/ptm/m/n/1
0 ar-gu-ment's spec-i-fi-ca-tion should be fol-
Underfull \hbox (badness 2735) in paragraph at lines 10904--10913
\T1/ptm/m/n/10 to the \T1/pcr/m/n/10 strict.width \T1/ptm/m/n/10 com-po-nent of
op-tion \T1/pcr/m/n/10 "str" \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][
][]\T1/ptm/m/n/10 )
Underfull \hbox (badness 1859) in paragraph at lines 10904--10913
\T1/ptm/m/n/10 which de-faults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back c
om-pat-i-bil-ity rea-sons; \T1/pcr/m/n/10 "wrap" \T1/ptm/m/n/10 uses
Underfull \hbox (badness 10000) in paragraph at lines 10904--10913
[][]\T1/pcr/m/n/10 strwrap[][][](*, width = width) \T1/ptm/m/n/10 whereas \T1/p
cr/m/n/10 "cut" \T1/ptm/m/n/10 cuts di-rectly to
Underfull \hbox (badness 1661) in paragraph at lines 10904--10913
\T1/pcr/m/n/10 width\T1/ptm/m/n/10 . Note that a small \T1/pcr/m/n/10 vec.lengt
h \T1/ptm/m/n/10 may be bet-ter than set-ting
[1892]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10948--10948
[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
[1893] [1894]
Underfull \hbox (badness 10000) in paragraph at lines 11072--11074
[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
[1895] [1896]
Underfull \hbox (badness 4492) in paragraph at lines 11226--11233
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
then the avail-able syn-tax ob-jects are con-sulted in
Underfull \hbox (badness 6252) in paragraph at lines 11226--11233
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 2452) in paragraph at lines 11226--11233
\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
[1897] [1898] [1899]
Underfull \hbox (badness 2020) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[1900]
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[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Tar _ (file _ fo
rmat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[1901] [1902] [1903] [1904] [1905] [1906] [1907]
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\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Overfull \hbox (36.87935pt too wide) in paragraph at lines 11987--11991
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be passed to
Underfull \hbox (badness 1052) in paragraph at lines 11996--11998
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
[1908]
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[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
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[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
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\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with
Underfull \hbox (badness 10000) in paragraph at lines 12055--12058
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[1909] [1910] [1911] [1912] [1913]
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[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
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[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
ex-am-ple,
[1914]
Underfull \hbox (badness 1715) in paragraph at lines 12383--12386
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
Underfull \hbox (badness 3271) in paragraph at lines 12440--12444
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
\T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[1915] [1916] [1917]) [1918] [1919] [1920] (./KernSmooth-pkg.tex
Chapter 15.
[1921]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[1922] [1923] [1924] [1925] [1926]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[1927] [1928] [1929] [1930]) (./MASS-pkg.tex
Chapter 16.
[1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772
[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
[1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952]
[1953]
Underfull \hbox (badness 7256) in paragraph at lines 1601--1603
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962] [1963] [1964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2409--2409
[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2413--2413
[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
[1965] [1966] [1967] [1968]
Underfull \hbox (badness 6559) in paragraph at lines 2691--2694
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
graph-i-cal pa-ram-e-ters. Note that
[1969] [1970] [1971]
Underfull \hbox (badness 7362) in paragraph at lines 2861--2866
\T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "lognormal"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3557) in paragraph at lines 2897--2905
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
Underfull \hbox (badness 3118) in paragraph at lines 2897--2905
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
\T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[1972] [1973]
Underfull \hbox (badness 4686) in paragraph at lines 3029--3031
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
Underfull \hbox (badness 1515) in paragraph at lines 3043--3047
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[1974] [1975] [1976]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3224--3224
[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
Underfull \hbox (badness 5817) in paragraph at lines 3231--3233
[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[1977]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3354--3354
[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
[1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988]
[1989]
Underfull \hbox (badness 1845) in paragraph at lines 4160--4162
[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[1990] [1991] [1992] [1993] [1994] [1995] [1996]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4656--4656
[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
[1997] [1998]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[1999]
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[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2000] [2001] [2002] [2003] [2004]
Underfull \hbox (badness 5681) in paragraph at lines 5286--5288
[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
Underfull \hbox (badness 5022) in paragraph at lines 5290--5293
[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2005]
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[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
the case of
[2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5925--5925
[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2014]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5987--5987
[]\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log")
[2015] [2016]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6129 ...sical N, P, K Factorial Experiment}{npk}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again>
\relax
l.6129 ...sical N, P, K Factorial Experiment}{npk}
[2017]
Underfull \hbox (badness 1783) in paragraph at lines 6247--6251
[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space.
That is
[2018] [2019] [2020] [2021]
Underfull \vbox (badness 10000) has occurred while \output is active [2022]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6545--6545
[] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[]
[2023]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6633--6633
[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2024] [2025] [2026] [2027] [2028] [2029]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7072--7072
[]\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7089--7089
[] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2030]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
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[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2031]
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2032] [2033]
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\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2034] [2035]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7476--7476
[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2036]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2037] [2038] [2039] [2040] [2041] [2042]
Underfull \hbox (badness 4686) in paragraph at lines 7979--7981
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
Underfull \hbox (badness 1515) in paragraph at lines 7995--7999
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2043] [2044]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8098--8098
[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
Underfull \hbox (badness 1590) in paragraph at lines 8122--8126
[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055]
[2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9501--9501
[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2065]
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[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
"Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2066]
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[]\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25)
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9712--9712
[]\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9715--9715
[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
[2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077]
[2078] [2079]) (./Matrix-pkg.tex [2080]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 42--45
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
Underfull \hbox (badness 10000) in paragraph at lines 42--45
\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2081]
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[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2082]
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[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
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\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2083]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
Underfull \hbox (badness 10000) in paragraph at lines 264--266
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2084] [2085]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 487--487
[]\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE)
Underfull \hbox (badness 5147) in paragraph at lines 494--496
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal
mean-ing as in
[2086]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
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[]\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 544--544
[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[]
[2087] [2088]
Underfull \hbox (badness 3189) in paragraph at lines 681--685
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2089]
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[]\T1/ptm/m/n/10 In some ver-sions of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 eigen[][][](CAex) \T1/ptm/m/n/10 fell into an in-fi-nite loop (where
as
[2090] [2091]
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[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2092]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
Underfull \hbox (badness 10000) in paragraph at lines 971--976
[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of
the lower tri-
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\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
de-com-po-si-tion. This method is equiv-a-lent to
Underfull \hbox (badness 1092) in paragraph at lines 971--976
\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in
the above de-scrip-tion of
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical")
[2093]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again>
\relax
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again>
\relax
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
[2094pdfTeX warning (ext4):
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1082 \end{Description}
pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate i
gnored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1082 \end{Description}
pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate i
gnored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1082 \end{Description}
] [2095]
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[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2096]
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[]\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
0, ...)
[2097]
Underfull \hbox (badness 2277) in paragraph at lines 1314--1317
[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
Underfull \hbox (badness 1609) in paragraph at lines 1361--1365
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2098]
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[]\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[]
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[]\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[]
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[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1420--1420
[]\T1/pcr/m/n/9 ## each has a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n
/9 matrix %% FIXME !! --- "check" them __unfinished__[]
[2099]
Underfull \hbox (badness 6445) in paragraph at lines 1457--1464
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky", ...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3861) in paragraph at lines 1457--1464
\T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1492--1496
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
Underfull \hbox (badness 1221) in paragraph at lines 1508--1514
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2100]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again>
\relax
l.1549 ... Row and Column Sums and Means}{colSums}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again>
\relax
l.1549 ... Row and Column Sums and Means}{colSums}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.1550 \aliasA{colMeans}{colSums}{colMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again>
\relax
l.1571 \aliasA{rowMeans}{colSums}{rowMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again>
\relax
l.1582 \aliasA{rowSums}{colSums}{rowSums}
[2101] [2102]
Underfull \hbox (badness 3547) in paragraph at lines 1757--1760
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
, the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2103] [2104] [2105] [2106]
Underfull \hbox (badness 10000) in paragraph at lines 1994--1996
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2107]
Underfull \hbox (badness 10000) in paragraph at lines 2116--2118
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
Underfull \hbox (badness 3068) in paragraph at lines 2177--2181
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
or sim-i-lar. Of-ten how-ever, more eas-ily via
[2108]
Underfull \hbox (badness 4713) in paragraph at lines 2212--2214
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2109]
Underfull \hbox (badness 10000) in paragraph at lines 2327--2330
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10
or
[2110] [2111]
Underfull \hbox (badness 10000) in paragraph at lines 2429--2433
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix", ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2429--2433
\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
Underfull \hbox (badness 2707) in paragraph at lines 2486--2490
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
[2112]
Underfull \hbox (badness 2689) in paragraph at lines 2546--2548
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
If miss-ing,
[2113]
Underfull \hbox (badness 1097) in paragraph at lines 2572--2575
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
[2114]
Underfull \hbox (badness 3646) in paragraph at lines 2818--2821
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 2840--2841
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
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[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
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[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2115]
Underfull \hbox (badness 1371) in paragraph at lines 2857--2863
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 :
the re-sult is from class
Underfull \hbox (badness 10000) in paragraph at lines 2864--2868
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 2874--2878
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2116] [2117]
Underfull \hbox (badness 1859) in paragraph at lines 3054--3056
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3099--3101
[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2118]
Underfull \hbox (badness 1168) in paragraph at lines 3214--3217
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
, via
[2119] [2120]
Underfull \hbox (badness 4967) in paragraph at lines 3376--3380
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix", ...) \T1/ptm/m/n/10 or
Overfull \hbox (2.39853pt too wide) in paragraph at lines 3381--3383
[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 .
[2121]
Underfull \hbox (badness 6364) in paragraph at lines 3423--3426
[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2122] [2123]
Underfull \hbox (badness 10000) in paragraph at lines 3573--3578
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3573--3578
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 10000) in paragraph at lines 3583--3585
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
triv-ial
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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
if
[2124]
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[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
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[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
[2125]
Underfull \hbox (badness 6364) in paragraph at lines 3700--3703
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2126]
Underfull \hbox (badness 4060) in paragraph at lines 3817--3820
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse
tri-an-gu-lar solve (aka
[2127]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3857--3857
[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
Underfull \hbox (badness 3635) in paragraph at lines 3923--3927
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
Underfull \hbox (badness 10000) in paragraph at lines 3932--3935
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 3932--3935
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
[2128]
Underfull \hbox (badness 10000) in paragraph at lines 3937--3941
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2129] [2130] [2131] [2132]
Underfull \hbox (badness 10000) in paragraph at lines 4225--4230
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite
Tay-lor se-ries
[2133] [2134]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4359--4359
[] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[]
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[] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[]
[2135] [2136] [2137] [2138]
Underfull \hbox (badness 10000) in paragraph at lines 4670--4675
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2139]
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[]\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons"
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4753--4753
[] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2,
dimnames=dns))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4757--4757
[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4764--4764
[] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[]
[2140] [2141]
Underfull \hbox (badness 4120) in paragraph at lines 4892--4895
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4921--4921
[]\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[]
[2142]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4926--4926
[]\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4933--4933
[]\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[]
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[] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[]
[2143]
Underfull \hbox (badness 1817) in paragraph at lines 5024--5033
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
the
Underfull \hbox (badness 5637) in paragraph at lines 5065--5067
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2144]
Underfull \hbox (badness 3138) in paragraph at lines 5091--5093
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2145]
Underfull \hbox (badness 1603) in paragraph at lines 5175--5177
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2146] [2147] [2148]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5411--5411
[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[]
[2149]
Underfull \hbox (badness 10000) in paragraph at lines 5487--5490
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[]
[2150]
Underfull \hbox (badness 1622) in paragraph at lines 5535--5540
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
\T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
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\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2151] [2152]
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[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2153]
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2154]
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[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2155]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2156] [2157]
Underfull \hbox (badness 10000) in paragraph at lines 6140--6143
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2158]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
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[]\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
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[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
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[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
sin-gu-lar,
[2159]
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[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
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[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2160] [2161]
Underfull \hbox (badness 6268) in paragraph at lines 6480--6483
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2162]
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[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
. How-ever,
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\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2163]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again>
\relax
l.6596 \aliasA{det}{Matrix-class}{det}
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[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
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[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
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[2164] [2165]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn..Rpcent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again>
\relax
l.6761 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again>
\relax
l.6851 ...A{crossprod}{matrix-products}{crossprod}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again>
\relax
l.6933 ...tcrossprod}{matrix-products}{tcrossprod}
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\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
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\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2166pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7076 \item[crossprod]
\code{signature(x = "dgeMatrix", y = "dgeMatrix")}:pdfT
eX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rd
ash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7076 \item[crossprod]
\code{signature(x = "dgeMatrix", y = "dgeMatrix")}:]
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[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10
and
[2167]
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[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2168]
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2169]
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[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
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\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2170] [2171]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[]
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[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 7500--7503
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2172] [2173]
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[]\T1/ptm/m/n/10 fast
[2174]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again>
\relax
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again>
\relax
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
[2175] [2176]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2177]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2178]
Underfull \hbox (badness 10000) in paragraph at lines 8137--8140
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
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[]\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
[2179] [2180]
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[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 :
co-er-cion to sparse
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\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2181]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
[2182]
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[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2183]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}
) has been already used, duplicate ignored
<to be read again>
\relax
l.8488 \aliasA{qr}{qr-methods}{qr}
[2184]
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[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
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[] \T1/pcr/m/n/9 c1=rep(c(1,0,0), 2), c2=rep(c(0,1,0), 2), c3
=rep(c(0,0,1),2)),[]
[2185]
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
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[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2186]
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[]\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
free"[]
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[]\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # wa
rning + ~1.5 sec[]
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[]\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.8723 ... the Reciprocal Condition Number}{rcond}
[2187] [2188]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2189] [2190] [2191]
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[]\T1/ptm/m/n/10 the ran-dom num-ber gen-er-a-tor for the \T1/pcr/m/n/10 x \T1/
ptm/m/n/10 slot, a [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 such that
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[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
[2192] [2193]
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[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2194]
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[] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[]
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[]\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[]
[2195]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again>
\relax
l.9292 \aliasA{solve}{solve-methods}{solve}
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[] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[]
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[] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[]
[2196]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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[]\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2197]
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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[]\T1/ptm/m/n/10 works via
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via
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[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and
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[]\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][]
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[] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
[FIXME ??] only[]
[2198]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
Underfull \hbox (badness 10000) in paragraph at lines 9622--9625
[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
er-ca-ble to)
Underfull \hbox (badness 2591) in paragraph at lines 9622--9625
\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
Underfull \hbox (badness 2828) in paragraph at lines 9633--9637
\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
[2199]
Underfull \hbox (badness 6592) in paragraph at lines 9644--9646
[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
[2200]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0, 0),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9722--9722
[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
== c(3, 0),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9723--9723
[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2201]
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[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2202]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 9900--9900
[] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij =
FALSE)[]
[2203]
Underfull \hbox (badness 4621) in paragraph at lines 9937--9941
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2204]
Underfull \hbox (badness 10000) in paragraph at lines 10008--10011
[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10025--10025
[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10028--10028
[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 10052--10052
[]\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x =
1:6, dimnames = dn)[]
[2205]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10096--10096
[]\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[]
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[] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
X@dimension)[]
[2206]
Underfull \hbox (badness 10000) in paragraph at lines 10193--10201
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject
of S3 class
Underfull \hbox (badness 1325) in paragraph at lines 10214--10218
[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
Underfull \hbox (badness 10000) in paragraph at lines 10244--10248
[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or
[2207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again>
\relax
l.10284 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2208]
Underfull \hbox (badness 1430) in paragraph at lines 10394--10396
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
[2209]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10420--10420
[] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[]
[2210]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.toe
plitz}) has been already used, duplicate ignored
<to be read again>
\relax
l.10559 ...toeplitz}{sparseVector-class}{toeplitz}
Underfull \hbox (badness 2970) in paragraph at lines 10571--10577
[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-
Underfull \hbox (badness 3679) in paragraph at lines 10571--10577
\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 10622--10625
[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
[2211]
Underfull \hbox (badness 10000) in paragraph at lines 10644--10647
[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
Underfull \hbox (badness 10000) in paragraph at lines 10660--10665
[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 10671--10673
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2212] [2213]
Underfull \hbox (badness 3525) in paragraph at lines 10767--10771
[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
[2214]
Underfull \hbox (badness 2591) in paragraph at lines 10868--10873
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2215]
Underfull \hbox (badness 2057) in paragraph at lines 10930--10932
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2216]
Underfull \hbox (badness 6641) in paragraph at lines 10999--11002
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
Underfull \hbox (badness 5133) in paragraph at lines 11036--11040
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
vir-tual class of all sparse ma-tri-ces coded in
Underfull \hbox (badness 2818) in paragraph at lines 11036--11040
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2217] [2218] [2219]
Underfull \hbox (badness 7362) in paragraph at lines 11245--11247
[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
sparse ma-trix (i.e., of sub-class of
[2220]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 11284--11284
[]\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x =
1:6, dimnames = dn)[]
[2221] [2222]
Underfull \hbox (badness 6910) in paragraph at lines 11533--11535
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2223] [2224]) (./boot-pkg.tex
Chapter 18.
[2225] [2226] [2227] [2228] [2229] [2230] [2231]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2232]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
Underfull \hbox (badness 1275) in paragraph at lines 583--588
[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
Underfull \hbox (badness 1264) in paragraph at lines 583--588
\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2233]
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[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2234]
Underfull \hbox (badness 6268) in paragraph at lines 797--807
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2235]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 6493) in paragraph at lines 851--855
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2236]
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[]\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt,
data = nuke)[]
Underfull \vbox (badness 10000) has occurred while \output is active [2237]
[2238]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
[2239]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
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\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to
Underfull \hbox (badness 2150) in paragraph at lines 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2240] [2241] [2242] [2243] [2244]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2245] [2246] [2247] [2248]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2249] [2250] [2251] [2252]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
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Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2254] [2255] [2256] [2257]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
[2258]
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2437--2438
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2259]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
sam-ple
Underfull \hbox (badness 1112) in paragraph at lines 2533--2537
\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
is used. This is mul-ti-plied by
[2260] [2261] [2262] [2263] [2264]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
[]\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894
[]\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,[]
[2265] [2266] [2267]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2268]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2269] [2270] [2271]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
[2272] [2273] [2274] [2275] [2276] [2277] [2278]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2279] [2280]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2281] [2282] [2283]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault
is
[2284]
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[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2285] [2286]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
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\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294] [2295]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2296] [2297] [2298] [2299]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2300]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2301] [2302] [2303] [2304] [2305] [2306] [2307] [2308]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5861--5861
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2309]
Underfull \hbox (badness 1127) in paragraph at lines 5983--6001
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2310]
Underfull \hbox (badness 2837) in paragraph at lines 6016--6019
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2311] [2312] [2313] [2314]
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[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2315] [2316]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6490--6490
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
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[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
[2317] [2318] [2319]
Underfull \hbox (badness 1596) in paragraph at lines 6737--6741
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2320] [2321]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6897--6897
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2322] [2323] [2324] [2325] [2326] [2327] [2328] [2329]) (./class-pkg.tex
[2330]
Chapter 19.
[2331] [2332] [2333] [2334] [2335] [2336] [2337] [2338]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2339] [2340] [2341] [2342] [2343] [2344] [2345] [2346]) (./cluster-pkg.tex
Chapter 20.
[2347]
Underfull \hbox (badness 10000) in paragraph at lines 133--140
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when
us-ing \T1/pcr/m/n/10 method = "flexible"
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 par-tic-u-larly for the case when \T1/pcr/m/n/10 par.method \T1/
ptm/m/n/10 is spec-i-fied of longer length
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 than one. The \T1/ptm/m/it/10 weighted av-er-age \T1/ptm/m/n/10
(\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n/10 . Fur-ther, \T
1/pcr/m/n/10 method= "single" \T1/ptm/m/n/10 is
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c
(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 .
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 165--167
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2349]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 250--250
[] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC]) ,[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 251--251
[] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, -.5))[iC]),[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 252--252
[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
[2350] [2351]
Underfull \vbox (badness 7685) has occurred while \output is active [2352]
[2353]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 516--516
[] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
= axes,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 520--520
[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2354]
Underfull \hbox (badness 5374) in paragraph at lines 537--539
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2355] [2356]
Underfull \hbox (badness 3078) in paragraph at lines 680--683
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2357]
Underfull \hbox (badness 2941) in paragraph at lines 761--764
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10
,
[2358]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 799--799
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
[2359]
Underfull \hbox (badness 10000) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
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[]\T1/pcr/m/n/10 clusGap(x, FUNcluster, K.max, B = 100, verbose = interactive(
), ...)
[2360]
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[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
[2361]
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[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
[2362] [2363]
Underfull \hbox (badness 4144) in paragraph at lines 1112--1116
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
e.g., for
[2364]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1188--1188
[] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
cex.txt = cex,[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1194--1194
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2365] [2366]
Underfull \hbox (badness 10000) in paragraph at lines 1394--1398
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
[2367]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1412--1412
[]\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1421--1421
[] \T1/pcr/m/n/9 axes=FALSE,ann=FALSE, sub="", col.p=NA, col.txt="dark
green", labels=3)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1429--1429
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2368]
Underfull \hbox (badness 5741) in paragraph at lines 1469--1472
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2369] [2370]
Underfull \hbox (badness 5008) in paragraph at lines 1645--1653
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1736--1736
[]\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1755--1755
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2372] [2373] [2374] [2375] [2376]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
Underfull \hbox (badness 3179) in paragraph at lines 2081--2087
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2377] [2378]
Underfull \hbox (badness 10000) in paragraph at lines 2239--2242
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2379]
Underfull \hbox (badness 1292) in paragraph at lines 2307--2310
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
[2380]
Underfull \hbox (badness 6675) in paragraph at lines 2316--2318
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2339--2342
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
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[2381] [2382] [2383]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2546--2546
[]\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[]
[2384] [2385] [2386]
Underfull \hbox (badness 1067) in paragraph at lines 2734--2739
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
\T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2387] [2388]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2889--2889
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2389] [2390] [2391]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3085--3085
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3086--3086
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2392]
Underfull \hbox (badness 10000) in paragraph at lines 3153--3156
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2393]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3203--3203
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3204--3204
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2394] [2395] [2396]
Underfull \hbox (badness 10000) in paragraph at lines 3389--3392
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
Underfull \hbox (badness 3471) in paragraph at lines 3389--3392
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2397]
Underfull \hbox (badness 10000) in paragraph at lines 3452--3457
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2398]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "twins"\T1/ptm/m/n/10 , typ
-i-cally cre-ated by ei-ther [][]\T1/pcr/m/n/10 agnes[][][]() \T1/ptm/m/n/10 or
Underfull \hbox (badness 4621) in paragraph at lines 3538--3543
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1990) in paragraph at lines 3538--3543
\T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1
/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider
Underfull \hbox (badness 6268) in paragraph at lines 3550--3553
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2399]
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[]\T1/ptm/m/n/10 currently [][]$\T1/pcr/m/n/10 http : / / www . agoras . ua . a
c . be / datasets / clusplot-[]examples . tar .
[2400] [2401]
Underfull \hbox (badness 10000) in paragraph at lines 3733--3736
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2402]
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[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2403]
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[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
Underfull \hbox (badness 2035) in paragraph at lines 3828--3830
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2404] [2405] [2406]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4021--4021
[] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[]
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[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2407]
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[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
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[]\T1/ptm/m/n/10 numeric (rank 1) ar-ray of clus-ter-wise \T1/ptm/m/it/10 means
\T1/ptm/m/n/10 of sil-hou-ette widths where
[2408]
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\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4160--4160
[]\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4169--4169
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4171--4171
[] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[]
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[]\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4176--4176
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE,[]
[2409]
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[] \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t
olerance = 0))[]
[2410] [2411] [2412] [2413] [2414] [2415] [2416]) (./codetools-pkg.tex
Chapter 21.
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[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
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[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
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[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2417]
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[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2418]
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[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2419] [2420] [2421]) (./foreign-pkg.tex [2422]
Chapter 22.
[2423]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2424] [2425]
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[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2426]
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[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2427] [2428] [2429]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 459--459
[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame)[]
[2430]
Underfull \hbox (badness 10000) in paragraph at lines 515--523
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
[2431]
Underfull \hbox (badness 7613) in paragraph at lines 533--539
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2432] [2433] [2434]
Underfull \hbox (badness 10000) in paragraph at lines 730--731
Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2435]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 816--816
[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2436]
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[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2437] [2438]
Underfull \hbox (badness 10000) in paragraph at lines 989--990
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1025--1025
[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2439]
Underfull \hbox (badness 1286) in paragraph at lines 1110--1114
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates =
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2440]
Underfull \hbox (badness 10000) in paragraph at lines 1183--1189
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2441] [2442]) (./lattice-pkg.tex
Chapter 23.
[2443] [2444] [2445]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 287--287
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 291--291
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[]
[2446]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 335--335
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 339--339
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[]
[2447]
Underfull \hbox (badness 4060) in paragraph at lines 358--370
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
Underfull \hbox (badness 10000) in paragraph at lines 358--370
\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 398--413
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
both
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[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
one can ei-ther set
[2448]
Underfull \hbox (badness 7631) in paragraph at lines 480--485
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2449] [2450]
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[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
ar-gu-ments to
[2451] [2452] [2453] [2454]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of
fac-tors will be
Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a
use-ful lay-out.
[2455]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2456] [2457]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
Underfull \hbox (badness 1917) in paragraph at lines 1239--1240
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2458] [2459] [2460]
Underfull \hbox (badness 1540) in paragraph at lines 1479--1485
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2461]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2462]
Underfull \vbox (badness 10000) has occurred while \output is active [2463]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671
[] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[]
Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2464]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
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[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10
, etc; see
[2465]
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
An-drews
[2466] [2467] [2468]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2469]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2470] [2471] [2472]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2347--2347
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2351--2351
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[]
Underfull \hbox (badness 4441) in paragraph at lines 2364--2368
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2473] [2474] [2475]
Underfull \hbox (badness 4441) in paragraph at lines 2549--2556
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2476] [2477]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2691--2691
[] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[]
[2478]
Underfull \hbox (badness 10000) in paragraph at lines 2763--2768
[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2479]
Underfull \hbox (badness 2913) in paragraph at lines 2793--2798
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2793--2798
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
Underfull \hbox (badness 6758) in paragraph at lines 2879--2883
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
Underfull \hbox (badness 7576) in paragraph at lines 2879--2883
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2885--2887
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2480]
Underfull \hbox (badness 1609) in paragraph at lines 2937--2943
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
Underfull \hbox (badness 2772) in paragraph at lines 2937--2943
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
Underfull \hbox (badness 1400) in paragraph at lines 2937--2943
\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2961--2965
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for
the de-fault panel func-tion
[2481] [2482]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
[] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3063--3063
[] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3064--3064
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3075--3075
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3087--3087
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
[2483]
Underfull \hbox (badness 10000) in paragraph at lines 3112--3120
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
Underfull \hbox (badness 2913) in paragraph at lines 3145--3152
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3145--3152
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2484] [2485] [2486] [2487]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3433 \aliasA{parallel}{B\_08\_splom}{parallel}
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3475--3475
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
[2488]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3498--3498
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2489] [2490] [2491] [2492] [2493]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3834--3834
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2494]
Underfull \hbox (badness 10000) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
Underfull \hbox (badness 2435) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2495] [2496]
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[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
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[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
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[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
Underfull \hbox (badness 1728) in paragraph at lines 4107--4111
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2497]
Underfull \hbox (badness 5161) in paragraph at lines 4172--4176
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4172--4176
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2498] [2499]
Underfull \hbox (badness 1067) in paragraph at lines 4286--4296
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1735) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
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\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
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[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4314--4316
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2500] [2501] [2502] [2503] [2504] [2505]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4718--4718
[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2506] [2507]
Underfull \hbox (badness 10000) in paragraph at lines 4905--4908
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2508] [2509]
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[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2510] [2511] [2512] [2513] [2514] [2515]
Underfull \hbox (badness 3646) in paragraph at lines 5369--5372
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 ,
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
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[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
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[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2516]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
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\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
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[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
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\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
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\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
though this can be
[2517]
Underfull \hbox (badness 1635) in paragraph at lines 5514--5519
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2518]
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[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
[2519]
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[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
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[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5681--5681
[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5684--5684
[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5686--5686
[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5694--5694
[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5695--5695
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5696--5696
[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
Underfull \hbox (badness 10000) in paragraph at lines 5712--5714
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
[2520]
Underfull \hbox (badness 2376) in paragraph at lines 5723--5725
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2521]
Underfull \hbox (badness 2538) in paragraph at lines 5848--5852
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5859--5866
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5859--5866
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
used (in com-bi-na-tion with
[2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 6012--6016
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2524] [2525]
Underfull \hbox (badness 4242) in paragraph at lines 6159--6164
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2526] [2527]
Underfull \hbox (badness 3601) in paragraph at lines 6275--6280
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6275--6280
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2528] [2529]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6362--6362
[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2530]
Underfull \hbox (badness 1888) in paragraph at lines 6494--6501
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2531]
Underfull \hbox (badness 10000) in paragraph at lines 6551--6554
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
Underfull \hbox (badness 1558) in paragraph at lines 6551--6554
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2532]
Underfull \hbox (badness 1005) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
Underfull \hbox (badness 1571) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2533] [2534] [2535] [2536] [2537]
Underfull \hbox (badness 1320) in paragraph at lines 6957--6964
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 6957--6964
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
ef-fi-cient. When us-ing
[2538]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7027--7027
[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
[2539]
Underfull \hbox (badness 10000) in paragraph at lines 7057--7060
[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
to
Underfull \hbox (badness 1584) in paragraph at lines 7057--7060
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2540]
Underfull \hbox (badness 10000) in paragraph at lines 7161--7164
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2541] [2542]
Underfull \hbox (badness 2012) in paragraph at lines 7327--7330
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2543]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7373--7373
[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2544] [2545]
Underfull \hbox (badness 2644) in paragraph at lines 7514--7518
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on
to
Underfull \hbox (badness 2772) in paragraph at lines 7527--7530
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a
list of ar-gu-ments to be sup-plied to
Underfull \hbox (badness 4242) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
Underfull \hbox (badness 1147) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
co-erced to a list. This al-lows ar-
Underfull \hbox (badness 2351) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
Underfull \hbox (badness 1675) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1
/ptm/m/n/10 , which adds the
Underfull \hbox (badness 1769) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
e.g.,
[2546]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7597--7597
[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7607--7607
[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2547]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7668--7668
[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7673--7673
[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2548] [2549] [2550]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7854--7854
[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2551]
Underfull \hbox (badness 1436) in paragraph at lines 7909--7915
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
Underfull \hbox (badness 1231) in paragraph at lines 7909--7915
\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2552] [2553] [2554] [2555] [2556] [2557] [2558] [2559]
Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2560] [2561]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8642--8642
[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8643--8643
[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8655--8655
[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
[2562]
Underfull \hbox (badness 3118) in paragraph at lines 8674--8677
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2563]
Underfull \hbox (badness 1515) in paragraph at lines 8750--8754
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2564]
Underfull \hbox (badness 6316) in paragraph at lines 8856--8861
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2565] [2566]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8963--8963
[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2567] [2568]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9102--9102
[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2569]
Overfull \hbox (84.94879pt too wide) in paragraph at lines 9161--9165
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left, right, left.name, right.name, condition
Overfull \hbox (104.63074pt too wide) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left, right.x, right.y, left.name
, right.x.name, right.y.name, condition
[2570] [2571] [2572] [2573] [2574] [2575] [2576]
Underfull \hbox (badness 4205) in paragraph at lines 9619--9623
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4518) in paragraph at lines 9619--9623
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 6300) in paragraph at lines 9624--9627
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2577] [2578] [2579]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9850 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2580] [2581] [2582] [2583])
(./mgcv-pkg.tex [2584]
Chapter 24.
Underfull \hbox (badness 1052) in paragraph at lines 40--42
[]\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term
p-values. See
[2585] [2586]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147
[]\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,
Overfull \hbox (6.78088pt too wide) in paragraph at lines 150--150
[] \T1/pcr/m/n/10 chunk.size=10000,rho=0,AR.start=NULL,sparse=FALSE,cluster
=NULL,[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 151--151
[] \T1/pcr/m/n/10 gc.level=1,use.chol=FALSE,samfrac=1,drop.unused.levels=TR
UE,...)[]
[2587]
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
Underfull \hbox (badness 1043) in paragraph at lines 193--198
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2588]
Underfull \hbox (badness 2626) in paragraph at lines 248--251
[]\T1/ptm/m/n/10 If all smooths are P-splines and all ten-sor prod-ucts are of
the form
[2589] [2590]
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2591] [2592] [2593]
Underfull \hbox (badness 2922) in paragraph at lines 521--522
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
Underfull \hbox (badness 1158) in paragraph at lines 563--565
[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2594] [2595]
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[2597] [2598] [2599] [2600]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 956--956
[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 982--982
[]\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[]
[2601] [2602] [2603] [2604] [2605] [2606] [2607]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1382--1382
[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2608] [2609] [2610] [2611] [2612] [2613]
Underfull \hbox (badness 1221) in paragraph at lines 1743--1749
\T1/ptm/m/n/10 de-grees of free-dom (mix-tures of the two are per-mit-ted). Mul
ti-dimensional smooths are
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[]\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1762--1762
[] \T1/pcr/m/n/10 fit=TRUE,paraPen=NULL,G=NULL,in.out,drop.unused.levels=TR
UE,...)[]
Underfull \hbox (badness 1142) in paragraph at lines 1783--1787
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2614]
Underfull \hbox (badness 1043) in paragraph at lines 1806--1811
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2615] [2616]
Underfull \hbox (badness 1043) in paragraph at lines 1966--1972
\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2619]
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Underfull \vbox (badness 10000) has occurred while \output is active [2621]
Underfull \vbox (badness 10000) has occurred while \output is active [2622]
[2623] [2624] [2625] [2626] [2627] [2628]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2720--2720
[] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
[] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[]
[2629] [2630] [2631] [2632] [2633]
Underfull \hbox (badness 5189) in paragraph at lines 3038--3042
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2634] [2635]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3155--3155
[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[2637] [2638] [2639] [2640] [2641] [2642] [2643] [2644]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3709--3709
[] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[]
[2645] [2646]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3824--3824
[]\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[]
Underfull \hbox (badness 1142) in paragraph at lines 3855--3859
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2647] [2648] [2649]
Underfull \hbox (badness 5970) in paragraph at lines 4035--4041
[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
[2650]
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[2652] [2653]
Underfull \hbox (badness 1577) in paragraph at lines 4280--4283
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
Underfull \hbox (badness 2181) in paragraph at lines 4287--4288
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
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[2665]
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[2667] [2668]
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[]\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
to rule the world.",[]
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[] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[]
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[2691] [2692] [2693]
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[2695]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2696]
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[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 3108) in paragraph at lines 6979--6982
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
be
[2697] [2698] [2699]
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[]\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s
cale=-1,[]
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[] \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla
b=NULL,[]
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[] \T1/pcr/m/n/10 shift=0,trans=I,seWithMean=FALSE,unconditional=FALSE
,by.resids=FALSE,[]
[2700] [2701] [2702]
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\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
some-times to clone the
[2703] [2704] [2705]
Overfull \hbox (114.78088pt too wide) in paragraph at lines 7554--7554
[] \T1/pcr/m/n/10 block.size=50000,newdata.guaranteed=FALSE,na.action=n
a.pass,cluster=NULL,...)[]
[2706] [2707]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 7704--7704
[] \T1/pcr/m/n/10 block.size=NULL,newdata.guaranteed=FALSE,na.action=na
.pass,[]
[2708] [2709] [2710]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 7945--7945
[] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[]
[2712]
Underfull \hbox (badness 1205) in paragraph at lines 7983--7985
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
Underfull \hbox (badness 1975) in paragraph at lines 7989--7994
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2713]
Underfull \hbox (badness 1205) in paragraph at lines 8073--8075
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
[2714]
Underfull \hbox (badness 10000) in paragraph at lines 8142--8145
[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2715] [2716]
Underfull \hbox (badness 1253) in paragraph at lines 8272--8274
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion
cri-te-rion re-ported is one of GCV,
[2717] [2718] [2719] [2720]
Underfull \hbox (badness 1946) in paragraph at lines 8450--8457
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
Underfull \hbox (badness 2221) in paragraph at lines 8450--8457
\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
Underfull \hbox (badness 2042) in paragraph at lines 8450--8457
\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee
Underfull \hbox (badness 2846) in paragraph at lines 8458--8461
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
Underfull \hbox (badness 5862) in paragraph at lines 8458--8461
\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2721]
Underfull \hbox (badness 10000) in paragraph at lines 8537--8540
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
"deviance"\T1/ptm/m/n/10 ,
[2722] [2723] [2724] [2725] [2726] [2727] [2728] [2729]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9044--9044
[] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[]
Underfull \hbox (badness 1975) in paragraph at lines 9055--9060
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2730] [2731]
Underfull \hbox (badness 1803) in paragraph at lines 9132--9136
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 9144--9156
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
Underfull \hbox (badness 2401) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able.
Plot meth-ods can be
Underfull \hbox (badness 2970) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2732] [2733] [2734]
Underfull \hbox (badness 6876) in paragraph at lines 9354--9360
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one
or two vari-ables, spec-i-fied via terms like
[2735]
Underfull \hbox (badness 10000) in paragraph at lines 9395--9396
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2736] [2737]
Underfull \hbox (badness 10000) in paragraph at lines 9524--9526
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
Underfull \hbox (badness 10000) in paragraph at lines 9524--9526
\T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs",
...) \T1/ptm/m/n/10 or
[2738] [2739]
Underfull \hbox (badness 10000) in paragraph at lines 9652--9653
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2740] [2741]
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[]\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first
deriv penalty[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9734--9734
[]\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[]
Underfull \hbox (badness 7613) in paragraph at lines 9772--9775
\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2742] [2743] [2744] [2745]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9985--9985
[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[2746]
Underfull \hbox (badness 10000) in paragraph at lines 10030--10032
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2747] [2748]
Underfull \hbox (badness 10000) in paragraph at lines 10138--10141
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method
a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 10138--10141
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 10138--10141
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[2749]
Underfull \hbox (badness 10000) in paragraph at lines 10237--10243
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 2698) in paragraph at lines 10237--10243
\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[2750] [2751] [2752]
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Overfull \hbox (36.7804pt too wide) in paragraph at lines 10451--10451
[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10453--10453
[] \T1/pcr/m/n/9 te(v,w,t,bs=c("sf","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))+[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 10454--10454
[] \T1/pcr/m/n/9 te(v,w,t,bs=c("sw","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))[]
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Overfull \hbox (90.78033pt too wide) in paragraph at lines 10535--10535
[]\T1/pcr/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax)
),knots=knots,method="REML")[]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 10541--10541
[] \T1/pcr/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax))
,knots=knots,method="REML")[]
[2755]
Underfull \hbox (badness 10000) in paragraph at lines 10555--10563
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the
sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 10581--10582
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2756] [2757]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 10683--10683
[]\T1/pcr/m/n/9 bk <- gam(y~s(la,lo,bs="sos",k=60),knots=list(la=dat$la[ind],l
o=dat$lo[ind]),data=dat)[]
[2758] [2759]
Underfull \hbox (badness 3396) in paragraph at lines 10841--10846
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any
num-ber of vari-ables, spec-i-fied via terms like
[2760]
Underfull \hbox (badness 10000) in paragraph at lines 10886--10888
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2761] [2762] [2763] [2764]
Underfull \hbox (badness 10000) in paragraph at lines 11074--11077
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
Underfull \hbox (badness 3068) in paragraph at lines 11074--11077
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
Underfull \hbox (badness 10000) in paragraph at lines 11107--11111
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 5652) in paragraph at lines 11107--11111
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , code[][]soap[][][], code[][]Spheri
cal.Spline[][][], [][]\T1/pcr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 ,
[2765] [2766]
Underfull \hbox (badness 2158) in paragraph at lines 11259--11259
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2767] [2768]
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[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[2769] [2770]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11468--11468
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[2771] [2772]
Underfull \hbox (badness 4846) in paragraph at lines 11604--11607
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or
es-ti-ma-tors if
[2773] [2774] [2775] [2776] [2777] [2778] [2779] [2780] [2781] [2782] [2783]
[2784] [2785] [2786] [2787]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 12501--12501
[]\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[]
[2788] [2789] [2790] [2791] [2792] [2793] [2794]) (./nlme-pkg.tex
Chapter 25.
[2795]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2796]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2797] [2798] [2799] [2800] [2801]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
[] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[2802] [2803] [2804] [2805] [2806] [2807] [2808] [2809] [2810] [2811]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1094--1094
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[]
[2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819]
Underfull \hbox (badness 10000) in paragraph at lines 1633--1636
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[2820]
Underfull \hbox (badness 3780) in paragraph at lines 1650--1652
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[2821] [2822] [2823] [2824] [2825]
Underfull \hbox (badness 2042) in paragraph at lines 1997--2003
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[2826]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2059--2059
[]\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla
pse = "Dog")[]
[2827]
Underfull \hbox (badness 1132) in paragraph at lines 2147--2149
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[2828] [2829]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[2830]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[2831] [2832] [2833] [2834] [2835] [2836] [2837] [2838]
Underfull \hbox (badness 10000) in paragraph at lines 2846--2850
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849]
[2850]
Underfull \hbox (badness 6493) in paragraph at lines 3582--3590
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[2851] [2852] [2853] [2854] [2855] [2856] [2857] [2858] [2859] [2860] [2861]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 4348--4348
[]\T1/pcr/m/n/10 fdHess(pars, fun, ..., .relStep=(.Machine$double.eps)^(1/3),
minAbsPar=0)
[2862] [2863] [2864] [2865] [2866] [2867] [2868] [2869] [2870] [2871] [2872]
[2873] [2874]
Underfull \hbox (badness 10000) in paragraph at lines 5158--5162
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[2875] [2876] [2877] [2878] [2879]
Underfull \hbox (badness 10000) in paragraph at lines 5475--5479
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
Underfull \hbox (badness 2671) in paragraph at lines 5475--5479
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[2880] [2881]
Underfull \hbox (badness 10000) in paragraph at lines 5590--5593
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890]
Underfull \hbox (badness 2799) in paragraph at lines 6096--6102
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[2891]
Underfull \hbox (badness 7133) in paragraph at lines 6157--6161
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2892]
Underfull \hbox (badness 2057) in paragraph at lines 6241--6252
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[2893]
Underfull \hbox (badness 10000) in paragraph at lines 6305--6307
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6334--6334
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2894] [2895] [2896] [2897]
Underfull \hbox (badness 7133) in paragraph at lines 6553--6557
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2898]
Underfull \hbox (badness 10000) in paragraph at lines 6652--6658
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
[2899]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6718
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2900]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6743--6743
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2901] [2902] [2903]
Underfull \hbox (badness 10000) in paragraph at lines 6986--6993
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7003--7003
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7011--7011
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
[2904]
Underfull \hbox (badness 2875) in paragraph at lines 7033--7035
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[2905] [2906] [2907]
Underfull \hbox (badness 10000) in paragraph at lines 7248--7253
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[2908] [2909]
Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 1817) in paragraph at lines 7400--7408
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that
20 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7423--7426
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[2910] [2911] [2912] [2913]
Underfull \hbox (badness 3354) in paragraph at lines 7638--7640
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
which \T1/ptm/m/n/10 is not equal to
[2914] [2915] [2916] [2917] [2918] [2919]
Underfull \hbox (badness 1642) in paragraph at lines 8030--8052
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2920] [2921]
Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8193--8193
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
Underfull \hbox (badness 1642) in paragraph at lines 8202--8224
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2922] [2923] [2924] [2925] [2926]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8466--8466
[]\T1/pcr/m/n/10 lmeControl(maxIter, msMaxIter, tolerance, niterEM, msMaxEval,
msTol,
Underfull \hbox (badness 10000) in paragraph at lines 8509--8511
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2927]
Underfull \hbox (badness 1320) in paragraph at lines 8522--8526
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][] \T1/ptm/m/n/10 (those from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8544--8544
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2928] [2929] [2930]
Underfull \hbox (badness 10000) in paragraph at lines 8707--8719
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[2931] [2932] [2933] [2934] [2935] [2936] [2937] [2938] [2939]
Underfull \hbox (badness 10000) in paragraph at lines 9297--9304
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9308--9308
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[2940]
Underfull \hbox (badness 6300) in paragraph at lines 9390--9393
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[2941] [2942] [2943] [2944]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[2945]
Underfull \hbox (badness 10000) in paragraph at lines 9679--9682
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
[2946]
Underfull \hbox (badness 3108) in paragraph at lines 9727--9730
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
Underfull \hbox (badness 2521) in paragraph at lines 9727--9730
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[2947] [2948]
Underfull \hbox (badness 2435) in paragraph at lines 9900--9905
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[2949] [2950] [2951] [2952] [2953]
Underfull \hbox (badness 7291) in paragraph at lines 10190--10192
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[2954] [2955] [2956]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10406--10406
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[2957]
Underfull \hbox (badness 1596) in paragraph at lines 10435--10461
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[2958] [2959] [2960]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10611--10611
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[2961] [2962] [2963]
Underfull \hbox (badness 10000) in paragraph at lines 10808--10810
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Underfull \hbox (badness 1092) in paragraph at lines 10818--10821
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10840--10840
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2964] [2965] [2966]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10996--10996
[]\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool)
[2967]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11091--11091
[]\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool)[]
[2968] [2969] [2970] [2971] [2972] [2973] [2974] [2975] [2976] [2977] [2978]
Underfull \hbox (badness 6268) in paragraph at lines 11852--11862
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[2979] [2980] [2981] [2982]
Underfull \hbox (badness 10000) in paragraph at lines 12113--12119
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[2983] [2984] [2985] [2986] [2987] [2988] [2989]
Underfull \hbox (badness 2452) in paragraph at lines 12576--12583
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[2990]
Underfull \hbox (badness 10000) in paragraph at lines 12641--12647
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001]
[3002] [3003] [3004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13593--13593
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3005]
Underfull \hbox (badness 10000) in paragraph at lines 13620--13623
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 6016) in paragraph at lines 13648--13651
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13648--13651
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13655--13658
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13663--13670
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13663--13670
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
[3006]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13720--13720
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
Underfull \hbox (badness 10000) in paragraph at lines 13727--13730
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13727--13730
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
[3007]
Underfull \hbox (badness 4582) in paragraph at lines 13755--13758
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13755--13758
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,
"labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13759--13762
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3008]
Underfull \hbox (badness 10000) in paragraph at lines 13835--13838
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 1472) in paragraph at lines 13860--13867
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3009]
Underfull \hbox (badness 10000) in paragraph at lines 13929--13931
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3010] [3011] [3012] [3013]
Underfull \hbox (badness 1540) in paragraph at lines 14144--14149
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
Underfull \hbox (badness 1215) in paragraph at lines 14191--14193
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
De-faults to
[3014] [3015] [3016] [3017] [3018]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14434--14434
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been
already used, duplicate ignored
<to be read again>
\relax
l.15072 ...Extract Random Effects}{random.effects}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again>
\relax
l.15072 ...Extract Random Effects}{random.effects}
[3028] [3029] [3030]
[3031] [3032] [3033] [3034] [3035] [3036] [3037]
Underfull \hbox (badness 1009) in paragraph at lines 15729--15738
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3038] [3039] [3040]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15876--15876
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3041] [3042] [3043] [3044]
Underfull \hbox (badness 10000) in paragraph at lines 16154--16172
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16154--16172
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3045]
Underfull \hbox (badness 10000) in paragraph at lines 16211--16217
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 1728) in paragraph at lines 16731--16734
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3054] [3055] [3056] [3057] [3058]
Underfull \hbox (badness 1867) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal"
Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3059]
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 ,
[3060] [3061] [3062] [3063]
Underfull \hbox (badness 10000) in paragraph at lines 17375--17382
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3064] [3065] [3066] [3067] [3068] [3069] [3070]
Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3071]
Underfull \hbox (badness 3579) in paragraph at lines 17942--17947
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3072]
Underfull \hbox (badness 3579) in paragraph at lines 18006--18011
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3073]
Underfull \hbox (badness 3579) in paragraph at lines 18069--18074
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3074]
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
Underfull \hbox (badness 3579) in paragraph at lines 18132--18137
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3075]
Underfull \hbox (badness 3579) in paragraph at lines 18195--18200
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3076]
Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3579) in paragraph at lines 18267--18272
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3077] [3078]
Underfull \hbox (badness 1009) in paragraph at lines 18416--18425
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3079] [3080] [3081]
Underfull \hbox (badness 1009) in paragraph at lines 18550--18559
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089]) (./nnet-pkg.tex
[3090]
Chapter 26.
[3091]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3092] [3093] [3094] [3095]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 383--383
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 440--440
[]\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 443--443
[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3096]
Underfull \hbox (badness 4013) in paragraph at lines 488--491
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if
the net was gen-er-ated by
[3097]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 523--523
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3098]) (./rpart-pkg.tex
Chapter 27.
[3099] [3100] [3101] [3102]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324
[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3103]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3104] [3105] [3106]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
at the hor-i-zon-tal plot co-or-di-nates of
[3107] [3108]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
[3109]
Underfull \hbox (badness 2941) in paragraph at lines 785--787
[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
if
[3110]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902
[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
[3111]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921
[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[]
[3112] [3113] [3114]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
[]\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164
[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3115]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3116]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270
[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286
[]\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01,
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287
[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
[3117] [3118] [3119] [3120] [3121] [3122]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3123] [3124]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3125] [3126] [3127]) (./spatial-pkg.tex [3128]
Chapter 28.
[3129] [3130] [3131] [3132] [3133] [3134]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3135] [3136] [3137] [3138] [3139] [3140] [3141] [3142] [3143] [3144] [3145]
[3146] [3147]) (./survival-pkg.tex [3148]
Chapter 29.
[3149] [3150]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171
[]\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
= lung, nmin = 1[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190
[]\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t
he last point[]
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[]\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a
nd Grambsch.[]
[3151]
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[]\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)
Overfull \hbox (42.78088pt too wide) in paragraph at lines 227--227
[]\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
been already used, duplicate ignored
<to be read again>
\relax
l.267 ... Myelogenous Leukemia survival data}{aml}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again>
\relax
l.267 ... Myelogenous Leukemia survival data}{aml}
[3152] [3153]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 364--364
[]\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian)
Overfull \hbox (4.38043pt too wide) in paragraph at lines 366--366
[]\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[]
[3154]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 403--403
[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3155] [3156]
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Overfull \hbox (36.78088pt too wide) in paragraph at lines 597--597
[]\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size,
Overfull \hbox (48.78088pt too wide) in paragraph at lines 598--598
[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3158] [3159]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 741--741
[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3160] [3161]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 891--891
[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3162]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again>
\relax
l.957 ...herapy for Stage B/C colon cancer}{colon}
[3163] [3164] [3165]
[3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1747--1747
[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
[3174] [3175]
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[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3176] [3177] [3178] [3179]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
Underfull \hbox (badness 1389) in paragraph at lines 2172--2174
[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
[3180] [3181]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2274--2274
[]\T1/pcr/m/n/9 lines(fit[1], lwd=2, xscale=365.24) #darken the first curve
and add marks[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2280--2280
[]\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[]
[3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191]
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[] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[]
[3192] [3193]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3072--3072
[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3194] [3195]
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[]\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[]
[3196]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3197] [3198]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3199] [3200]
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[]\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod,
[3201] [3202]
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[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3203]
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[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
[3204]
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[]\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age
+ sex, mgus,[]
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[]\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[]
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[]\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[]
[3205] [3206]
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[]\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[]
[3207] [3208] [3209] [3210] [3211]
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[]\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[]
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[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3212] [3213]
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[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[]
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[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[]
[3214] [3215] [3216] [3217] [3218] [3219] [3220]
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[] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[]
[3221] [3222] [3223]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
form
[3224] [3225]
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[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
Underfull \hbox (badness 3000) in paragraph at lines 5341--5343
[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3226]
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[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3227]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5457--5457
[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3228] [3229]
Underfull \hbox (badness 10000) in paragraph at lines 5591--5595
[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5611--5611
[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[]
[3230] [3231] [3232]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3233]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3234] [3235]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3236] [3237]
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[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3238]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3239] [3240]
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\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1297) in paragraph at lines 6463--6470
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3241]
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[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3242] [3243] [3244]
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[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3245] [3246]
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[] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[]
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[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3247] [3248] [3249] [3250]
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[3252]) (./fullrefman.ind [3253] [3254] [3255] [3256] [3257] [3258] [3259]
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[3271] [3272]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 ,
[3273] [3274] [3275] [3276] [3277]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 ,
[3278]
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[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 ,
[3279]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
[3280] [3281] [3282] [3283]
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[3285] [3286]
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,missing,logical-method
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[]\T1/pcr/m/n/10 [,CsparseMatrix,missing,index,logical-method
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[]\T1/pcr/m/n/10 [,Matrix,index,index,missing-method
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[]\T1/pcr/m/n/10 [,Matrix,index,missing,missing-method
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[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,ANY-method
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[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,missing-method
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[]\T1/pcr/m/n/10 [,Matrix,logical,missing,ANY-method
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[]\T1/pcr/m/n/10 [,Matrix,logical,missing,missing-method
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[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x, parent = emptyenv())
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[]\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[30] [31]
Underfull \hbox (badness 10000) in paragraph at lines 1993--1995
[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[32] [33]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2100--2100
[]\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[]
[34] [35]
Underfull \hbox (badness 1107) in paragraph at lines 2233--2235
[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[36] [37] [38] [39] [40]
Underfull \hbox (badness 5878) in paragraph at lines 2562--2567
[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-
Underfull \hbox (badness 10000) in paragraph at lines 2562--2567
\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53]
Underfull \hbox (badness 10000) in paragraph at lines 3446--3448
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[54] [55] [56] [57] [58] [59] [60]
Underfull \hbox (badness 4927) in paragraph at lines 3896--3900
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an
ob-ject
Underfull \hbox (badness 2012) in paragraph at lines 3896--3900
\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[61]
Underfull \hbox (badness 5260) in paragraph at lines 4004--4009
[]\T1/ptm/m/n/10 Are the \T1/pcr/m/n/10 R.app \T1/ptm/m/n/10 GUI com-po-nents a
nd the [][]\T1/pcr/m/n/10 quartz[][][] \T1/ptm/m/n/10 func-tion op-er-a-
Underfull \hbox (badness 1354) in paragraph at lines 4004--4009
\T1/ptm/m/n/10 tional? Only on some OS X builds. Note that this is dis-tinct fr
om
[62] [63] [64]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4172--4172
[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
[65]
Underfull \hbox (badness 10000) in paragraph at lines 4273--4278
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for
Underfull \hbox (badness 10000) in paragraph at lines 4273--4278
[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-
Underfull \hbox (badness 2181) in paragraph at lines 4273--4278
\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
columns to fac-tors un-less
[66]
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
[67] [68] [69] [70]
Underfull \hbox (badness 2521) in paragraph at lines 4589--4591
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[71] [72] [73] [74] [75]
Underfull \hbox (badness 10000) in paragraph at lines 4922--4930
[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is
ap-plied to an ob-ject with class at-tribute
[76] [77] [78] [79] [80] [81] [82] [83]
Underfull \hbox (badness 2443) in paragraph at lines 5465--5472
[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 http : / /
[84] [85] [86] [87]
Underfull \hbox (badness 1635) in paragraph at lines 5777--5780
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
Underfull \hbox (badness 3009) in paragraph at lines 5781--5784
[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols.
They can be es-tab-lished us-ing
Underfull \hbox (badness 1102) in paragraph at lines 5798--5811
[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
Underfull \hbox (badness 1308) in paragraph at lines 5812--5820
[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[88] [89] [90] [91]
Underfull \hbox (badness 2158) in paragraph at lines 6032--6036
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 '). Prox-ies can be spe
c-i-fied for HTTP and FTP \T1/pcr/m/n/10 url \T1/ptm/m/n/10 con-nec-tions: see
[92]
Underfull \hbox (badness 10000) in paragraph at lines 6120--6123
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
Underfull \hbox (badness 2057) in paragraph at lines 6120--6123
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[93] [94]
Underfull \hbox (badness 3815) in paragraph at lines 6284--6290
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
Underfull \hbox (badness 2343) in paragraph at lines 6284--6290
\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
and web-pages gen-er-
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\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If it is re-quired (it is n
ot rec-om-mended) when writ-ing
Underfull \hbox (badness 10000) in paragraph at lines 6303--6305
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[95]
Underfull \hbox (badness 1067) in paragraph at lines 6345--6352
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[96]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 6518--6518
[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[98] [99] [100] [101] [102]
Underfull \hbox (badness 10000) in paragraph at lines 6844--6846
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[103] [104]
Underfull \hbox (badness 4595) in paragraph at lines 6950--6953
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[105] [106] [107]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7143--7143
[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
[108]
Underfull \hbox (badness 8132) in paragraph at lines 7239--7243
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
Underfull \hbox (badness 4543) in paragraph at lines 7239--7243
\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
but this can be changed by set-ting
[109]
Underfull \hbox (badness 10000) in paragraph at lines 7258--7269
[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
a data frame by call-ing
Underfull \hbox (badness 1062) in paragraph at lines 7258--7269
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
is a generic func-tion, meth-ods can be
Overfull \hbox (4.63962pt too wide) in paragraph at lines 7291--7295
[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[110] [111] [112] [113] [114] [115]
Underfull \hbox (badness 10000) in paragraph at lines 7733--7745
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 7733--7745
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz =
"UTC") \T1/ptm/m/n/10 will give
[116] [117]
Underfull \hbox (badness 5802) in paragraph at lines 7938--7942
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10
reads the file byte-by-byte. This al-lows a
[118] [119]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8053--8057
\T1/pcr/m/n/10 trace("plot", browser, exit = browser, signature = c("track", "m
issing"))
[120]
Underfull \hbox (badness 10000) in paragraph at lines 8106--8110
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[121]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8187--8187
[]\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(1+2, "y", {cat(" HO
! "); pi+2})[]
[122] [123]
Underfull \hbox (badness 4254) in paragraph at lines 8340--8344
[]\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so
urce \T1/ptm/m/n/10 at-tribute), use
[124]
Underfull \hbox (badness 1132) in paragraph at lines 8383--8390
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
make the re-sult parseable.
[125]
Underfull \hbox (badness 1603) in paragraph at lines 8492--8495
[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
[126] [127] [128] [129] [130] [131] [132] [133] [134]
Underfull \hbox (badness 1917) in paragraph at lines 9077--9080
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
Overfull \hbox (36.7804pt too wide) in paragraph at lines 9130--9130
[]\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9131--9131
[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
[135] [136]
Underfull \hbox (badness 1168) in paragraph at lines 9231--9236
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[137] [138]
Underfull \hbox (badness 10000) in paragraph at lines 9369--9373
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / IEEE _ 754-[]198
5$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / en . wikipedia .
Underfull \hbox (badness 10000) in paragraph at lines 9369--9373
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 http : / / en . wikipedia . org / wiki / Double _
[139] [140] [141]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9588--9588
[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
[142]
Underfull \hbox (badness 1629) in paragraph at lines 9661--9665
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[143] [144]
Underfull \hbox (badness 2150) in paragraph at lines 9760--9763
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
from the re-verse
Underfull \hbox (badness 3690) in paragraph at lines 9774--9782
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
Underfull \hbox (badness 10000) in paragraph at lines 9783--9785
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent
to but faster than
[145]
Underfull \hbox (badness 3735) in paragraph at lines 9815--9822
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[146] [147]
Underfull \hbox (badness 10000) in paragraph at lines 10010--10013
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[148] [149] [150] [151] [152] [153] [154] [155] [156]
Underfull \hbox (badness 5288) in paragraph at lines 10669--10671
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
Underfull \hbox (badness 3039) in paragraph at lines 10679--10684
[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
and
[157]
Underfull \hbox (badness 10000) in paragraph at lines 10737--10739
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[158] [159]
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[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
passed as an ar-gu-ment
Underfull \hbox (badness 2401) in paragraph at lines 10854--10858
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[160]
Underfull \hbox (badness 10000) in paragraph at lines 10965--10967
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[161] [162] [163]
Underfull \hbox (badness 4048) in paragraph at lines 11151--11161
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
Underfull \hbox (badness 3657) in paragraph at lines 11151--11161
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[164] [165] [166]
Underfull \hbox (badness 5460) in paragraph at lines 11398--11407
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
Underfull \hbox (badness 2221) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[167] [168] [169] [170] [171]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11761--11761
[]\T1/pcr/m/n/9 A <- data.frame(x = 1:3, y = I(matrix(4:6)), z = I(matrix(lett
ers[1:9], 3, 3)))[]
[172] [173] [174] [175] [176]
Underfull \hbox (badness 2221) in paragraph at lines 12121--12127
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[177] [178] [179] [180]
Underfull \hbox (badness 2253) in paragraph at lines 12350--12352
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
[181]
Underfull \hbox (badness 10000) in paragraph at lines 12454--12456
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[182] [183]
Underfull \hbox (badness 10000) in paragraph at lines 12602--12604
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[184] [185]
Underfull \hbox (badness 10000) in paragraph at lines 12700--12704
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (30.78088pt too wide) in paragraph at lines 12750--12750
[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")
[186] [187]
Underfull \hbox (badness 10000) in paragraph at lines 12839--12842
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12849--12849
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive TRUE)[]
[188]
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[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE)
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 12950--12957
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
of fact, the in-ter-nal al-go-
Underfull \hbox (badness 3965) in paragraph at lines 12958--12962
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[189] [190]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13066--13066
[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13067--13067
[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
[191]
Underfull \hbox (badness 10000) in paragraph at lines 13148--13152
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
Underfull \hbox (badness 1389) in paragraph at lines 13148--13152
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[192]
Underfull \hbox (badness 1314) in paragraph at lines 13208--13210
[]\T1/ptm/m/n/10 In re-cent ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 most u
n-nec-es-sary copy-ing is avoided: on the other hand us-ing
[193] [194] [195]
Underfull \hbox (badness 1168) in paragraph at lines 13402--13406
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real
or com-plex vec-
Underfull \hbox (badness 2012) in paragraph at lines 13402--13406
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
[196]
Underfull \hbox (badness 6944) in paragraph at lines 13496--13499
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13521--13521
[]\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[]
[197] [198] [199]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13668--13668
[] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx
= NA,[]
Underfull \hbox (badness 2790) in paragraph at lines 13675--13678
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
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[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 13706--13710
[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[200]
Underfull \hbox (badness 10000) in paragraph at lines 13761--13763
[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so
Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point,
Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
Underfull \hbox (badness 10000) in paragraph at lines 13772--13780
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
com-plex (or
[201]
Underfull \hbox (badness 1009) in paragraph at lines 13806--13809
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 is
not ap-pro-pri-ate for use within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/1
0 meth-ods: use
[202]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13869--13869
[]\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[]
[203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214]
[215]
Underfull \hbox (badness 2418) in paragraph at lines 14776--14780
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
,
Underfull \hbox (badness 6510) in paragraph at lines 14783--14786
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
Underfull \hbox (badness 2326) in paragraph at lines 14811--14818
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[216] [217] [218] [219]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15057--15057
[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
Underfull \hbox (badness 1867) in paragraph at lines 15082--15089
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[220] [221] [222] [223]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15316--15316
[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 15343--15343
[]\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[]
Underfull \vbox (badness 10000) has occurred while \output is active [224]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15387--15387
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
Underfull \hbox (badness 10000) in paragraph at lines 15393--15397
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
Underfull \hbox (badness 1028) in paragraph at lines 15393--15397
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[225] [226] [227] [228] [229] [230] [231]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15921--15921
[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[232] [233] [234] [235]
Underfull \hbox (badness 2435) in paragraph at lines 16174--16176
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
. unicode . org / reports / tr35 /
Underfull \hbox (badness 2285) in paragraph at lines 16227--16229
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16235--16235
[]\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[]
[236]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16245--16245
[] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16265--16265
[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[237] [238] [239] [240] [241] [242] [243]
Underfull \hbox (badness 10000) in paragraph at lines 16701--16703
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[244]
Underfull \hbox (badness 4217) in paragraph at lines 16785--16794
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2057) in paragraph at lines 16800--16816
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[245] [246] [247] [248] [249] [250]
Underfull \hbox (badness 4699) in paragraph at lines 17207--17210
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the atomic types (\T1/pcr
/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[251] [252]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17329--17329
[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[253] [254]
Underfull \hbox (badness 4739) in paragraph at lines 17460--17462
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[255] [256] [257] [258] [259] [260]
Underfull \hbox (badness 1430) in paragraph at lines 17858--17863
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 17858--17863
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is the same as
[261]
Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
Underfull \hbox (badness 5008) in paragraph at lines 17919--17924
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[262]
Underfull \hbox (badness 10000) in paragraph at lines 17979--17986
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 17979--17986
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
Underfull \hbox (badness 5064) in paragraph at lines 17979--17986
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
with
Underfull \hbox (badness 5908) in paragraph at lines 17979--17986
\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
Underfull \hbox (badness 10000) in paragraph at lines 17995--17997
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
is equiv-a-lent to
[263]
Underfull \hbox (badness 1975) in paragraph at lines 18067--18070
[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[264] [265] [266] [267] [268]
Underfull \hbox (badness 10000) in paragraph at lines 18364--18368
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[269]
Underfull \hbox (badness 10000) in paragraph at lines 18494--18498
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
Underfull \hbox (badness 1454) in paragraph at lines 18494--18498
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
[270] [271]
Underfull \hbox (badness 10000) in paragraph at lines 18589--18596
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[272] [273]
Underfull \hbox (badness 10000) in paragraph at lines 18710--18714
[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use
Underfull \hbox (badness 5161) in paragraph at lines 18765--18770
[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
Underfull \hbox (badness 6592) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of
Underfull \hbox (badness 5133) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion
3 of the li-cense can be dis-played by
[274] [275] [276]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 18927--18927
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 18931--18931
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[277]
Underfull \hbox (badness 3343) in paragraph at lines 18987--18991
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
many more file han-dling func-tions and
[278]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19073--19073
[] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments
as for lists[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19084--19084
[] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
pr = 0.2))),[]
[279] [280]
Underfull \hbox (badness 6380) in paragraph at lines 19229--19234
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
[281]
Underfull \hbox (badness 10000) in paragraph at lines 19258--19261
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/pcr/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only \T1/pcr/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "LC
_CTYPE"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1337) in paragraph at lines 19287--19294
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
Underfull \hbox (badness 2229) in paragraph at lines 19287--19294
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, OS X) or
Underfull \hbox (badness 1043) in paragraph at lines 19287--19294
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
Underfull \hbox (badness 2564) in paragraph at lines 19306--19309
[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
[282]
Underfull \hbox (badness 1205) in paragraph at lines 19359--19364
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[283] [284] [285] [286]
Underfull \hbox (badness 2469) in paragraph at lines 19668--19674
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 1939) in paragraph at lines 19668--19674
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing names.
Underfull \hbox (badness 10000) in paragraph at lines 19668--19674
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[287] [288] [289] [290] [291]
Underfull \hbox (badness 10000) in paragraph at lines 19977--19979
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[292] [293] [294] [295] [296] [297]
Underfull \hbox (badness 1655) in paragraph at lines 20374--20378
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
[298] [299] [300] [301] [302] [303] [304] [305] [306]
Underfull \hbox (badness 4366) in paragraph at lines 20965--20971
\T1/pcr/m/n/10 www . bzip . org/$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http
: / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n
/10 http : / / tukaani .
[307] [308]
Underfull \hbox (badness 10000) in paragraph at lines 21094--21100
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
space can-not ex-ceed
Underfull \hbox (badness 6316) in paragraph at lines 21094--21100
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
[309] [310]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 21203--21203
[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
[311]
Underfull \hbox (badness 10000) in paragraph at lines 21254--21258
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
Underfull \hbox (badness 10000) in paragraph at lines 21254--21258
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
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Underfull \hbox (badness 3849) in paragraph at lines 21797--21802
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[319]
Underfull \hbox (badness 10000) in paragraph at lines 21877--21880
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute
via the gen-eral rules:
Underfull \hbox (badness 10000) in paragraph at lines 21877--21880
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
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Underfull \hbox (badness 10000) in paragraph at lines 22025--22027
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[323] [324] [325] [326] [327] [328] [329] [330]
Underfull \hbox (badness 2197) in paragraph at lines 22624--22628
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
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\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
[331]
Underfull \hbox (badness 2846) in paragraph at lines 22638--22642
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the
pack-
Underfull \hbox (badness 1990) in paragraph at lines 22638--22642
\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
[332]
Underfull \hbox (badness 10000) in paragraph at lines 22722--22728
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
Underfull \hbox (badness 1168) in paragraph at lines 22722--22728
\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
[333] [334] [335]
Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of
Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[336]
Underfull \hbox (badness 4120) in paragraph at lines 22997--23004
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[337]
Underfull \hbox (badness 1694) in paragraph at lines 23107--23110
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
(see `De-tails');
[338] [339] [340]
Underfull \hbox (badness 1603) in paragraph at lines 23346--23348
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[341] [342]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 23464--23473
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",
"methods")\T1/ptm/m/n/10 .
[343]
Underfull \hbox (badness 5475) in paragraph at lines 23559--23569
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 3271) in paragraph at lines 23578--23581
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
Underfull \hbox (badness 10000) in paragraph at lines 23593--23595
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[344] [345] [346]
Underfull \hbox (badness 3138) in paragraph at lines 23833--23839
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4132) in paragraph at lines 23833--23839
\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "http://www.bioconductor.org"\
T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror
Underfull \hbox (badness 4001) in paragraph at lines 23833--23839
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T
1/ptm/m/n/10 '. Can be set by
Underfull \hbox (badness 1194) in paragraph at lines 23845--23848
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
and
Underfull \hbox (badness 1389) in paragraph at lines 23869--23871
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[347]
Underfull \hbox (badness 10000) in paragraph at lines 23886--23892
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
Underfull \hbox (badness 1009) in paragraph at lines 23897--23900
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 23907--23914
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
Underfull \hbox (badness 10000) in paragraph at lines 23916--23923
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 10000) in paragraph at lines 23916--23923
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a
Underfull \hbox (badness 6380) in paragraph at lines 23916--23923
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
Overfull \hbox (34.78088pt too wide) in paragraph at lines 23916--23923
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
Underfull \hbox (badness 1881) in paragraph at lines 23930--23935
[]\T1/ptm/m/n/10 a char-ac-ter string, the path of the com-mand used for un-zip
-ping help files, or
[348] [349] [350] [351]
Underfull \vbox (badness 10000) has occurred while \output is active [352]
Underfull \hbox (badness 10000) in paragraph at lines 24227--24231
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
Underfull \hbox (badness 10000) in paragraph at lines 24227--24231
\T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10
A[c(arrayindex.x, arrayindex.y)]
[353] [354] [355] [356]
Underfull \hbox (badness 4341) in paragraph at lines 24550--24552
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
[357] [358] [359] [360] [361] [362] [363]
Underfull \hbox (badness 10000) in paragraph at lines 24977--24981
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully,
[364]
Underfull \hbox (badness 1796) in paragraph at lines 25040--25043
[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
see
[365] [366] [367]
Underfull \hbox (badness 10000) in paragraph at lines 25235--25238
[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[368] [369] [370] [371] [372] [373] [374] [375] [376]
Underfull \hbox (badness 1226) in paragraph at lines 25855--25860
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[377]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25900--25900
[] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 =
rep(c(0,0,1),2))[]
[378] [379] [380] [381]
Underfull \hbox (badness 7415) in paragraph at lines 26181--26185
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26202--26202
[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
[382] [383]
Underfull \hbox (badness 2418) in paragraph at lines 26350--26361
[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[384] [385] [386]
Underfull \hbox (badness 1533) in paragraph at lines 26583--26586
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[387]
Underfull \hbox (badness 1337) in paragraph at lines 26680--26683
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[388]
Underfull \hbox (badness 1038) in paragraph at lines 26745--26755
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[389]
Underfull \hbox (badness 10000) in paragraph at lines 26756--26759
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal:
for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and
[390]
Underfull \hbox (badness 1117) in paragraph at lines 26840--26846
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[391] [392] [393] [394] [395] [396]
Underfull \hbox (badness 4048) in paragraph at lines 27210--27215
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
Underfull \hbox (badness 4582) in paragraph at lines 27210--27215
\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
mode:
Underfull \hbox (badness 1824) in paragraph at lines 27210--27215
\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
"int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[397] [398] [399] [400] [401] [402] [403] [404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27743--27743
[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
[405] [406] [407] [408]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 28025--28027
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
* + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '.
[409] [410]
Underfull \hbox (badness 7558) in paragraph at lines 28234--28238
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 5417) in paragraph at lines 28250--28253
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
[411]
Underfull \hbox (badness 10000) in paragraph at lines 28254--28256
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 28257--28259
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[412] [413] [414] [415] [416] [417]
Underfull \hbox (badness 10000) in paragraph at lines 28664--28668
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[418] [419] [420] [421] [422] [423] [424] [425] [426] [427] [428] [429]
Underfull \hbox (badness 10000) in paragraph at lines 29470--29473
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,
Underfull \hbox (badness 1430) in paragraph at lines 29470--29473
\T1/pcr/m/n/10 save(list = ls(all = TRUE), file = ".RData")\T1/ptm/m/n/10 .
It is also what hap-
[430] [431] [432]
Underfull \hbox (badness 2302) in paragraph at lines 29681--29688
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
Underfull \hbox (badness 2837) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
Underfull \hbox (badness 3815) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[433]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 29733--29733
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[434]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
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[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[435]
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[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
Underfull \hbox (badness 6725) in paragraph at lines 29937--29942
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
will give an empty
[436]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30019--30019
[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[437] [438] [439] [440]
Underfull \hbox (badness 2809) in paragraph at lines 30282--30288
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2,
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
Underfull \hbox (badness 7759) in paragraph at lines 30289--30292
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less
[441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452]
Underfull \hbox (badness 1735) in paragraph at lines 31079--31085
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
Underfull \hbox (badness 4303) in paragraph at lines 31095--31098
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
out-put from
[453] [454] [455] [456] [457] [458] [459] [460]
Underfull \hbox (badness 2512) in paragraph at lines 31636--31638
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[461] [462] [463] [464]
Underfull \vbox (badness 10000) has occurred while \output is active [465]
[466]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 32030--32030
[]\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 32045--32045
[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
[467] [468] [469] [470] [471]
Underfull \hbox (badness 1087) in paragraph at lines 32416--32418
[]\T1/ptm/m/n/10 Markus Kuhn, ``ASCII and Uni-code quo-ta-tion marks''. [][]$\T
1/pcr/m/n/10 http : / / www . cl . cam . ac . uk /
[472]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32480--32480
[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32481--32481
[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
[473] [474] [475]
Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
Underfull \hbox (badness 8113) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
Underfull \hbox (badness 6542) in paragraph at lines 32696--32706
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
Underfull \hbox (badness 5189) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
Underfull \hbox (badness 4193) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 32740--32746
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 32740--32746
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
first in architecture-specific di-rec-to-ries,
Underfull \hbox (badness 1496) in paragraph at lines 32740--32746
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
[476]
Underfull \hbox (badness 1728) in paragraph at lines 32753--32760
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 32753--32760
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
Underfull \hbox (badness 2573) in paragraph at lines 32753--32760
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[477] [478] [479] [480]
Underfull \hbox (badness 10000) in paragraph at lines 33049--33055
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[481] [482]
Underfull \hbox (badness 1163) in paragraph at lines 33224--33231
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
Underfull \hbox (badness 8132) in paragraph at lines 33224--33231
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[483] [484] [485]
Underfull \hbox (badness 1142) in paragraph at lines 33440--33446
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
[486]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 33455--33455
[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
[487] [488] [489]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 33707--33707
[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
[490]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33751--33751
[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[491] [492] [493] [494] [495] [496] [497]
Underfull \hbox (badness 10000) in paragraph at lines 34212--34215
[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
signif[][][]() \T1/ptm/m/n/10 (for
[498]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34259--34259
[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[499] [500] [501] [502]
Underfull \hbox (badness 2762) in paragraph at lines 34489--34498
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
is a match then that el-e-ment is eval-u-ated un-less
Underfull \hbox (badness 1466) in paragraph at lines 34489--34498
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is
eval-u-ated, so for ex-am-ple
Overfull \hbox (31.3804pt too wide) in paragraph at lines 34548--34548
[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[503] [504] [505]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34688--34688
[]\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not.
[506]
Underfull \hbox (badness 3219) in paragraph at lines 34770--34775
[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 34770--34775
\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[507]
Underfull \hbox (badness 2452) in paragraph at lines 34864--34867
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
Underfull \hbox (badness 10000) in paragraph at lines 34864--34867
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[508] [509] [510]
Underfull \hbox (badness 10000) in paragraph at lines 35040--35044
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
Underfull \hbox (badness 1584) in paragraph at lines 35055--35058
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[511] [512] [513]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 35248--35248
[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used
[514] [515]
Underfull \hbox (badness 1082) in paragraph at lines 35377--35380
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[516] [517] [518]
Underfull \hbox (badness 1038) in paragraph at lines 35565--35568
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[519] [520] [521] [522] [523]
Underfull \hbox (badness 1515) in paragraph at lines 35904--35907
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies
[524]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36020--36020
[]\T1/pcr/m/n/10 table(..., exclude = if (useNA == "no") c(NA, NaN), useNA = c
("no",
[525]
Underfull \hbox (badness 1924) in paragraph at lines 36039--36042
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/pcr/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[526]
Underfull \hbox (badness 4096) in paragraph at lines 36123--36126
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[527] [528] [529]
Underfull \hbox (badness 10000) in paragraph at lines 36363--36365
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[530]
Underfull \hbox (badness 10000) in paragraph at lines 36443--36446
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$http : / / developer .
[531] [532]
Underfull \hbox (badness 5475) in paragraph at lines 36564--36568
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http : / /
[533]
Underfull \hbox (badness 10000) in paragraph at lines 36626--36630
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http :
[534] [535] [536] [537] [538] [539]
Underfull \hbox (badness 5637) in paragraph at lines 37038--37047
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the Ol-son/IANA
Underfull \hbox (badness 1629) in paragraph at lines 37038--37047
\T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion
in the file sys-tem varies,
[540]
Underfull \hbox (badness 3460) in paragraph at lines 37092--37094
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Time _ zone$[][]
\T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / www . twinsun . com /
[541] [542] [543]
Underfull \hbox (badness 10000) in paragraph at lines 37299--37301
[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[544] [545] [546] [547] [548] [549]
Underfull \hbox (badness 6542) in paragraph at lines 37718--37720
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
, and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[550] [551]
Underfull \hbox (badness 1708) in paragraph at lines 37841--37849
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 37841--37849
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
Underfull \hbox (badness 10000) in paragraph at lines 37850--37854
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
Underfull \hbox (badness 10000) in paragraph at lines 37850--37854
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
some-thing like
Underfull \hbox (badness 3281) in paragraph at lines 37850--37854
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
Underfull \hbox (badness 4859) in paragraph at lines 37864--37869
[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
and sup-press-ing the print-ing of er-ror mes-sages;
[552]
Underfull \hbox (badness 3895) in paragraph at lines 37926--37938
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in
Underfull \hbox (badness 1303) in paragraph at lines 37926--37938
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
"integer"\T1/ptm/m/n/10 ,
[553] [554] [555]
Underfull \hbox (badness 1515) in paragraph at lines 38113--38118
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[556] [557]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 38252--38252
[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[558] [559] [560] [561] [562] [563]
Underfull \hbox (badness 1803) in paragraph at lines 38707--38710
[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
Underfull \hbox (badness 2334) in paragraph at lines 38711--38718
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 4726) in paragraph at lines 38737--38741
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
Underfull \hbox (badness 1122) in paragraph at lines 38737--38741
\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[564] [565] [566]
Underfull \hbox (badness 3668) in paragraph at lines 38915--38917
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[567] [568] [569] [570]
Underfull \hbox (badness 6220) in paragraph at lines 39189--39194
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
Underfull \hbox (badness 3098) in paragraph at lines 39189--39194
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
Underfull \hbox (badness 1533) in paragraph at lines 39189--39194
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
Underfull \hbox (badness 6592) in paragraph at lines 39205--39210
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[571]
Underfull \hbox (badness 1603) in paragraph at lines 39224--39228
[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[572] [573] [574] [575] [576] [577]
Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
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\T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[578]
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[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[579]
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[]\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[]
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[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[580]) (./compiler-pkg.tex
Chapter 2.
[581] [582] [583]) (./datasets-pkg.tex [584]
Chapter 3.
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[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[585] [586] [587] [588] [589]
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[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[590]
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[]\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[]
[591] [592] [593] [594] [595]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[596] [597]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[598] [599] [600] [601]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[602] [603] [604] [605] [606]
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[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[607] [608]
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[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[609]
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[]\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[610] [611]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[612]
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[]\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[]
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[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
[613] [614]
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[] \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[]
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[] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[]
[615] [616] [617] [618]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[619] [620] [621] [622] [623] [624] [625] [626]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[627]
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[628]
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[630]
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[631] [632]
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[633]
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[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[634] [635] [636] [637] [638] [639] [640]
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[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[641]
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[]\T1/ptm/m/n/10 Files for all 182 dis-tricts in 1888 and other years have been
avail-able at [][]$\T1/pcr/m/n/10 http :
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\T1/pcr/m/n/10 / / opr . princeton . edu / archive / eufert / switz . html$[][]
\T1/ptm/m/n/10 or [][]$\T1/pcr/m/n/10 http : / / opr .
[642]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[643]
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[644]
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[645]
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[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
[646] [647] [648] [649] [650] [651] [652] [653] [654] [655]
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[657] [658]) (./grDevices-pkg.tex
Chapter 4.
[659] [660] [661] [662] [663]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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[][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[664] [665]
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[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[666] [667] [668] [669] [670] [671] [672] [673] [674]
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[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[675]
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\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[676]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
. com / Lab / Graphics / Colors /
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[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[677]
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[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[678] [679] [680]
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[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
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\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
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\T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
,
[681]
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
oth-er-wise a ma-trix of color names (for
[682]
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[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
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[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[683] [684] [685]
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[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
pro-duce and print a postscript copy. This will not
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\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10
for how to set this up. Win-dows users may pre-fer to use
[686]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
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[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-
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\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[687] [688]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the
set-ting of
[689] [690]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
[691] [692]
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\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
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\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
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\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
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\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[693]
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
[694] [695] [696] [697] [698]
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[699] [700] [701] [702] [703] [704]
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[]\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv",
scale.in = 255))[]
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[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
[705]
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[706] [707] [708]
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[]\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1)
[709] [710]
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[711] [712] [713] [714]
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[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[715] [716] [717] [718] [719] [720] [721]
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[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[722]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the
type of anti-aliasing (if any) to be
[723] [724]
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[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
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[]\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024,
height = 768)[]
[725]
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[726]
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[727]
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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East
Asian lan-guages -- see
[728] [729]
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[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
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[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[730] [731]
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\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
[732]
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\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
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[]\T1/pcr/m/n/10 Baekmuk-Batang \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m/n
/10 ftp : / / ftp . mizi . com / pub / baekmuk/$[][]\T1/ptm/m/n/10 .
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\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m
/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /
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[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
[734] [735] [736]
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[737]
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[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
for on-screen de-vices and to
[738]
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[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots
due to cor-rupted or du-pli-
[739] [740] [741] [742]
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[]\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
sep = "."))[]
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[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[743] [744] [745] [746] [747] [748]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[749] [750]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK
lan-guages and
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[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s
ys-tems which have the Wine
[751]
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[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[752]
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
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[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[753] [754]
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\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[755] [756] [757]
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\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
via
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[758] [759] [760]) (./graphics-pkg.tex
Chapter 5.
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[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use
[761] [762] [763] [764]
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[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[765] [766] [767]
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
lo-ca-tions are com-puted in-ter-nally (the same way
[768] [769] [770]
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[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or
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[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
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[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[771]
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[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
[772] [773]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[774] [775] [776] [777] [778] [779] [780]
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[] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names =
NULL,[]
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\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
[781]
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\T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
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\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and
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[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) +
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[782]
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[]\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[]
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[]\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi
s=..,main=..)")[]
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[]\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
= "grey40",[]
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[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[783] [784] [785] [786] [787]
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[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10
contourplot[][][] \T1/ptm/m/n/10 (and
[788]
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[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
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[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
[789]
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[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[790] [791]
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[]\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[]
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[]\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[]
[792] [793] [794] [795] [796]
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\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[797] [798] [799] [800] [801]
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[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[802] [803]
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
[804] [805]
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[806] [807] [808]
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[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[809]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
raster im-ages are used when the
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the
grid is reg-u-lar and ei-ther
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[810] [811] [812]
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[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
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[] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col =
par("fg"),[]
[813]
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[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[814] [815]
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[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
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[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
[816]
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[] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
= c(0, 0.3))[]
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[]\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[]
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[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
[818]
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[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for
[819] [820]
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[821] [822] [823]
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[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a
mul-ti-ple of
[824] [825] [826] [827]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[828]
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\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10
oma \T1/ptm/m/n/10 when chang-ing
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are
to be used: see
[829]
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[]\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel
= panel.cor)[]
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[] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[]
[830]
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[]\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue") # hmm...[]
[831]
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\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[832] [833]
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[834]
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</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf, id=27864, 28
9.08pt x 289.08pt>
<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf> [835 </u
sr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf>]
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[837 </usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf>]
[838]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[839]
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[]\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9,
physicians = 9,[]
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[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
[840]
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[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
[841]
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[842] [843] [844] [845]
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[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing
or an er-ror; us-ing, e.g.,
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\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[846] [847] [848] [849]
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[]\T1/pcr/m/n/9 axis(2, at = at.y, labels = formatC(at.y, format = "fg"), col.
axis = "red")[]
[850] [851]
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[]\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v
ector ~ factor[]
[852]
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[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[853] [854] [855] [856] [857]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[858] [859]
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[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of
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[][]
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[]\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[]
[861]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
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[863]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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[] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[]
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[]\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[]
[864]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[865] [866] [867]
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[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[868]
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[]\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[]
[869] [870] [871] [872] [873] [874]
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[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE))[]
[875] [876] [877] [878] [879] [880]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc = 0:1,[]
[881] [882] [883]
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[]\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)
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[]\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)[]
[884] [885]
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[]\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
...,[]
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[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[886]
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[]\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[]
[887]
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[]\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100,
lambda = 2),[]
[888] [889]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
[890]
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[]\T1/ptm/m/n/10 The Euro sym-bol was in-tro-duced rel-a-tively re-cently and m
ay not be avail-able in
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\T1/ptm/m/n/10 older fonts. In re-cent ver-sions of Adobe sym-bol fonts it is c
har-ac-ter 160, so
[891]
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[] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile:
Règles, Liberté, Egalité, Fraternité...")[]
[892]
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[]\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex-
pan-sion)
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[]\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[893]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again>
\relax
l.8643 \HeaderA{units}{Graphical Units}{units}
[894]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[895] [896]
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[]\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code =
2, length = 0.1)[]
[897]) (./grid-pkg.tex [898]
Chapter 6.
[899] [900] [901] [902] [903] [904]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
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\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[]
Underfull \vbox (badness 10000) has occurred while \output is active [915]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[916] [917] [918]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject
de-scrib-ing a cir-cle), but only
[919] [920] [921] [922] [923] [924] [925]
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
[926] [927] [928]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[]
[929]
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[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 ,
[930]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
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[]\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10
to al-low a grob to per-form cus-tom ac-tions and
[931] [932] [933]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
[934] [935] [936]
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[]\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global =
FALSE)[]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[937] [938] [939]
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[] \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[]
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[] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
NULL)[]
[940] [941] [942] [943]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
[944] [945] [946] [947] [948]
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[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
[949]
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[]\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
"bottom")))[]
[950]
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[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[951]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
[952]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
[953] [954] [955]
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[] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[]
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[] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other
anti-clockwise")[]
[956] [957] [958] [959] [960] [961] [962] [963] [964]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[965] [966] [967]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[968]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[969] [970] [971]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[972] [973] [974] [975] [976] [977] [978] [979] [980]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
[981] [982] [983] [984] [985] [986] [987] [988] [989] [990]
Underfull \hbox (badness 3449) in paragraph at lines 5856--5862
\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
"npc") - unit(1, "inches")\T1/ptm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 5856--5862
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[991] [992] [993] [994] [995]
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[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for
use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or
[996]
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[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[997] [998]
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
do-ing some-thing like
[999] [1000] [1001]
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[]\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[]
[1002]) (./methods-pkg.tex
Chapter 7.
[1003] [1004] [1005]
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[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
\T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-
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\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the
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\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about
it, you'll prob-a-bly agree that you wouldn't
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\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,
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\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1006] [1007] [1008] [1009] [1010] [1011]
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[]\T1/ptm/m/n/10 Note that the pre-ced-ing def-i-ni-tion means that the next me
thod is de-fined uniquely when
[1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022]
[1023] [1024] [1025] [1026]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1027] [1028]
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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class
[1029] [1030] [1031] [1032] [1033]
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
[1034] [1035] [1036]
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1037]
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[]\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10
(a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
[1038] [1039] [1040]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1050]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these
classes takes spe-cial ar-gu-ments
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[]
[1051]
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1052]
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\T1/ptm/m/n/10 If ar-gu-ment \T1/pcr/m/n/10 fullInfo \T1/ptm/m/n/10 is \T1/pcr/
m/n/10 TRUE\T1/ptm/m/n/10 , the call re-turns a named list of ob-jects of class
[1053] [1054] [1055]
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[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
[1056] [1057] [1058]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method
ex-ists for
[1059]
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\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is
to mod-ify a field ex-plic-itly by
[1060]
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[]\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(),
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[] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[]
[1061]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1062] [1063] [1064] [1065] [1066] [1067]
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[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
[1068]
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[1070]
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
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[]\T1/pcr/m/n/9 stopifnot(identical(abs(y), 1:10)) # (version 2.9.0 or earlier
fails here)[]
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[]\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[]
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[1072]
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\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
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[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1073] [1074] [1075] [1076] [1077]
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[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1078]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5723--5727
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1079] [1080]
Underfull \hbox (badness 10000) in paragraph at lines 5900--5916
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1081] [1082] [1083]
Underfull \hbox (badness 1248) in paragraph at lines 6186--6190
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
Underfull \hbox (badness 1960) in paragraph at lines 6186--6190
\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1084]
Underfull \hbox (badness 4647) in paragraph at lines 6274--6276
[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1085]
Underfull \hbox (badness 1072) in paragraph at lines 6348--6355
[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1086] [1087] [1088] [1089] [1090]pdfTeX warning (ext4): destination with the s
ame identifier (name{Rfn.S4}) has been already used, duplicate ignored
<to be read again>
\relax
l.6707 \aliasA{S4}{S3Part}{S4}
[1091] [1092] [1093]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6948--6948
[]\T1/pcr/m/n/9 ## note the these classes can insert an S3 subclass of "lm" as
the S3 part:[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6953--6953
[]\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c
("mlm", "lm")[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex})
has been already used, duplicate ignored
<to be read again>
\relax
l.6983 \aliasA{Complex}{S4groupGeneric}{Complex}
pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
ignored
<to be read again>
\relax
l.6985 \aliasA{Logic}{S4groupGeneric}{Logic}
pdfTeX warning (ext4): destination
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again>
\relax
l.6986 \aliasA{Math}{S4groupGeneric}{Math}
pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again>
\relax
l.6988 \aliasA{Ops}{S4groupGeneric}{Ops}
pdfTeX warning (ext4): destination with
the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again>
\relax
l.6989 \aliasA{Summary}{S4groupGeneric}{Summary}
[1094]
Underfull \hbox (badness 2050) in paragraph at lines 7050--7054
[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic
can be ob-tained by call-ing
Underfull \hbox (badness 6708) in paragraph at lines 7063--7075
[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3209) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1095] [1096]
Underfull \hbox (badness 1694) in paragraph at lines 7223--7225
[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
[1097]
Underfull \hbox (badness 10000) in paragraph at lines 7247--7250
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1098] [1099] [1100] [1101] [1102] [1103]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7702--7702
[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),[]
[1104] [1105]
Underfull \hbox (badness 2277) in paragraph at lines 7838--7846
[]\T1/ptm/m/n/10 Note that call-ing \T1/pcr/m/n/10 setGeneric() \T1/ptm/m/n/10
in this form is not strictly nec-es-sary be-fore call-ing
Underfull \hbox (badness 3128) in paragraph at lines 7879--7884
[]\T1/ptm/m/n/10 If you \T1/ptm/m/it/10 don't \T1/ptm/m/n/10 want the ex-ist-in
g func-tion to be taken as de-fault, sup-ply the ar-gu-ment
[1106]
Underfull \hbox (badness 1052) in paragraph at lines 7916--7923
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
\T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1107] [1108] [1109] [1110]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8236--8236
[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
[1111]
Underfull \hbox (badness 1755) in paragraph at lines 8270--8273
[]\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the
method. For
[1112]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8413--8413
[]\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li
nk{setClass})[]
[1113] [1114] [1115] [1116] [1117]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8819--8819
[]\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date
= "POSIXt"))[]
[1118]
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[]\T1/pcr/m/n/9 # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
s class, then calls the S3 print method.[]
[1119]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8930--8930
[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8941--8941
[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128]
Underfull \hbox (badness 10000) in paragraph at lines 9634--9636
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
Underfull \hbox (badness 1852) in paragraph at lines 9642--9646
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
Underfull \hbox (badness 1681) in paragraph at lines 9642--9646
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1129] [1130] [1131] [1132]) (./parallel-pkg.tex
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 15--17
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1133]
Underfull \hbox (badness 4242) in paragraph at lines 94--96
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1134] [1135]
Underfull \hbox (badness 1024) in paragraph at lines 194--197
[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1136]
Underfull \hbox (badness 5077) in paragraph at lines 281--284
[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, OS X, FreeBSD, So-laris, I
rix and Win-dows.
[1137] [1138]
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1139] [1140] [1141] [1142]
Underfull \hbox (badness 1917) in paragraph at lines 702--711
[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class
Underfull \hbox (badness 1178) in paragraph at lines 702--711
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1143] [1144]
Underfull \hbox (badness 10000) in paragraph at lines 839--842
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1145] [1146] [1147]
Underfull \hbox (badness 5388) in paragraph at lines 1028--1033
[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1148]
Underfull \hbox (badness 10000) in paragraph at lines 1052--1060
[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1088--1088
[]\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[]
[1149] [1150]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1203--1203
[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1217--1217
[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
Underfull \hbox (badness 1577) in paragraph at lines 1246--1249
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1151]
Underfull \hbox (badness 3375) in paragraph at lines 1292--1294
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
[1152] [1153]) (./splines-pkg.tex [1154]
Chapter 9.
Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1155] [1156] [1157] [1158] [1159] [1160] [1161]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 467--467
[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1162] [1163] [1164]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 678--678
[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1165] [1166] [1167]) (./stats-pkg.tex [1168]
Chapter 10.
[1169]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of
\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
[1170] [1171] [1172] [1173] [1174]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 416--416
[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 437--437
[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
[1175] [1176] [1177] [1178] [1179] [1180]
Underfull \hbox (badness 1024) in paragraph at lines 843--845
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189]
Underfull \hbox (badness 10000) in paragraph at lines 1387--1389
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1190]
Underfull \hbox (badness 10000) in paragraph at lines 1503--1507
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1503--1507
\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
Underfull \hbox (badness 1490) in paragraph at lines 1503--1507
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199]
Underfull \hbox (badness 10000) in paragraph at lines 2076--2081
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
Underfull \hbox (badness 10000) in paragraph at lines 2076--2081
\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
Underfull \hbox (badness 1371) in paragraph at lines 2076--2081
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
Underfull \hbox (badness 1221) in paragraph at lines 2082--2088
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2082--2088
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1200]
Underfull \hbox (badness 3965) in paragraph at lines 2163--2165
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1201] [1202] [1203] [1204]
Underfull \hbox (badness 1221) in paragraph at lines 2418--2423
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2418--2423
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1205]
Underfull \hbox (badness 3965) in paragraph at lines 2495--2497
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1206] [1207]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2630--2630
[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1208] [1209] [1210] [1211]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2866--2866
[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1212] [1213] [1214]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3059--3061
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 .
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3106--3106
[]\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3107--3107
[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1215] [1216] [1217] [1218] [1219] [1220]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3485--3485
[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1221] [1222] [1223] [1224]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3755--3755
[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1225] [1226] [1227] [1228] [1229]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4040--4040
[]\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4041--4041
[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1230] [1231] [1232]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4276--4276
[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1233] [1234] [1235]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4439--4439
[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1236]
Underfull \hbox (badness 3989) in paragraph at lines 4528--4535
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1237] [1238] [1239] [1240] [1241]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4876--4876
[]\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4878--4878
[]\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
= c(-0.9,0.1))[]
[1242]
Underfull \hbox (badness 7397) in paragraph at lines 4965--4969
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an
ar-gu-ment to all these con-trast func-tions, how-ever
Underfull \hbox (badness 7326) in paragraph at lines 4965--4969
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1243] [1244]
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[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
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[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
[1245]
Underfull \hbox (badness 2680) in paragraph at lines 5144--5146
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is
given by
Underfull \hbox (badness 10000) in paragraph at lines 5149--5151
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1246] [1247] [1248]
Underfull \hbox (badness 1436) in paragraph at lines 5327--5332
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
Underfull \hbox (badness 1377) in paragraph at lines 5327--5332
\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
Underfull \hbox (badness 1448) in paragraph at lines 5327--5332
\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1249] [1250]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5513--5513
[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1251]
Underfull \hbox (badness 1168) in paragraph at lines 5585--5590
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1252] [1253]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5679--5679
[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1254] [1255] [1256]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5864--5864
[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
[1257] [1258] [1259]
Underfull \hbox (badness 10000) in paragraph at lines 6027--6032
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When
[1260] [1261] [1262]
Underfull \hbox (badness 5954) in paragraph at lines 6215--6217
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1263]
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[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
Underfull \hbox (badness 5563) in paragraph at lines 6301--6303
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6304--6309
\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
Underfull \hbox (badness 7238) in paragraph at lines 6339--6342
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1264]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6374--6374
[]\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE,
type = "tr")[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6389--6389
[]\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6404--6404
[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
Underfull \vbox (badness 10000) has occurred while \output is active [1265]
[1266] [1267] [1268]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6645--6645
[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
[1269] [1270] [1271] [1272] [1273] [1274]
Underfull \hbox (badness 10000) in paragraph at lines 7012--7016
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1275]
Underfull \hbox (badness 6493) in paragraph at lines 7109--7112
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1276] [1277]
Underfull \hbox (badness 1430) in paragraph at lines 7246--7249
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tp : / / cran . r-[]project . org / web / views /
[1278] [1279] [1280] [1281] [1282] [1283]
Underfull \hbox (badness 10000) in paragraph at lines 7656--7661
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1284] [1285]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7794--7796
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
= TRUE)\T1/ptm/m/n/10 .
[1286] [1287] [1288]
Underfull \hbox (badness 1210) in paragraph at lines 8011--8013
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1289] [1290] [1291] [1292] [1293] [1294] [1295]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8455--8455
[] \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8477--8477
[]\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link
= "log")) # fails[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8480--8480
[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
[1296] [1297]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8618--8618
[]\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
.90) # ~= 7e-9[]
Underfull \hbox (badness 1859) in paragraph at lines 8655--8660
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
i.e., if
[1298] [1299] [1300] [1301] [1302]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8987--8987
[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate
S", "VeryS")))[]
[1303] [1304] [1305]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9155--9157
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
homogeneity of variances"\T1/ptm/m/n/10 .
[1306] [1307] [1308] [1309] [1310] [1311] [1312]
Underfull \hbox (badness 2443) in paragraph at lines 9607--9613
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1313] [1314] [1315]
Underfull \hbox (badness 10000) in paragraph at lines 9821--9824
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org /
wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1316] [1317] [1318] [1319]
Underfull \hbox (badness 4518) in paragraph at lines 10081--10086
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1320]
Underfull \hbox (badness 4132) in paragraph at lines 10120--10124
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1321]
Underfull \hbox (badness 10000) in paragraph at lines 10223--10226
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
fitted.values \T1/ptm/m/n/10 and
[1322] [1323] [1324]
Underfull \hbox (badness 2142) in paragraph at lines 10423--10426
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1325]
Underfull \hbox (badness 1708) in paragraph at lines 10504--10507
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1326]
Underfull \hbox (badness 10000) in paragraph at lines 10545--10551
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 10583--10588
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1327] [1328]
Underfull \hbox (badness 2635) in paragraph at lines 10716--10719
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1329] [1330]
Underfull \hbox (badness 1694) in paragraph at lines 10883--10886
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
[1331]
Underfull \hbox (badness 1337) in paragraph at lines 10902--10911
[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
den-dro-gram is re-ordered ac-cord-
Underfull \hbox (badness 3049) in paragraph at lines 10902--10911
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1332]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 10984--10984
[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11017--11017
[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
[1333]
Underfull \hbox (badness 10000) in paragraph at lines 11030--11034
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1334] [1335] [1336] [1337] [1338]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11334--11334
[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
been already used, duplicate ignored
<to be read again>
\relax
l.11349 \aliasA{hat}{influence.measures}{hat}
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11401--11401
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
[1339]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11413--11413
[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
Underfull \hbox (badness 1062) in paragraph at lines 11460--11465
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11471--11473
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1340] [1341]
Underfull \hbox (badness 3623) in paragraph at lines 11600--11602
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if
[1342] [1343]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11688--11688
[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
[1344]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11781--11781
[] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
= "tobacco",[]
[1345]
Underfull \hbox (badness 10000) in paragraph at lines 11829--11832
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1346] [1347] [1348]
Underfull \hbox (badness 4441) in paragraph at lines 12024--12026
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
fit-ted to
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[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
[1349] [1350]
Underfull \hbox (badness 2753) in paragraph at lines 12121--12123
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
/ / bugs . r-[]project . org / bugzilla3 /
[1351] [1352]
Underfull \hbox (badness 1292) in paragraph at lines 12246--12250
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
\T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1353]
Underfull \hbox (badness 10000) in paragraph at lines 12359--12361
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of
Underfull \hbox (badness 2894) in paragraph at lines 12365--12369
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
Underfull \hbox (badness 1038) in paragraph at lines 12365--12369
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364]
Underfull \hbox (badness 4518) in paragraph at lines 13059--13064
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1365] [1366] [1367]
Underfull \hbox (badness 10000) in paragraph at lines 13253--13257
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
,
[1368] [1369]
Underfull \hbox (badness 6995) in paragraph at lines 13438--13440
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1370] [1371] [1372]
Underfull \hbox (badness 1163) in paragraph at lines 13586--13594
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1373]
Underfull \hbox (badness 4518) in paragraph at lines 13706--13711
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1374] [1375] [1376]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13884--13884
[]\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13885--13885
[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1377]
Underfull \hbox (badness 10000) in paragraph at lines 13940--13943
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
Underfull \hbox (badness 1715) in paragraph at lines 13940--13943
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1378] [1379] [1380] [1381]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14226--14226
[]\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14227--14227
[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1382]
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[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
\OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
[1383] [1384] [1385] [1386] [1387] [1388] [1389]
Underfull \hbox (badness 2726) in paragraph at lines 14722--14725
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1401] [1402] [1403]
Underfull \hbox (badness 1648) in paragraph at lines 15627--15629
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
Underfull \hbox (badness 2591) in paragraph at lines 15641--15650
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
sup-ply vari-ables with the same names as would
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\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1404]
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[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b
= "contr.poly"))[]
[1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16258--16258
[]\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects
with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[]
[1413] [1414] [1415] [1416]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16486--16486
[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
[1417] [1418] [1419] [1420] [1421] [1422]
Underfull \hbox (badness 2772) in paragraph at lines 16922--16925
[]\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate
s. When
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\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr
/m/n/10 start \T1/ptm/m/n/10 is tried (if
[1423] [1424]
Underfull \hbox (badness 2359) in paragraph at lines 17041--17043
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1425]
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Underfull \vbox (badness 10000) has occurred while \output is active [1427]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17213--17213
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
[1428]
Underfull \hbox (badness 10000) in paragraph at lines 17293--17297
[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1429] [1430]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17373--17373
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1431]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439]
Underfull \hbox (badness 1248) in paragraph at lines 17957--17960
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
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\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
Underfull \hbox (badness 1478) in paragraph at lines 17978--17982
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and
[1440]
Underfull \hbox (badness 2042) in paragraph at lines 18031--18033
[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1441]
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[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
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[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
[1443]
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1444]
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[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
[1445] [1446] [1447]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18518--18518
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1448]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1449] [1450] [1451] [1452] [1453] [1454]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18910--18910
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1455]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 18997--18997
[] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
vs Leverage " * h[ii] / (1 - h[ii]))),[]
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[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1456] [1457] [1458] [1459] [1460]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19313--19313
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
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[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1461]
Underfull \hbox (badness 1107) in paragraph at lines 19381--19383
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1462]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19436--19436
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
[1463]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 19443--19443
[]\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty =
1, y.intersp = 1)[]
Underfull \hbox (badness 10000) in paragraph at lines 19492--19495
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
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\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1464]
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[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1465] [1466]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19658--19658
[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1467]
Underfull \hbox (badness 10000) in paragraph at lines 19716--19718
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
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[1479] [1480] [1481]
Underfull \hbox (badness 6859) in paragraph at lines 20681--20688
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 20692--20698
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492]
[1493] [1494] [1495] [1496] [1497] [1498]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21684--21684
[] \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) ==
"Pr(",[]
[1499] [1500] [1501] [1502] [1503]
Underfull \hbox (badness 1337) in paragraph at lines 22007--22013
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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Underfull \hbox (badness 1028) in paragraph at lines 22690--22693
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1514] [1515]
Underfull \hbox (badness 10000) in paragraph at lines 22800--22803
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 5091) in paragraph at lines 22800--22803
\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
ef-fi-ciency if
[1516] [1517] [1518]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23011--23011
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1519] [1520] [1521]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23230--23230
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1522] [1523]
Underfull \hbox (badness 10000) in paragraph at lines 23375--23378
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1524]
Underfull \hbox (badness 2134) in paragraph at lines 23426--23430
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
end point rule and is called by de-fault from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23439--23439
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1525] [1526] [1527] [1528]
Underfull \hbox (badness 7667) in paragraph at lines 23692--23694
[]\T1/ptm/m/n/10 a nu-meric vec-tor or an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-je
ct which is co-ercible to one by
[1529] [1530] [1531]
Underfull \hbox (badness 2591) in paragraph at lines 23895--23901
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][
][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/
ptm/m/n/10 mod-els (with ex-am-
[1532] [1533] [1534] [1535] [1536] [1537]
Underfull \hbox (badness 1412) in paragraph at lines 24301--24303
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1538] [1539]
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[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
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[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
Underfull \hbox (badness 2435) in paragraph at lines 24443--24448
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1540] [1541]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 24600--24600
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) /
tol) ))[]
[1542] [1543] [1544]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24770--24770
[]\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
sep = " = "),[]
[1545]
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[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1546] [1547] [1548] [1549] [1550] [1551]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 25213--25213
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
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[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of
an
[1552] [1553]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 25392--25392
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[]
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[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
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Underfull \hbox (badness 2922) in paragraph at lines 25459--25464
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1555]
Underfull \hbox (badness 2922) in paragraph at lines 25521--25526
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Underfull \hbox (badness 3240) in paragraph at lines 25533--25537
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
[1556]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1557]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1558]
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[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25677--25677
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
[1559] [1560]
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[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25814--25814
[]\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response
and gradient[]
[1561]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1562]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Underfull \hbox (badness 2922) in paragraph at lines 25965--25970
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1563]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1564]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26041--26041
[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1565]
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[]\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
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[]\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
[1566] [1567] [1568] [1569] [1570] [1571] [1572]
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[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
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\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1573] [1574] [1575] [1576] [1577] [1578] [1579]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
, usu-ally, a re-sult of a call to
[1580] [1581] [1582]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
, usu-ally the re-sult of a call to
[1585]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1586] [1587] [1588]
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[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low)
[1589] [1590]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1591] [1592]
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[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1593] [1594]
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[]\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200,
main = t.tit,[]
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[] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[]
[1595]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
resid-u-als, when
[1596]
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[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
[1597]
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[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
TRUE,[]
[1598]
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
is re-turned. The ob-ject it-self is the re-ordered (un-less
[1599]
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[]\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv
en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
[1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607]
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[]\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)
[1608]
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[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1609] [1610]
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[]\T1/ptm/m/n/10 In \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.2 and ear-lier the re-
sults were \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 for fits with \T1/pcr/m/n/10 na.act
ion \T1/ptm/m/n/10 meth-ods such as
[1611] [1612]
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[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
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[] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[]
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[] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
= 0)[]
[1613] [1614]
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[]\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[]
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[]\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[]
[1615] [1616] [1617] [1618]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1627]
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
ar-gu-ment
[1628] [1629] [1630] [1631] [1632]
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
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[] \T1/pcr/m/n/10 na.action, exclude = c(NA, NaN), drop.unused.levels = F
ALSE)[]
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[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1633] [1634]
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[] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[]
[1635]) (./stats4-pkg.tex [1636]
Chapter 11.
[1637] [1638] [1639]
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[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
[1640] [1641] [1642]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again>
\relax
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
[1643]
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[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1644] [1645]) (./tcltk-pkg.tex [1646]
Chapter 12.
[1647] [1648] [1649] [1650]
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
ref in here[]
[1651] [1652] [1653]
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[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
any Tk or Tcl com-mand by sim-ply run-ning
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665]
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[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept
on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1666]) (./tools-pkg.tex
Chapter 13.
[1667]
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
[1668]
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[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
which will be eval-u-ated via
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[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1669]
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
[1670]
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[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1671]
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[]\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine
to use. Over-rides any
[1672] [1673] [1674]
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[][][]$\T1/pcr/m/n/10 http : / / partners . adobe . com / public / developer /
en / opentype / glyphlist .
[1675] [1676] [1677] [1678] [1679] [1680]
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[]\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[]
[1681]
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[]\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[]
[1682]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1683]
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[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:
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\T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen
-den-cies (de-fault:
[1684]
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[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
[1685] [1686]
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[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and
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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1687] [1688] [1689]
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[] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
sub-set of
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1690] [1691] [1692]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again>
\relax
l.1666 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
[1693] [1694]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if
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\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
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\T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R
\T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
[1699] [1700]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
sub-set of
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1701]
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[] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[]
[1702] [1703] [1704] [1705] [1706] [1707] [1708]
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to
r of links, as re-turned by
[1709] [1710] [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718]
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[] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1719] [1720] [1721] [1722] [1723]
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[]\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright,
bugs)
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[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
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[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1724]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-
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\T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie
d (for in-stance if there was
[1725] [1726]
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[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
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\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
[1727]
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[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for
R pack-ages, ex-tracts in-for-ma-tion from
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[]\T1/ptm/m/n/10 Invisibly re-turns the num-ber of pack-ages de-scribed in the
re-sult-ing `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ' and
[1728] [1729] [1730]) (./utils-pkg.tex
Chapter 14.
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1731] [1732] [1733]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 by de-
[1734]
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[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1735] [1736] [1737]
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[]\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"),
[1738]
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[]\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
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[]\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Underfull \hbox (badness 10000) in paragraph at lines 536--542
[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
, \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4416) in paragraph at lines 536--542
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1739] [1740]
Underfull \hbox (badness 4505) in paragraph at lines 647--653
\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1741]
Underfull \hbox (badness 1603) in paragraph at lines 764--770
\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
Underfull \hbox (badness 3029) in paragraph at lines 764--770
\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1742]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 817--817
[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1743] [1744] [1745]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1026--1026
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1746] [1747] [1748] [1749] [1750]
Underfull \hbox (badness 1859) in paragraph at lines 1379--1388
[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1751] [1752]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1506--1506
[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1753] [1754]
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[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1672--1672
[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL)
[1755]
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[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL)
[1756] [1757]
Underfull \hbox (badness 10000) in paragraph at lines 1841--1843
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
[1758]
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[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
Underfull \hbox (badness 5189) in paragraph at lines 1931--1933
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1759]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2006--2006
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1760]
Underfull \hbox (badness 1082) in paragraph at lines 2080--2084
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
[1761]
Underfull \hbox (badness 1057) in paragraph at lines 2146--2153
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1762]
Underfull \hbox (badness 10000) in paragraph at lines 2158--2160
[]\T1/ptm/m/n/10 Factors \T1/pcr/m/n/10 x \T1/ptm/m/n/10 are ac-cepted from \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.0 (al-though co-in-ci-den-tally they worked fo
r
[1763] [1764] [1765]
Underfull \hbox (badness 10000) in paragraph at lines 2336--2338
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1766] [1767] [1768]
Underfull \hbox (badness 10000) in paragraph at lines 2568--2571
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
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[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";")\T1/ptm/m/n/10 ,
[1769]
Underfull \hbox (badness 10000) in paragraph at lines 2621--2624
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set
[1770]
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[]\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[]
[1771]
Underfull \hbox (badness 2452) in paragraph at lines 2769--2772
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1772] [1773] [1774] [1775] [1776]
Underfull \hbox (badness 1077) in paragraph at lines 3116--3118
[]\T1/ptm/m/n/10 character vec-tor of ad-di-tional command-line ar-gu-ments for
the \T1/pcr/m/n/10 "wget"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1072) in paragraph at lines 3155--3161
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
Underfull \hbox (badness 1377) in paragraph at lines 3155--3161
\T1/pcr/m/n/10 internet.info \T1/ptm/m/n/10 op-tion. The de-tails de-pend on th
e plat-form and scheme, but set-ting
[1777]
Underfull \hbox (badness 1057) in paragraph at lines 3180--3194
[]\T1/ptm/m/n/10 Proxies can be spec-i-fied via en-vi-ron-ment vari-ables. Set-
ting \T1/pcr/m/n/10 "no_proxy" \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "*" \T1/ptm/m/n
/10 stops
Underfull \hbox (badness 1742) in paragraph at lines 3180--3194
\T1/ptm/m/n/10 fail-ing that, the all upper-case ver-sion) is con-sulted and if
non-empty used as a proxy
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\T1/ptm/m/n/10 site. For FTP trans-fers, the user-name and pass-word on the pro
xy can be spec-i-fied by
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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers
via en-vi-ron-ment vari-able
[1778]
Underfull \hbox (badness 4660) in paragraph at lines 3266--3269
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
[1779] [1780] [1781]
Underfull \hbox (badness 1565) in paragraph at lines 3472--3476
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
Underfull \hbox (badness 10000) in paragraph at lines 3493--3499
[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1782]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3555--3555
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
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\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 .
[1783] [1784] [1785] [1786] [1787]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3896--3896
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1788]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.3967 ...mat Unordered and Ordered Lists}{format}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.3967 ...mat Unordered and Ordered Lists}{format}
[1789] [1790] [1791]
[1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802]
[1803]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4871--4871
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[1804]
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[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 http : / / www . r-[]p
roject . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1805]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[1806] [1807]
Underfull \hbox (badness 10000) in paragraph at lines 5166--5175
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10
', which can be re-made by
[1808] [1809]
Underfull \hbox (badness 3118) in paragraph at lines 5283--5285
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
sub-architecture used by
[1810] [1811]
Underfull \hbox (badness 1348) in paragraph at lines 5434--5439
[]\T1/ptm/m/n/10 logical in-di-cat-ing to also in-stall unin-stalled pack-ages
which these pack-
Underfull \hbox (badness 3884) in paragraph at lines 5434--5439
\T1/ptm/m/n/10 ages de-pend on/link to/import/suggest (and so on re-cur-sively)
. Not
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\T1/ptm/m/n/10 used if \T1/pcr/m/n/10 repos = NULL\T1/ptm/m/n/10 . Can also be
a char-ac-ter vec-tor, a sub-set of
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\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
Overfull \hbox (48.30977pt too wide) in paragraph at lines 5447--5454
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
Underfull \hbox (badness 10000) in paragraph at lines 5460--5464
[]\T1/ptm/m/n/10 Possible val-ues are (cur-rently) \T1/pcr/m/n/10 "source"\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2073) in paragraph at lines 5460--5464
\T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "win.bi
nary"\T1/ptm/m/n/10 : the bi-nary types
[1812]
Underfull \hbox (badness 10000) in paragraph at lines 5518--5521
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed
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\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1813]
Underfull \hbox (badness 1314) in paragraph at lines 5628--5635
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
[1814]
Underfull \hbox (badness 10000) in paragraph at lines 5649--5654
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
Underfull \hbox (badness 5133) in paragraph at lines 5706--5710
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
pack-age's
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[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1815]
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[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[1816]
Underfull \hbox (badness 4132) in paragraph at lines 5796--5798
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[1817] [1818]
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[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[1819] [1820] [1821]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6097--6097
[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
[1822] [1823] [1824]
Underfull \hbox (badness 10000) in paragraph at lines 6270--6272
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
[1825] [1826] [1827] [1828]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 6537--6537
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[1829] [1830] [1831] [1832]
Underfull \hbox (badness 10000) in paragraph at lines 6810--6812
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut,
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 6815--6820
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
given pack-age is found and can suc-cess-fully be read,
[1833] [1834]
Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1835] [1836]
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[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
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[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[1837] [1838] [1839] [1840]
Underfull \hbox (badness 1789) in paragraph at lines 7353--7355
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
more dis-cus-sion of the
[1841]
Underfull \hbox (badness 10000) in paragraph at lines 7411--7415
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1842]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7524--7528
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1843] [1844]
Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1845] [1846] [1847] [1848]
Underfull \hbox (badness 5203) in paragraph at lines 7914--7917
[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
ex-trac-tor are de-ter-mined by the generic func-tion
[1849] [1850] [1851]
Underfull \hbox (badness 1776) in paragraph at lines 8136--8143
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
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[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[1852] [1853]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8316--8316
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[1854] [1855] [1856]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8491--8491
[]\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23
456 98 76 54[]
[1857]
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[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
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[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
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[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[1858]
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[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[1859] [1860] [1861] [1862] [1863] [1864]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9094--9094
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[1865] [1866]
Underfull \hbox (badness 10000) in paragraph at lines 9181--9183
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1867] [1868]
Underfull \hbox (badness 10000) in paragraph at lines 9313--9317
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1869] [1870]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9454--9454
[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[1871] [1872] [1873] [1874]
Underfull \hbox (badness 6725) in paragraph at lines 9694--9703
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
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\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
Underfull \hbox (badness 10000) in paragraph at lines 9694--9703
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 9694--9703
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[1875] [1876]
Underfull \hbox (badness 10000) in paragraph at lines 9820--9822
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Ctags$[][]\T1/pt
m/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / www . gnu . org / software /
[1877] [1878] [1879]
Underfull \hbox (badness 10000) in paragraph at lines 9998--10002
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 10029--10035
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1880]
Underfull \hbox (badness 2012) in paragraph at lines 10124--10130
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
for fig-ures should be auto-generated. Use
Underfull \hbox (badness 2096) in paragraph at lines 10137--10139
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 2698) in paragraph at lines 10140--10142
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1527) in paragraph at lines 10147--10150
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1067) in paragraph at lines 10151--10154
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
[1881]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10205--10205
[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
Underfull \hbox (badness 10000) in paragraph at lines 10212--10214
[]\T1/ptm/m/n/10 A re-place-ment for [][]\T1/pcr/m/n/10 dev.off[][][] \T1/ptm/m
/n/10 can be pro-vided as a func-tion with suf-fix \T1/pcr/m/n/10 .off\T1/ptm/m
/n/10 ,
Underfull \hbox (badness 1009) in paragraph at lines 10217--10228
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[1882] [1883]
Underfull \hbox (badness 2846) in paragraph at lines 10304--10314
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1884] [1885]
Underfull \hbox (badness 10000) in paragraph at lines 10443--10446
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form. For re-cent v
er-
Underfull \hbox (badness 10000) in paragraph at lines 10443--10446
\T1/ptm/m/n/10 sions where sub-architectures are in use this is of the form
Underfull \hbox (badness 10000) in paragraph at lines 10451--10454
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1886]
Underfull \hbox (badness 10000) in paragraph at lines 10504--10508
\T1/ptm/m/n/10 That file can be edited for a site, or a user can have a per-son
al copy in
Underfull \hbox (badness 2158) in paragraph at lines 10524--10527
[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
[1887] [1888]
Underfull \hbox (badness 3333) in paragraph at lines 10704--10706
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[1889] [1890] [1891]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10865--10865
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
Underfull \hbox (badness 5970) in paragraph at lines 10893--10896
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
Underfull \hbox (badness 2600) in paragraph at lines 10893--10896
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
Underfull \hbox (badness 2401) in paragraph at lines 10904--10913
[]\T1/ptm/m/n/10 string in-di-cat-ing if the \T1/pcr/m/n/10 width \T1/ptm/m/n/1
0 ar-gu-ment's spec-i-fi-ca-tion should be fol-
Underfull \hbox (badness 2735) in paragraph at lines 10904--10913
\T1/ptm/m/n/10 to the \T1/pcr/m/n/10 strict.width \T1/ptm/m/n/10 com-po-nent of
op-tion \T1/pcr/m/n/10 "str" \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][
][]\T1/ptm/m/n/10 )
Underfull \hbox (badness 1859) in paragraph at lines 10904--10913
\T1/ptm/m/n/10 which de-faults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back c
om-pat-i-bil-ity rea-sons; \T1/pcr/m/n/10 "wrap" \T1/ptm/m/n/10 uses
Underfull \hbox (badness 10000) in paragraph at lines 10904--10913
[][]\T1/pcr/m/n/10 strwrap[][][](*, width = width) \T1/ptm/m/n/10 whereas \T1/p
cr/m/n/10 "cut" \T1/ptm/m/n/10 cuts di-rectly to
Underfull \hbox (badness 1661) in paragraph at lines 10904--10913
\T1/pcr/m/n/10 width\T1/ptm/m/n/10 . Note that a small \T1/pcr/m/n/10 vec.lengt
h \T1/ptm/m/n/10 may be bet-ter than set-ting
[1892]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10948--10948
[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
[1893] [1894]
Underfull \hbox (badness 10000) in paragraph at lines 11072--11074
[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
[1895] [1896]
Underfull \hbox (badness 4492) in paragraph at lines 11226--11233
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
then the avail-able syn-tax ob-jects are con-sulted in
Underfull \hbox (badness 6252) in paragraph at lines 11226--11233
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 2452) in paragraph at lines 11226--11233
\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
[1897] [1898] [1899]
Underfull \hbox (badness 2020) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[1900]
Underfull \hbox (badness 10000) in paragraph at lines 11469--11472
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Tar _ (file _ fo
rmat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 11469--11472
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[1901] [1902] [1903] [1904] [1905] [1906] [1907]
Underfull \hbox (badness 4660) in paragraph at lines 11974--11977
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Overfull \hbox (36.87935pt too wide) in paragraph at lines 11987--11991
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .
Underfull \hbox (badness 3557) in paragraph at lines 11993--11995
[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be passed to
Underfull \hbox (badness 1052) in paragraph at lines 11996--11998
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
[1908]
Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 12047--12052
[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with
Underfull \hbox (badness 10000) in paragraph at lines 12055--12058
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[1909] [1910] [1911] [1912] [1913]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12331--12331
[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
Underfull \hbox (badness 1454) in paragraph at lines 12358--12362
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
ex-am-ple,
[1914]
Underfull \hbox (badness 1715) in paragraph at lines 12383--12386
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 12428--12430
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
Underfull \hbox (badness 3271) in paragraph at lines 12440--12444
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
\T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[1915] [1916] [1917]) [1918] [1919] [1920] (./KernSmooth-pkg.tex
Chapter 15.
[1921]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[1922] [1923] [1924] [1925] [1926]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[1927] [1928] [1929] [1930]) (./MASS-pkg.tex
Chapter 16.
[1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772
[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
[1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952]
[1953]
Underfull \hbox (badness 7256) in paragraph at lines 1601--1603
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962] [1963] [1964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2409--2409
[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2413--2413
[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
[1965] [1966] [1967] [1968]
Underfull \hbox (badness 6559) in paragraph at lines 2691--2694
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
graph-i-cal pa-ram-e-ters. Note that
[1969] [1970] [1971]
Underfull \hbox (badness 7362) in paragraph at lines 2861--2866
\T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "lognormal"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3557) in paragraph at lines 2897--2905
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
Underfull \hbox (badness 3118) in paragraph at lines 2897--2905
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
\T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[1972] [1973]
Underfull \hbox (badness 4686) in paragraph at lines 3029--3031
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
Underfull \hbox (badness 1515) in paragraph at lines 3043--3047
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[1974] [1975] [1976]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3224--3224
[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
Underfull \hbox (badness 5817) in paragraph at lines 3231--3233
[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[1977]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3354--3354
[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
[1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988]
[1989]
Underfull \hbox (badness 1845) in paragraph at lines 4160--4162
[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[1990] [1991] [1992] [1993] [1994] [1995] [1996]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4656--4656
[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
[1997] [1998]
Underfull \hbox (badness 10000) in paragraph at lines 4808--4811
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[1999]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4878--4878
[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
Underfull \hbox (badness 10000) in paragraph at lines 4886--4889
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2000] [2001] [2002] [2003] [2004]
Underfull \hbox (badness 5681) in paragraph at lines 5286--5288
[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
Underfull \hbox (badness 5022) in paragraph at lines 5290--5293
[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2005]
Underfull \hbox (badness 1975) in paragraph at lines 5339--5341
[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
the case of
[2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5925--5925
[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2014]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5987--5987
[]\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log")
[2015] [2016]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6129 ...sical N, P, K Factorial Experiment}{npk}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again>
\relax
l.6129 ...sical N, P, K Factorial Experiment}{npk}
[2017]
Underfull \hbox (badness 1783) in paragraph at lines 6247--6251
[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space.
That is
[2018] [2019] [2020] [2021]
Underfull \vbox (badness 10000) has occurred while \output is active [2022]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6545--6545
[] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[]
[2023]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2024] [2025] [2026] [2027] [2028] [2029]
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[]\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[]
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[] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2030]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
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[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2031]
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2032] [2033]
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\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2034] [2035]
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[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2036]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2037] [2038] [2039] [2040] [2041] [2042]
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
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[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2043] [2044]
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[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
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[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055]
[2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9501--9501
[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2065]
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[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
"Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2066]
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[]\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25)
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[]\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9715--9715
[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
[2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077]
[2078] [2079]) (./Matrix-pkg.tex [2080]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 42--45
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2081]
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[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2082]
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[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
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\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2083]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
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[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2084] [2085]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 487--487
[]\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE)
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[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal
mean-ing as in
[2086]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
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[]\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[]
[2087] [2088]
Underfull \hbox (badness 3189) in paragraph at lines 681--685
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2089]
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[]\T1/ptm/m/n/10 In some ver-sions of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 eigen[][][](CAex) \T1/ptm/m/n/10 fell into an in-fi-nite loop (where
as
[2090] [2091]
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[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2092]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
Underfull \hbox (badness 10000) in paragraph at lines 971--976
[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of
the lower tri-
Underfull \hbox (badness 10000) in paragraph at lines 971--976
\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
de-com-po-si-tion. This method is equiv-a-lent to
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\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in
the above de-scrip-tion of
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical")
[2093]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again>
\relax
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again>
\relax
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
[2094pdfTeX warning (ext4):
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1082 \end{Description}
pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate i
gnored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1082 \end{Description}
pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate i
gnored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1082 \end{Description}
] [2095]
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[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2096]
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[]\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
0, ...)
[2097]
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[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
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[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2098]
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[]\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[]
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[]\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[]
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[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
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[]\T1/pcr/m/n/9 ## each has a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n
/9 matrix %% FIXME !! --- "check" them __unfinished__[]
[2099]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky", ...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3861) in paragraph at lines 1457--1464
\T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1492--1496
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
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\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2100]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again>
\relax
l.1549 ... Row and Column Sums and Means}{colSums}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again>
\relax
l.1549 ... Row and Column Sums and Means}{colSums}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.1550 \aliasA{colMeans}{colSums}{colMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again>
\relax
l.1571 \aliasA{rowMeans}{colSums}{rowMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again>
\relax
l.1582 \aliasA{rowSums}{colSums}{rowSums}
[2101] [2102]
Underfull \hbox (badness 3547) in paragraph at lines 1757--1760
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
, the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2103] [2104] [2105] [2106]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2107]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
Underfull \hbox (badness 3068) in paragraph at lines 2177--2181
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
or sim-i-lar. Of-ten how-ever, more eas-ily via
[2108]
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[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2109]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10
or
[2110] [2111]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix", ...)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
Underfull \hbox (badness 2707) in paragraph at lines 2486--2490
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
[2112]
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[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
If miss-ing,
[2113]
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[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
[2114]
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[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
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[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
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[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
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[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2115]
Underfull \hbox (badness 1371) in paragraph at lines 2857--2863
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 :
the re-sult is from class
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[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 2874--2878
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2116] [2117]
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[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
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[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2118]
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[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
, via
[2119] [2120]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix", ...) \T1/ptm/m/n/10 or
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[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 .
[2121]
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[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2122] [2123]
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[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3573--3578
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 10000) in paragraph at lines 3583--3585
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
triv-ial
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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
if
[2124]
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[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
Underfull \hbox (badness 10000) in paragraph at lines 3696--3699
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
[2125]
Underfull \hbox (badness 6364) in paragraph at lines 3700--3703
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2126]
Underfull \hbox (badness 4060) in paragraph at lines 3817--3820
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse
tri-an-gu-lar solve (aka
[2127]
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[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
Underfull \hbox (badness 3635) in paragraph at lines 3923--3927
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
Underfull \hbox (badness 10000) in paragraph at lines 3932--3935
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 3932--3935
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
[2128]
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[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2129] [2130] [2131] [2132]
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[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite
Tay-lor se-ries
[2133] [2134]
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[] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[]
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[] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[]
[2135] [2136] [2137] [2138]
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[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2139]
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[]\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons"
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[] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2,
dimnames=dns))[]
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[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
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[] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[]
[2140] [2141]
Underfull \hbox (badness 4120) in paragraph at lines 4892--4895
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4921--4921
[]\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[]
[2142]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4926--4926
[]\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[]
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[]\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[]
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[] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[]
[2143]
Underfull \hbox (badness 1817) in paragraph at lines 5024--5033
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
the
Underfull \hbox (badness 5637) in paragraph at lines 5065--5067
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2144]
Underfull \hbox (badness 3138) in paragraph at lines 5091--5093
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2145]
Underfull \hbox (badness 1603) in paragraph at lines 5175--5177
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2146] [2147] [2148]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5411--5411
[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[]
[2149]
Underfull \hbox (badness 10000) in paragraph at lines 5487--5490
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5498--5498
[]\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[]
[2150]
Underfull \hbox (badness 1622) in paragraph at lines 5535--5540
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
\T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
Underfull \hbox (badness 1418) in paragraph at lines 5535--5540
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2151] [2152]
Underfull \hbox (badness 1062) in paragraph at lines 5720--5723
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2153]
Underfull \hbox (badness 2809) in paragraph at lines 5749--5752
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2154]
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[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 5861--5866
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 5869--5872
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2155]
Underfull \hbox (badness 1184) in paragraph at lines 6042--6045
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2156] [2157]
Underfull \hbox (badness 10000) in paragraph at lines 6140--6143
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2158]
Underfull \hbox (badness 10000) in paragraph at lines 6215--6218
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6231--6231
[]\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
Underfull \hbox (badness 2443) in paragraph at lines 6269--6275
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
Underfull \hbox (badness 1776) in paragraph at lines 6269--6275
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
sin-gu-lar,
[2159]
Underfull \hbox (badness 1675) in paragraph at lines 6286--6289
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6344--6344
[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2160] [2161]
Underfull \hbox (badness 6268) in paragraph at lines 6480--6483
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2162]
Underfull \hbox (badness 5036) in paragraph at lines 6504--6508
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
. How-ever,
Underfull \hbox (badness 10000) in paragraph at lines 6504--6508
\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2163]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again>
\relax
l.6596 \aliasA{det}{Matrix-class}{det}
Underfull \hbox (badness 1348) in paragraph at lines 6670--6673
[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
Underfull \hbox (badness 10000) in paragraph at lines 6675--6678
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
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[2164] [2165]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn..Rpcent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again>
\relax
l.6761 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again>
\relax
l.6851 ...A{crossprod}{matrix-products}{crossprod}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again>
\relax
l.6933 ...tcrossprod}{matrix-products}{tcrossprod}
Underfull \hbox (badness 1881) in paragraph at lines 7015--7021
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
Underfull \hbox (badness 10000) in paragraph at lines 7068--7071
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 7068--7071
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 5637) in paragraph at lines 7071--7076
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2166pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7076 \item[crossprod]
\code{signature(x = "dgeMatrix", y = "dgeMatrix")}:pdfT
eX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rd
ash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7076 \item[crossprod]
\code{signature(x = "dgeMatrix", y = "dgeMatrix")}:]
Underfull \hbox (badness 10000) in paragraph at lines 7080--7082
[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10
and
[2167]
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[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2168]
Underfull \hbox (badness 2809) in paragraph at lines 7237--7240
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 10000) in paragraph at lines 7289--7291
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2169]
Underfull \hbox (badness 1406) in paragraph at lines 7329--7333
[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
Underfull \hbox (badness 1019) in paragraph at lines 7329--7333
\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2170] [2171]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7427--7427
[]\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[]
Underfull \hbox (badness 2635) in paragraph at lines 7492--7497
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 7492--7497
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 7500--7503
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2172] [2173]
Underfull \hbox (badness 10000) in paragraph at lines 7686--7688
[]\T1/ptm/m/n/10 fast
[2174]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again>
\relax
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again>
\relax
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
[2175] [2176]
Underfull \hbox (badness 1184) in paragraph at lines 7971--7974
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2177]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2178]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
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[]\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
[2179] [2180]
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[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 :
co-er-cion to sparse
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\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2181]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
[2182]
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[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2183]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}
) has been already used, duplicate ignored
<to be read again>
\relax
l.8488 \aliasA{qr}{qr-methods}{qr}
[2184]
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[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
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[] \T1/pcr/m/n/9 c1=rep(c(1,0,0), 2), c2=rep(c(0,1,0), 2), c3
=rep(c(0,0,1),2)),[]
[2185]
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
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[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2186]
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[]\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
free"[]
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[]\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # wa
rning + ~1.5 sec[]
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[]\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.8723 ... the Reciprocal Condition Number}{rcond}
[2187] [2188]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2189] [2190] [2191]
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[]\T1/ptm/m/n/10 the ran-dom num-ber gen-er-a-tor for the \T1/pcr/m/n/10 x \T1/
ptm/m/n/10 slot, a [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 such that
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[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
[2192] [2193]
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[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2194]
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[] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[]
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[]\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[]
[2195]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again>
\relax
l.9292 \aliasA{solve}{solve-methods}{solve}
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[] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[]
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[] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[]
[2196]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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[]\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2197]
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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[]\T1/ptm/m/n/10 works via
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via
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[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and
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[]\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][]
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[] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
[FIXME ??] only[]
[2198]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
er-ca-ble to)
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\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
[2199]
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[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
[2200]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
== c(3, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2201]
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[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2202]
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[] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij =
FALSE)[]
[2203]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2204]
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[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
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[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
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[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
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[]\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x =
1:6, dimnames = dn)[]
[2205]
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[]\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[]
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[] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
X@dimension)[]
[2206]
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[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject
of S3 class
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[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
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[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or
[2207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again>
\relax
l.10284 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2208]
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[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
[2209]
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[] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[]
[2210]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.toe
plitz}) has been already used, duplicate ignored
<to be read again>
\relax
l.10559 ...toeplitz}{sparseVector-class}{toeplitz}
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[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-
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\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
[2211]
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[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
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[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or
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[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2212] [2213]
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[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
[2214]
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\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2215]
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[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2216]
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[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
vir-tual class of all sparse ma-tri-ces coded in
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\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2217] [2218] [2219]
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[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
sparse ma-trix (i.e., of sub-class of
[2220]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
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[]\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x =
1:6, dimnames = dn)[]
[2221] [2222]
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2223] [2224]) (./boot-pkg.tex
Chapter 18.
[2225] [2226] [2227] [2228] [2229] [2230] [2231]
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[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2232]
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[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
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\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2233]
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[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2234]
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\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2235]
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[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
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[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2236]
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[]\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt,
data = nuke)[]
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[2238]
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[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
[2239]
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[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
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\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2240] [2241] [2242] [2243] [2244]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2245] [2246] [2247] [2248]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2249] [2250] [2251] [2252]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
Underfull \vbox (badness 10000) has occurred while \output is active [2253]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2254] [2255] [2256] [2257]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
[2258]
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2437--2438
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2259]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
sam-ple
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\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
is used. This is mul-ti-plied by
[2260] [2261] [2262] [2263] [2264]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
[]\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,
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[]\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,[]
[2265] [2266] [2267]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2268]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2269] [2270] [2271]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
[2272] [2273] [2274] [2275] [2276] [2277] [2278]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2279] [2280]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2281] [2282] [2283]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault
is
[2284]
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[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2285] [2286]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
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\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294] [2295]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2296] [2297] [2298] [2299]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2300]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2301] [2302] [2303] [2304] [2305] [2306] [2307] [2308]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5861--5861
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2309]
Underfull \hbox (badness 1127) in paragraph at lines 5983--6001
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2310]
Underfull \hbox (badness 2837) in paragraph at lines 6016--6019
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2311] [2312] [2313] [2314]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6301--6301
[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2315] [2316]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6490--6490
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6492--6492
[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
[2317] [2318] [2319]
Underfull \hbox (badness 1596) in paragraph at lines 6737--6741
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2320] [2321]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6897--6897
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2322] [2323] [2324] [2325] [2326] [2327] [2328] [2329]) (./class-pkg.tex
[2330]
Chapter 19.
[2331] [2332] [2333] [2334] [2335] [2336] [2337] [2338]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2339] [2340] [2341] [2342] [2343] [2344] [2345] [2346]) (./cluster-pkg.tex
Chapter 20.
[2347]
Underfull \hbox (badness 10000) in paragraph at lines 133--140
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when
us-ing \T1/pcr/m/n/10 method = "flexible"
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 par-tic-u-larly for the case when \T1/pcr/m/n/10 par.method \T1/
ptm/m/n/10 is spec-i-fied of longer length
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 than one. The \T1/ptm/m/it/10 weighted av-er-age \T1/ptm/m/n/10
(\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n/10 . Fur-ther, \T
1/pcr/m/n/10 method= "single" \T1/ptm/m/n/10 is
Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c
(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 .
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 165--167
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2349]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 250--250
[] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC]) ,[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 251--251
[] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, -.5))[iC]),[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 252--252
[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
[2350] [2351]
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[2353]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 516--516
[] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
= axes,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 520--520
[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2354]
Underfull \hbox (badness 5374) in paragraph at lines 537--539
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2355] [2356]
Underfull \hbox (badness 3078) in paragraph at lines 680--683
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2357]
Underfull \hbox (badness 2941) in paragraph at lines 761--764
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10
,
[2358]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 799--799
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
[2359]
Underfull \hbox (badness 10000) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
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[]\T1/pcr/m/n/10 clusGap(x, FUNcluster, K.max, B = 100, verbose = interactive(
), ...)
[2360]
Underfull \hbox (badness 4872) in paragraph at lines 934--936
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
[2361]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1036--1036
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
[2362] [2363]
Underfull \hbox (badness 4144) in paragraph at lines 1112--1116
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
e.g., for
[2364]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1188--1188
[] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
cex.txt = cex,[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1194--1194
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2365] [2366]
Underfull \hbox (badness 10000) in paragraph at lines 1394--1398
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
[2367]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1412--1412
[]\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1421--1421
[] \T1/pcr/m/n/9 axes=FALSE,ann=FALSE, sub="", col.p=NA, col.txt="dark
green", labels=3)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1429--1429
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2368]
Underfull \hbox (badness 5741) in paragraph at lines 1469--1472
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2369] [2370]
Underfull \hbox (badness 5008) in paragraph at lines 1645--1653
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1736--1736
[]\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1755--1755
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2372] [2373] [2374] [2375] [2376]
Underfull \hbox (badness 10000) in paragraph at lines 2057--2059
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
Underfull \hbox (badness 3179) in paragraph at lines 2081--2087
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2377] [2378]
Underfull \hbox (badness 10000) in paragraph at lines 2239--2242
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2379]
Underfull \hbox (badness 1292) in paragraph at lines 2307--2310
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
[2380]
Underfull \hbox (badness 6675) in paragraph at lines 2316--2318
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2339--2342
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
Overfull \vbox (12.60576pt too high) has occurred while \output is active
[2381] [2382] [2383]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2546--2546
[]\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[]
[2384] [2385] [2386]
Underfull \hbox (badness 1067) in paragraph at lines 2734--2739
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
\T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2387] [2388]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2889--2889
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2389] [2390] [2391]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3085--3085
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3086--3086
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2392]
Underfull \hbox (badness 10000) in paragraph at lines 3153--3156
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2393]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3203--3203
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3204--3204
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2394] [2395] [2396]
Underfull \hbox (badness 10000) in paragraph at lines 3389--3392
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
Underfull \hbox (badness 3471) in paragraph at lines 3389--3392
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2397]
Underfull \hbox (badness 10000) in paragraph at lines 3452--3457
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2398]
Underfull \hbox (badness 1735) in paragraph at lines 3521--3523
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "twins"\T1/ptm/m/n/10 , typ
-i-cally cre-ated by ei-ther [][]\T1/pcr/m/n/10 agnes[][][]() \T1/ptm/m/n/10 or
Underfull \hbox (badness 4621) in paragraph at lines 3538--3543
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1990) in paragraph at lines 3538--3543
\T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1
/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider
Underfull \hbox (badness 6268) in paragraph at lines 3550--3553
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2399]
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[]\T1/ptm/m/n/10 currently [][]$\T1/pcr/m/n/10 http : / / www . agoras . ua . a
c . be / datasets / clusplot-[]examples . tar .
[2400] [2401]
Underfull \hbox (badness 10000) in paragraph at lines 3733--3736
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2402]
Underfull \hbox (badness 10000) in paragraph at lines 3764--3767
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2403]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3817--3817
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
Underfull \hbox (badness 2035) in paragraph at lines 3828--3830
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2404] [2405] [2406]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4021--4021
[] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 4023--4023
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2407]
Underfull \hbox (badness 1946) in paragraph at lines 4052--4057
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
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[]\T1/ptm/m/n/10 numeric (rank 1) ar-ray of clus-ter-wise \T1/ptm/m/it/10 means
\T1/ptm/m/n/10 of sil-hou-ette widths where
[2408]
Underfull \hbox (badness 10000) in paragraph at lines 4118--4126
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4160--4160
[]\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4169--4169
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4171--4171
[] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4174--4174
[]\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4176--4176
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE,[]
[2409]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4190--4190
[] \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t
olerance = 0))[]
[2410] [2411] [2412] [2413] [2414] [2415] [2416]) (./codetools-pkg.tex
Chapter 21.
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2417]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2418]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2419] [2420] [2421]) (./foreign-pkg.tex [2422]
Chapter 22.
[2423]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2424] [2425]
Underfull \hbox (badness 3601) in paragraph at lines 234--242
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2426]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 293--293
[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2427] [2428] [2429]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 459--459
[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame)[]
[2430]
Underfull \hbox (badness 10000) in paragraph at lines 515--523
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
[2431]
Underfull \hbox (badness 7613) in paragraph at lines 533--539
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2432] [2433] [2434]
Underfull \hbox (badness 10000) in paragraph at lines 730--731
Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2435]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 816--816
[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2436]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 879--879
[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
Underfull \hbox (badness 6708) in paragraph at lines 905--908
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
www . cs . waikato . ac . nz / ~ml / weka / arff .
[2437] [2438]
Underfull \hbox (badness 10000) in paragraph at lines 989--990
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1025--1025
[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2439]
Underfull \hbox (badness 1286) in paragraph at lines 1110--1114
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates =
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2440]
Underfull \hbox (badness 10000) in paragraph at lines 1183--1189
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2441] [2442]) (./lattice-pkg.tex
Chapter 23.
[2443] [2444] [2445]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 287--287
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 291--291
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[]
[2446]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 306--306
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 314--314
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 335--335
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 339--339
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[]
[2447]
Underfull \hbox (badness 4060) in paragraph at lines 358--370
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
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\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 398--413
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
both
Underfull \hbox (badness 10000) in paragraph at lines 414--416
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
one can ei-ther set
[2448]
Underfull \hbox (badness 7631) in paragraph at lines 480--485
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2449] [2450]
Underfull \hbox (badness 1221) in paragraph at lines 651--659
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
ar-gu-ments to
[2451] [2452] [2453] [2454]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of
fac-tors will be
Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a
use-ful lay-out.
[2455]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2456] [2457]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
Underfull \hbox (badness 1917) in paragraph at lines 1239--1240
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2458] [2459] [2460]
Underfull \hbox (badness 1540) in paragraph at lines 1479--1485
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2461]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2462]
Underfull \vbox (badness 10000) has occurred while \output is active [2463]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671
[] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[]
Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2464]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
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[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10
, etc; see
[2465]
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
An-drews
[2466] [2467] [2468]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2469]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2470] [2471] [2472]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2347--2347
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2351--2351
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[]
Underfull \hbox (badness 4441) in paragraph at lines 2364--2368
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2473] [2474] [2475]
Underfull \hbox (badness 4441) in paragraph at lines 2549--2556
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2476] [2477]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2691--2691
[] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[]
[2478]
Underfull \hbox (badness 10000) in paragraph at lines 2763--2768
[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2479]
Underfull \hbox (badness 2913) in paragraph at lines 2793--2798
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2793--2798
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
Underfull \hbox (badness 6758) in paragraph at lines 2879--2883
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
Underfull \hbox (badness 7576) in paragraph at lines 2879--2883
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2885--2887
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2480]
Underfull \hbox (badness 1609) in paragraph at lines 2937--2943
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
Underfull \hbox (badness 2772) in paragraph at lines 2937--2943
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
Underfull \hbox (badness 1400) in paragraph at lines 2937--2943
\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2961--2965
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for
the de-fault panel func-tion
[2481] [2482]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
[] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3063--3063
[] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3064--3064
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3075--3075
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3087--3087
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
[2483]
Underfull \hbox (badness 10000) in paragraph at lines 3112--3120
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
Underfull \hbox (badness 2913) in paragraph at lines 3145--3152
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3145--3152
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2484] [2485] [2486] [2487]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3433 \aliasA{parallel}{B\_08\_splom}{parallel}
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3475--3475
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
[2488]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3498--3498
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2489] [2490] [2491] [2492] [2493]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3834--3834
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2494]
Underfull \hbox (badness 10000) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
Underfull \hbox (badness 2435) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2495] [2496]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4054--4054
[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
Underfull \hbox (badness 1173) in paragraph at lines 4063--4067
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
Underfull \hbox (badness 3219) in paragraph at lines 4090--4092
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
Underfull \hbox (badness 1728) in paragraph at lines 4107--4111
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2497]
Underfull \hbox (badness 5161) in paragraph at lines 4172--4176
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4172--4176
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2498] [2499]
Underfull \hbox (badness 1067) in paragraph at lines 4286--4296
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1735) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4286--4296
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
Underfull \hbox (badness 1701) in paragraph at lines 4311--4314
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4314--4316
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2500] [2501] [2502] [2503] [2504] [2505]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4718--4718
[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2506] [2507]
Underfull \hbox (badness 10000) in paragraph at lines 4905--4908
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2508] [2509]
Underfull \hbox (badness 1442) in paragraph at lines 5037--5040
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2510] [2511] [2512] [2513] [2514] [2515]
Underfull \hbox (badness 3646) in paragraph at lines 5369--5372
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 ,
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5399--5399
[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5400--5400
[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2516]
Underfull \hbox (badness 10000) in paragraph at lines 5488--5491
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
Underfull \hbox (badness 2103) in paragraph at lines 5488--5491
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
Underfull \hbox (badness 6412) in paragraph at lines 5505--5511
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
though this can be
[2517]
Underfull \hbox (badness 1635) in paragraph at lines 5514--5519
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2518]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5663--5663
[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
[2519]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5677--5677
[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5678--5678
[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5681--5681
[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5684--5684
[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5686--5686
[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5694--5694
[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5695--5695
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5696--5696
[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
Underfull \hbox (badness 10000) in paragraph at lines 5712--5714
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
[2520]
Underfull \hbox (badness 2376) in paragraph at lines 5723--5725
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2521]
Underfull \hbox (badness 2538) in paragraph at lines 5848--5852
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5859--5866
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5859--5866
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
used (in com-bi-na-tion with
[2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 6012--6016
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2524] [2525]
Underfull \hbox (badness 4242) in paragraph at lines 6159--6164
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2526] [2527]
Underfull \hbox (badness 3601) in paragraph at lines 6275--6280
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6275--6280
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2528] [2529]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6362--6362
[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2530]
Underfull \hbox (badness 1888) in paragraph at lines 6494--6501
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2531]
Underfull \hbox (badness 10000) in paragraph at lines 6551--6554
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
Underfull \hbox (badness 1558) in paragraph at lines 6551--6554
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2532]
Underfull \hbox (badness 1005) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
Underfull \hbox (badness 1571) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2533] [2534] [2535] [2536] [2537]
Underfull \hbox (badness 1320) in paragraph at lines 6957--6964
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 6957--6964
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
ef-fi-cient. When us-ing
[2538]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7027--7027
[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
[2539]
Underfull \hbox (badness 10000) in paragraph at lines 7057--7060
[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
to
Underfull \hbox (badness 1584) in paragraph at lines 7057--7060
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2540]
Underfull \hbox (badness 10000) in paragraph at lines 7161--7164
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2541] [2542]
Underfull \hbox (badness 2012) in paragraph at lines 7327--7330
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2543]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7373--7373
[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2544] [2545]
Underfull \hbox (badness 2644) in paragraph at lines 7514--7518
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on
to
Underfull \hbox (badness 2772) in paragraph at lines 7527--7530
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a
list of ar-gu-ments to be sup-plied to
Underfull \hbox (badness 4242) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
Underfull \hbox (badness 1147) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
co-erced to a list. This al-lows ar-
Underfull \hbox (badness 2351) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
Underfull \hbox (badness 1675) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1
/ptm/m/n/10 , which adds the
Underfull \hbox (badness 1769) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
e.g.,
[2546]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7597--7597
[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7607--7607
[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2547]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7668--7668
[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7673--7673
[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2548] [2549] [2550]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7854--7854
[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2551]
Underfull \hbox (badness 1436) in paragraph at lines 7909--7915
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
Underfull \hbox (badness 1231) in paragraph at lines 7909--7915
\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2552] [2553] [2554] [2555] [2556] [2557] [2558] [2559]
Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2560] [2561]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8642--8642
[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8643--8643
[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8655--8655
[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
[2562]
Underfull \hbox (badness 3118) in paragraph at lines 8674--8677
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2563]
Underfull \hbox (badness 1515) in paragraph at lines 8750--8754
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2564]
Underfull \hbox (badness 6316) in paragraph at lines 8856--8861
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2565] [2566]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8963--8963
[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2567] [2568]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9102--9102
[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2569]
Overfull \hbox (84.94879pt too wide) in paragraph at lines 9161--9165
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left, right, left.name, right.name, condition
Overfull \hbox (104.63074pt too wide) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left, right.x, right.y, left.name
, right.x.name, right.y.name, condition
[2570] [2571] [2572] [2573] [2574] [2575] [2576]
Underfull \hbox (badness 4205) in paragraph at lines 9619--9623
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4518) in paragraph at lines 9619--9623
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2577] [2578] [2579]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9850 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2580] [2581] [2582] [2583])
(./mgcv-pkg.tex [2584]
Chapter 24.
Underfull \hbox (badness 1052) in paragraph at lines 40--42
[]\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term
p-values. See
[2585] [2586]
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[]\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,
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[] \T1/pcr/m/n/10 chunk.size=10000,rho=0,AR.start=NULL,sparse=FALSE,cluster
=NULL,[]
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[] \T1/pcr/m/n/10 gc.level=1,use.chol=FALSE,samfrac=1,drop.unused.levels=TR
UE,...)[]
[2587]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2588]
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[]\T1/ptm/m/n/10 If all smooths are P-splines and all ten-sor prod-ucts are of
the form
[2589] [2590]
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2591] [2592] [2593]
Underfull \hbox (badness 2922) in paragraph at lines 521--522
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
Underfull \hbox (badness 1158) in paragraph at lines 563--565
[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2594] [2595]
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[2597] [2598] [2599] [2600]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 982--982
[]\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[]
[2601] [2602] [2603] [2604] [2605] [2606] [2607]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1382--1382
[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2608] [2609] [2610] [2611] [2612] [2613]
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\T1/ptm/m/n/10 de-grees of free-dom (mix-tures of the two are per-mit-ted). Mul
ti-dimensional smooths are
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[]\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[]
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[] \T1/pcr/m/n/10 fit=TRUE,paraPen=NULL,G=NULL,in.out,drop.unused.levels=TR
UE,...)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2614]
Underfull \hbox (badness 1043) in paragraph at lines 1806--1811
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2615] [2616]
Underfull \hbox (badness 1043) in paragraph at lines 1966--1972
\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2619]
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[2623] [2624] [2625] [2626] [2627] [2628]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2720--2720
[] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
[] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[]
[2629] [2630] [2631] [2632] [2633]
Underfull \hbox (badness 5189) in paragraph at lines 3038--3042
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2634] [2635]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3155--3155
[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[2637] [2638] [2639] [2640] [2641] [2642] [2643] [2644]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3709--3709
[] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[]
[2645] [2646]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3824--3824
[]\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[]
Underfull \hbox (badness 1142) in paragraph at lines 3855--3859
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2647] [2648] [2649]
Underfull \hbox (badness 5970) in paragraph at lines 4035--4041
[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
[2650]
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[2652] [2653]
Underfull \hbox (badness 1577) in paragraph at lines 4280--4283
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
Underfull \hbox (badness 2181) in paragraph at lines 4287--4288
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
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[2665]
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[2667] [2668]
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[]\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
to rule the world.",[]
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[] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[]
[2669] [2670] [2671] [2672] [2673] [2674] [2675] [2676] [2677] [2678] [2679]
[2680] [2681] [2682] [2683] [2684] [2685] [2686] [2687] [2688] [2689] [2690]
[2691] [2692] [2693]
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[2695]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2696]
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[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 3108) in paragraph at lines 6979--6982
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
be
[2697] [2698] [2699]
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[]\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s
cale=-1,[]
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[] \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla
b=NULL,[]
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[] \T1/pcr/m/n/10 shift=0,trans=I,seWithMean=FALSE,unconditional=FALSE
,by.resids=FALSE,[]
[2700] [2701] [2702]
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\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
some-times to clone the
[2703] [2704] [2705]
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[] \T1/pcr/m/n/10 block.size=50000,newdata.guaranteed=FALSE,na.action=n
a.pass,cluster=NULL,...)[]
[2706] [2707]
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[] \T1/pcr/m/n/10 block.size=NULL,newdata.guaranteed=FALSE,na.action=na
.pass,[]
[2708] [2709] [2710]
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[] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[]
[2712]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2713]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
[2714]
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2715] [2716]
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[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion
cri-te-rion re-ported is one of GCV,
[2717] [2718] [2719] [2720]
Underfull \hbox (badness 1946) in paragraph at lines 8450--8457
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
Underfull \hbox (badness 2042) in paragraph at lines 8450--8457
\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
Underfull \hbox (badness 5862) in paragraph at lines 8458--8461
\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2721]
Underfull \hbox (badness 10000) in paragraph at lines 8537--8540
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
"deviance"\T1/ptm/m/n/10 ,
[2722] [2723] [2724] [2725] [2726] [2727] [2728] [2729]
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[] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[]
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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2730] [2731]
Underfull \hbox (badness 1803) in paragraph at lines 9132--9136
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 9144--9156
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
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\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able.
Plot meth-ods can be
Underfull \hbox (badness 2970) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2732] [2733] [2734]
Underfull \hbox (badness 6876) in paragraph at lines 9354--9360
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one
or two vari-ables, spec-i-fied via terms like
[2735]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2736] [2737]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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\T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs",
...) \T1/ptm/m/n/10 or
[2738] [2739]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2740] [2741]
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[]\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first
deriv penalty[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9734--9734
[]\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[]
Underfull \hbox (badness 7613) in paragraph at lines 9772--9775
\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2742] [2743] [2744] [2745]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9985--9985
[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[2746]
Underfull \hbox (badness 10000) in paragraph at lines 10030--10032
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2747] [2748]
Underfull \hbox (badness 10000) in paragraph at lines 10138--10141
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method
a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 10138--10141
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 10138--10141
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[2749]
Underfull \hbox (badness 10000) in paragraph at lines 10237--10243
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 2698) in paragraph at lines 10237--10243
\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[2750] [2751] [2752]
Underfull \vbox (badness 10000) has occurred while \output is active [2753]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10451--10451
[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10453--10453
[] \T1/pcr/m/n/9 te(v,w,t,bs=c("sf","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))+[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 10454--10454
[] \T1/pcr/m/n/9 te(v,w,t,bs=c("sw","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))[]
Underfull \vbox (badness 10000) has occurred while \output is active [2754]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 10535--10535
[]\T1/pcr/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax)
),knots=knots,method="REML")[]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 10541--10541
[] \T1/pcr/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax))
,knots=knots,method="REML")[]
[2755]
Underfull \hbox (badness 10000) in paragraph at lines 10555--10563
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the
sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 10581--10582
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2756] [2757]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 10683--10683
[]\T1/pcr/m/n/9 bk <- gam(y~s(la,lo,bs="sos",k=60),knots=list(la=dat$la[ind],l
o=dat$lo[ind]),data=dat)[]
[2758] [2759]
Underfull \hbox (badness 3396) in paragraph at lines 10841--10846
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any
num-ber of vari-ables, spec-i-fied via terms like
[2760]
Underfull \hbox (badness 10000) in paragraph at lines 10886--10888
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2761] [2762] [2763] [2764]
Underfull \hbox (badness 10000) in paragraph at lines 11074--11077
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
Underfull \hbox (badness 3068) in paragraph at lines 11074--11077
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
Underfull \hbox (badness 10000) in paragraph at lines 11107--11111
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 5652) in paragraph at lines 11107--11111
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , code[][]soap[][][], code[][]Spheri
cal.Spline[][][], [][]\T1/pcr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 ,
[2765] [2766]
Underfull \hbox (badness 2158) in paragraph at lines 11259--11259
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2767] [2768]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 11334--11334
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[2769] [2770]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11468--11468
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[2771] [2772]
Underfull \hbox (badness 4846) in paragraph at lines 11604--11607
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or
es-ti-ma-tors if
[2773] [2774] [2775] [2776] [2777] [2778] [2779] [2780] [2781] [2782] [2783]
[2784] [2785] [2786] [2787]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 12501--12501
[]\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[]
[2788] [2789] [2790] [2791] [2792] [2793] [2794]) (./nlme-pkg.tex
Chapter 25.
[2795]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2796]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2797] [2798] [2799] [2800] [2801]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
[] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[2802] [2803] [2804] [2805] [2806] [2807] [2808] [2809] [2810] [2811]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1094--1094
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[]
[2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819]
Underfull \hbox (badness 10000) in paragraph at lines 1633--1636
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[2820]
Underfull \hbox (badness 3780) in paragraph at lines 1650--1652
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[2821] [2822] [2823] [2824] [2825]
Underfull \hbox (badness 2042) in paragraph at lines 1997--2003
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[2826]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2059--2059
[]\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla
pse = "Dog")[]
[2827]
Underfull \hbox (badness 1132) in paragraph at lines 2147--2149
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[2828] [2829]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[2830]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[2831] [2832] [2833] [2834] [2835] [2836] [2837] [2838]
Underfull \hbox (badness 10000) in paragraph at lines 2846--2850
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849]
[2850]
Underfull \hbox (badness 6493) in paragraph at lines 3582--3590
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[2851] [2852] [2853] [2854] [2855] [2856] [2857] [2858] [2859] [2860] [2861]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 4348--4348
[]\T1/pcr/m/n/10 fdHess(pars, fun, ..., .relStep=(.Machine$double.eps)^(1/3),
minAbsPar=0)
[2862] [2863] [2864] [2865] [2866] [2867] [2868] [2869] [2870] [2871] [2872]
[2873] [2874]
Underfull \hbox (badness 10000) in paragraph at lines 5158--5162
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[2875] [2876] [2877] [2878] [2879]
Underfull \hbox (badness 10000) in paragraph at lines 5475--5479
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
Underfull \hbox (badness 2671) in paragraph at lines 5475--5479
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[2880] [2881]
Underfull \hbox (badness 10000) in paragraph at lines 5590--5593
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890]
Underfull \hbox (badness 2799) in paragraph at lines 6096--6102
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[2891]
Underfull \hbox (badness 7133) in paragraph at lines 6157--6161
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2892]
Underfull \hbox (badness 2057) in paragraph at lines 6241--6252
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[2893]
Underfull \hbox (badness 10000) in paragraph at lines 6305--6307
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6334--6334
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2894] [2895] [2896] [2897]
Underfull \hbox (badness 7133) in paragraph at lines 6553--6557
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2898]
Underfull \hbox (badness 10000) in paragraph at lines 6652--6658
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
[2899]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6718
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2900]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6743--6743
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2901] [2902] [2903]
Underfull \hbox (badness 10000) in paragraph at lines 6986--6993
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7003--7003
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7011--7011
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
[2904]
Underfull \hbox (badness 2875) in paragraph at lines 7033--7035
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[2905] [2906] [2907]
Underfull \hbox (badness 10000) in paragraph at lines 7248--7253
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[2908] [2909]
Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 1817) in paragraph at lines 7400--7408
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that
20 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7423--7426
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[2910] [2911] [2912] [2913]
Underfull \hbox (badness 3354) in paragraph at lines 7638--7640
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
which \T1/ptm/m/n/10 is not equal to
[2914] [2915] [2916] [2917] [2918] [2919]
Underfull \hbox (badness 1642) in paragraph at lines 8030--8052
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2920] [2921]
Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8193--8193
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
Underfull \hbox (badness 1642) in paragraph at lines 8202--8224
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2922] [2923] [2924] [2925] [2926]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8466--8466
[]\T1/pcr/m/n/10 lmeControl(maxIter, msMaxIter, tolerance, niterEM, msMaxEval,
msTol,
Underfull \hbox (badness 10000) in paragraph at lines 8509--8511
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2927]
Underfull \hbox (badness 1320) in paragraph at lines 8522--8526
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][] \T1/ptm/m/n/10 (those from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8544--8544
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2928] [2929] [2930]
Underfull \hbox (badness 10000) in paragraph at lines 8707--8719
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[2931] [2932] [2933] [2934] [2935] [2936] [2937] [2938] [2939]
Underfull \hbox (badness 10000) in paragraph at lines 9297--9304
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9308--9308
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[2940]
Underfull \hbox (badness 6300) in paragraph at lines 9390--9393
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[2941] [2942] [2943] [2944]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again>
\relax
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[2945]
Underfull \hbox (badness 10000) in paragraph at lines 9679--9682
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
[2946]
Underfull \hbox (badness 3108) in paragraph at lines 9727--9730
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
Underfull \hbox (badness 2521) in paragraph at lines 9727--9730
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[2947] [2948]
Underfull \hbox (badness 2435) in paragraph at lines 9900--9905
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[2949] [2950] [2951] [2952] [2953]
Underfull \hbox (badness 7291) in paragraph at lines 10190--10192
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[2954] [2955] [2956]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10406--10406
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[2957]
Underfull \hbox (badness 1596) in paragraph at lines 10435--10461
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[2958] [2959] [2960]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10611--10611
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[2961] [2962] [2963]
Underfull \hbox (badness 10000) in paragraph at lines 10808--10810
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Underfull \hbox (badness 1092) in paragraph at lines 10818--10821
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10840--10840
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[2964] [2965] [2966]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10996--10996
[]\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool)
[2967]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11091--11091
[]\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool)[]
[2968] [2969] [2970] [2971] [2972] [2973] [2974] [2975] [2976] [2977] [2978]
Underfull \hbox (badness 6268) in paragraph at lines 11852--11862
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[2979] [2980] [2981] [2982]
Underfull \hbox (badness 10000) in paragraph at lines 12113--12119
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[2983] [2984] [2985] [2986] [2987] [2988] [2989]
Underfull \hbox (badness 2452) in paragraph at lines 12576--12583
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[2990]
Underfull \hbox (badness 10000) in paragraph at lines 12641--12647
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001]
[3002] [3003] [3004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13593--13593
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3005]
Underfull \hbox (badness 10000) in paragraph at lines 13620--13623
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 6016) in paragraph at lines 13648--13651
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13648--13651
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13655--13658
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13663--13670
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13663--13670
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
[3006]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13720--13720
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
Underfull \hbox (badness 10000) in paragraph at lines 13727--13730
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13727--13730
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
[3007]
Underfull \hbox (badness 4582) in paragraph at lines 13755--13758
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13755--13758
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,
"labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13759--13762
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3008]
Underfull \hbox (badness 10000) in paragraph at lines 13835--13838
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 1472) in paragraph at lines 13860--13867
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3009]
Underfull \hbox (badness 10000) in paragraph at lines 13929--13931
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3010] [3011] [3012] [3013]
Underfull \hbox (badness 1540) in paragraph at lines 14144--14149
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
Underfull \hbox (badness 1215) in paragraph at lines 14191--14193
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
De-faults to
[3014] [3015] [3016] [3017] [3018]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14434--14434
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been
already used, duplicate ignored
<to be read again>
\relax
l.15072 ...Extract Random Effects}{random.effects}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again>
\relax
l.15072 ...Extract Random Effects}{random.effects}
[3028] [3029] [3030]
[3031] [3032] [3033] [3034] [3035] [3036] [3037]
Underfull \hbox (badness 1009) in paragraph at lines 15729--15738
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3038] [3039] [3040]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15876--15876
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3041] [3042] [3043] [3044]
Underfull \hbox (badness 10000) in paragraph at lines 16154--16172
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16154--16172
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3045]
Underfull \hbox (badness 10000) in paragraph at lines 16211--16217
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 1728) in paragraph at lines 16731--16734
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3054] [3055] [3056] [3057] [3058]
Underfull \hbox (badness 1867) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal"
Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3059]
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 ,
[3060] [3061] [3062] [3063]
Underfull \hbox (badness 10000) in paragraph at lines 17375--17382
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3064] [3065] [3066] [3067] [3068] [3069] [3070]
Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3071]
Underfull \hbox (badness 3579) in paragraph at lines 17942--17947
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3072]
Underfull \hbox (badness 3579) in paragraph at lines 18006--18011
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3073]
Underfull \hbox (badness 3579) in paragraph at lines 18069--18074
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3074]
Underfull \hbox (badness 1577) in paragraph at lines 18130--18132
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
Underfull \hbox (badness 3579) in paragraph at lines 18132--18137
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3075]
Underfull \hbox (badness 3579) in paragraph at lines 18195--18200
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3076]
Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3579) in paragraph at lines 18267--18272
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3077] [3078]
Underfull \hbox (badness 1009) in paragraph at lines 18416--18425
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3079] [3080] [3081]
Underfull \hbox (badness 1009) in paragraph at lines 18550--18559
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089]) (./nnet-pkg.tex
[3090]
Chapter 26.
[3091]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3092] [3093] [3094] [3095]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 383--383
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 440--440
[]\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 443--443
[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3096]
Underfull \hbox (badness 4013) in paragraph at lines 488--491
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if
the net was gen-er-ated by
[3097]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 523--523
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3098]) (./rpart-pkg.tex
Chapter 27.
[3099] [3100] [3101] [3102]
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[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3103]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3104] [3105] [3106]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
at the hor-i-zon-tal plot co-or-di-nates of
[3107] [3108]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
[3109]
Underfull \hbox (badness 2941) in paragraph at lines 785--787
[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
if
[3110]
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[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
[3111]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921
[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[]
[3112] [3113] [3114]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
[]\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164
[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3115]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3116]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270
[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286
[]\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01,
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287
[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
[3117] [3118] [3119] [3120] [3121] [3122]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3123] [3124]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3125] [3126] [3127]) (./spatial-pkg.tex [3128]
Chapter 28.
[3129] [3130] [3131] [3132] [3133] [3134]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3135] [3136] [3137] [3138] [3139] [3140] [3141] [3142] [3143] [3144] [3145]
[3146] [3147]) (./survival-pkg.tex [3148]
Chapter 29.
[3149] [3150]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171
[]\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
= lung, nmin = 1[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190
[]\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t
he last point[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193
[]\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a
nd Grambsch.[]
[3151]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 226--226
[]\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)
Overfull \hbox (42.78088pt too wide) in paragraph at lines 227--227
[]\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
been already used, duplicate ignored
<to be read again>
\relax
l.267 ... Myelogenous Leukemia survival data}{aml}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again>
\relax
l.267 ... Myelogenous Leukemia survival data}{aml}
[3152] [3153]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 364--364
[]\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian)
Overfull \hbox (4.38043pt too wide) in paragraph at lines 366--366
[]\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[]
[3154]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 403--403
[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3155] [3156]
Underfull \vbox (badness 10000) has occurred while \output is active [3157]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 597--597
[]\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size,
Overfull \hbox (48.78088pt too wide) in paragraph at lines 598--598
[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3158] [3159]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 741--741
[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3160] [3161]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 891--891
[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3162]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again>
\relax
l.957 ...herapy for Stage B/C colon cancer}{colon}
[3163] [3164] [3165]
[3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1747--1747
[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
[3174] [3175]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1877--1877
[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3176] [3177] [3178] [3179]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2159--2159
[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
Underfull \hbox (badness 1389) in paragraph at lines 2172--2174
[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
[3180] [3181]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2274--2274
[]\T1/pcr/m/n/9 lines(fit[1], lwd=2, xscale=365.24) #darken the first curve
and add marks[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2280--2280
[]\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[]
[3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2916--2916
[] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[]
[3192] [3193]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3072--3072
[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3194] [3195]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3163--3163
[]\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[]
[3196]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3253--3253
[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3197] [3198]
Underfull \hbox (badness 1852) in paragraph at lines 3401--3403
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3199] [3200]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3534--3534
[]\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod,
[3201] [3202]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3694--3694
[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3203]
Underfull \hbox (badness 1540) in paragraph at lines 3749--3752
[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
[3204]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3792--3792
[]\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age
+ sex, mgus,[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3813--3813
[]\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3815--3815
[]\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[]
[3205] [3206]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3960--3960
[]\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[]
[3207] [3208] [3209] [3210] [3211]
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[]\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[]
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[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4299--4304
\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4299--4304
\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3212] [3213]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4407--4407
[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4408--4408
[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[]
[3214] [3215] [3216] [3217] [3218] [3219] [3220]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4910--4910
[] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[]
[3221] [3222] [3223]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
form
[3224] [3225]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5280--5280
[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
Underfull \hbox (badness 1038) in paragraph at lines 5322--5328
\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
Underfull \hbox (badness 3000) in paragraph at lines 5341--5343
[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3226]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5371--5371
[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3227]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5457--5457
[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3228] [3229]
Underfull \hbox (badness 10000) in paragraph at lines 5591--5595
[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5611--5611
[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[]
[3230] [3231] [3232]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3233]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3234] [3235]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3236] [3237]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6246--6246
[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3238]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3239] [3240]
Underfull \hbox (badness 2035) in paragraph at lines 6463--6470
\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 6463--6470
\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1297) in paragraph at lines 6463--6470
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3241]
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[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3242] [3243] [3244]
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[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3245] [3246]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813
[] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6816--6816
[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3247] [3248] [3249] [3250]
Underfull \vbox (badness 10000) has occurred while \output is active [3251]
[3252]) (./fullrefman.ind [3253] [3254] [3255] [3256] [3257] [3258] [3259]
[3260] [3261] [3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270]
[3271] [3272]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2139--2141
[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 ,
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mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/html
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/html'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
installing doc/manual ...
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual/images
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/etc'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc
installing etc ...
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/etc'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/share'
installing share ...
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/R
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/dictionaries
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/encodings
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/java
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/licenses
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/make
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/sh
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/bibtex/bib
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/bibtex/bst
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/tex/latex
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/share'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/bin
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/include'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/include/R
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/include/R_ext'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/include/R_ext'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/include'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/blas'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/blas'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/bzip2'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/bzip2'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/pcre'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/pcre'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/xdr'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/xdr'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/xz'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/xz'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/zlib'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/zlib'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/intl'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/intl'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -L/usr/local/lib64 -DR_HOME='"/usr/lib64/R"' \
-o Rscript ./Rscript.c
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/pkgconfig
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/exec
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/modules
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/library
installing packages ...
building HTML index ...
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
installing R manuals in PDF format ...
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
ERROR: 'makeinfo' v4.7 or later needed but missing on your system.
make[1]: *** [R-FAQ.info] Error 1
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make: [install-info] Error 2 (ignored)
make: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2'
+ mv /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib/libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so
+ ln -s libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR-2.11.so
++ relative /usr/share/doc/R-3.1 /usr/lib64/R/doc
+ ln -s ../../share/doc/R-3.1 /usr/src/tmp/R-base-buildroot/usr/lib64/R/doc
++ relative /usr/include/R /usr/lib64/R/include
+ ln -s ../../include/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/include
+ cmp /usr/src/tmp/R-base-buildroot/usr/bin/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/R
++ relative /usr/lib64/R/bin/R /usr/bin/R
+ ln -snfv ../lib64/R/bin/R /usr/src/tmp/R-base-buildroot/usr/bin/R
'/usr/src/tmp/R-base-buildroot/usr/bin/R' -> '../lib64/R/bin/R'
+ cmp /usr/src/tmp/R-base-buildroot/usr/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/Rscript
++ relative /usr/lib64/R/bin/Rscript /usr/bin/Rscript
+ ln -snfv ../lib64/R/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/bin/Rscript
'/usr/src/tmp/R-base-buildroot/usr/bin/Rscript' -> '../lib64/R/bin/Rscript'
+ fgrep -r /usr/src/tmp/R-base-buildroot /usr/src/tmp/R-base-buildroot
+ mkdir -p /usr/src/tmp/R-base-buildroot/etc/R
+ mv /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/Makeconf /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/Renviron /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/javaconf /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/ldpaths /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/repositories /usr/src/tmp/R-base-buildroot/etc/R/
+ rmdir /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc
++ relative /etc/R /usr/lib64/R/etc
+ ln -s ../../../etc/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc
+ '[' -f /usr/src/tmp/R-base-buildroot/etc/R/ldpaths ']'
+ :
+ mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/applications
+ cat
+ '[' -f /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool ']'
++ relative /usr/bin/libtool /usr/lib64/R/bin/libtool
+ ln -snfv ../../../bin/libtool /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool
'/usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool' -> '../../../bin/libtool'
+ rm -fv '/usr/src/tmp/R-base-buildroot/usr/share/info/dir*'
+ /usr/lib/rpm/brp-alt
Cleaning files in /usr/src/tmp/R-base-buildroot (auto)
mode of './usr/lib64/libR.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/mgcv/libs/mgcv.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/class/libs/class.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/nlme/libs/nlme.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/cluster/libs/cluster.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/Matrix/libs/Matrix.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/nnet/libs/nnet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/KernSmooth/libs/KernSmooth.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/rpart/libs/rpart.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/MASS/libs/MASS.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/spatial/libs/spatial.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/foreign/libs/foreign.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/survival/libs/survival.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/lattice/libs/lattice.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/parallel/libs/parallel.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/tcltk/libs/tcltk.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grid/libs/grid.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/utils/libs/utils.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/splines/libs/splines.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grDevices/libs/cairo.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grDevices/libs/grDevices.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/methods/libs/methods.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/stats/libs/stats.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/graphics/libs/graphics.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/tools/libs/tools.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/R_de.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/R_X11.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/vfonts.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/lapack.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/internet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
Verifying and fixing files in /usr/src/tmp/R-base-buildroot (binconfig,pkgconfig,libtool,desktop)
/usr/lib64/pkgconfig/libR.pc: Libs: '-Wl,--export-dynamic -L/usr/local/lib64 -L${rlibdir} -lR' --> '-Wl,--export-dynamic -L${rlibdir} -lR'
Compressing files in /usr/src/tmp/R-base-buildroot (auto)
Adjusting library links in /usr/src/tmp/R-base-buildroot
./usr/lib64:
libR.so -> libR.so
./usr/lib64/R/lib:
Verifying ELF objects in /usr/src/tmp/R-base-buildroot (arch=normal,fhs=normal,lfs=relaxed,lint=relaxed,rpath=normal,stack=normal,textrel=normal,unresolved=normal)
Hardlinking identical .pyc and .pyo files
Executing(%check): /bin/sh -e /usr/src/tmp/rpm-tmp.67013
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.1.2
+ export TZ=GMT
+ TZ=GMT
+ make check
make: Entering directory `/usr/src/RPM/BUILD/R-3.1.2'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests/Examples'
Testing examples for package 'base'
Testing examples for package 'tools'
comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK
Testing examples for package 'utils'
Testing examples for package 'grDevices'
comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK
Testing examples for package 'graphics'
comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK
Testing examples for package 'stats'
comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ...
6484c6484
< Grand Mean: 291.5937
---
> Grand Mean: 291.5938
13041c13041
< 6 -0.5412 20.482886 -0.845157
---
> 6 -0.5412 20.482887 -0.845157
14625c14625
< Grand Mean: 291.5937
---
> Grand Mean: 291.5938
Testing examples for package 'datasets'
comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK
Testing examples for package 'methods'
Testing examples for package 'grid'
comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK
Testing examples for package 'splines'
comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK
Testing examples for package 'stats4'
comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK
Testing examples for package 'tcltk'
Testing examples for package 'compiler'
Testing examples for package 'parallel'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests/Examples'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running strict specific tests
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running code in 'eval-etc.R' ... OK
comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK
running code in 'simple-true.R' ... OK
comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK
running code in 'arith-true.R' ... OK
comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK
running code in 'arith.R' ... OK
comparing 'arith.Rout' to './arith.Rout.save' ... OK
running code in 'lm-tests.R' ... OK
comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK
running code in 'ok-errors.R' ... OK
comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK
running code in 'method-dispatch.R' ... OK
comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK
running code in 'array-subset.R' ... OK
comparing 'array-subset.Rout' to './array-subset.Rout.save' ... OK
running code in 'any-all.R' ... OK
comparing 'any-all.Rout' to './any-all.Rout.save' ... OK
running code in 'd-p-q-r-tests.R' ... OK
comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running sloppy specific tests
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running code in 'complex.R' ... OK
comparing 'complex.Rout' to './complex.Rout.save' ... OK
running code in 'print-tests.R' ... OK
comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK
running code in 'lapack.R' ... OK
comparing 'lapack.Rout' to './lapack.Rout.save' ... OK
running code in 'datasets.R' ... OK
comparing 'datasets.Rout' to './datasets.Rout.save' ... OK
running code in 'datetime.R' ... OK
comparing 'datetime.Rout' to './datetime.Rout.save' ... OK
running code in 'iec60559.R' ... OK
comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running regression tests ...
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running code in 'reg-tests-1a.R' ... OK
running code in 'reg-tests-1b.R' ... OK
running code in 'reg-tests-1c.R' ... OK
running code in 'reg-tests-2.R' ... OK
comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK
running code in 'reg-examples1.R' ... OK
running code in 'reg-examples2.R' ... OK
running code in 'reg-packages.R' ... OK
running code in 'reg-IO.R' ... OK
comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK
running code in 'reg-IO2.R' ... OK
comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK
running code in 'reg-plot.R' ... OK
comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK
running code in 'reg-S4.R' ... OK
comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK
running code in 'reg-BLAS.R' ... OK
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running code in 'reg-tests-3.R' ... OK
comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK
running code in 'reg-examples3.R' ... OK
comparing 'reg-examples3.Rout' to './reg-examples3.Rout.save' ... OK
running tests of plotting Latin-1
expect failure or some differences if not in a Latin-1 or UTF-8 locale
running code in 'reg-plot-latin1.R' ... FAILED
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running tests of Internet and socket functions
expect some differences
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running code in 'internet.R' ... OK
comparing 'internet.Rout' to './internet.Rout.save' ...14,16c14,355
< Warning message:
< In nsl("cran.r-project.org") :
< nsl() was unable to resolve host 'cran.r-project.org'
---
> >
> > # test do_download.
> > nrow(available.packages(contrib.url("http://cran.r-project.org")))
> [1] 5993
> >
> > # test url connections on http
> > zz <- url("http://cran.r-project.org/")
> > readLines(zz)
> [1] "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">"
> [2] "<html>"
> [3] "<head>"
> [4] "<title>The Comprehensive R Archive Network</title>"
> [5] "<META HTTP-EQUIV=\"content-type\" CONTENT=\"text/html; charset=utf-8\">"
> [6] "<link rel=\"icon\" href=\"favicon.ico\" type=\"image/x-icon\">"
> [7] "<link rel=\"shortcut icon\" href=\"favicon.ico\" type=\"image/x-icon\">"
> [8] "<link rel=\"stylesheet\" type=\"text/css\" href=\"R.css\">"
> [9] "</head>"
> [10] ""
> [11] "<FRAMESET cols=\"1*, 4*\" border=0>"
> [12] "<FRAMESET rows=\"120, 1*\">"
> [13] "<FRAME src=\"logo.html\" name=\"logo\" frameborder=0>"
> [14] "<FRAME src=\"navbar.html\" name=\"contents\" frameborder=0>"
> [15] "</FRAMESET>"
> [16] "<FRAME src=\"banner.shtml\" name=\"banner\" frameborder=0>"
> [17] "<noframes>"
> [18] "<h1>The Comprehensive R Archive Network</h1>"
> [19] ""
> [20] "Your browser seems not to support frames,"
> [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN."
> [22] "</noframes>"
> [23] "</FRAMESET>"
> > close(zz)
> >
> > ## check graceful failure:
> > try(zz <- url("http://foo.bar", "r"))
> Error in url("http://foo.bar", "r") : cannot open the connection
> In addition: Warning message:
> In url("http://foo.bar", "r") : unable to connect to 'foo.bar' on port 80.
> >
> > # and via read.table, test http and ftp.
> >
> > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
> V1 V2 V3 V4 V5
> 1 1 307 930 36.58 0
> 2 2 307 940 36.73 0
> 3 3 307 950 36.93 0
> 4 4 307 1000 37.15 0
> 5 5 307 1010 37.23 0
> 6 6 307 1020 37.24 0
> 7 7 307 1030 37.24 0
> 8 8 307 1040 36.90 0
> 9 9 307 1050 36.95 0
> 10 10 307 1100 36.89 0
> 11 11 307 1110 36.95 0
> 12 12 307 1120 37.00 0
> 13 13 307 1130 36.90 0
> 14 14 307 1140 36.99 0
> 15 15 307 1150 36.99 0
> 16 16 307 1200 37.01 0
> 17 17 307 1210 37.04 0
> 18 18 307 1220 37.04 0
> 19 19 307 1230 37.14 0
> 20 20 307 1240 37.07 0
> 21 21 307 1250 36.98 0
> 22 22 307 1300 37.01 0
> 23 23 307 1310 36.97 0
> 24 24 307 1320 36.97 0
> 25 25 307 1330 37.12 0
> 26 26 307 1340 37.13 0
> 27 27 307 1350 37.14 0
> 28 28 307 1400 37.15 0
> 29 29 307 1410 37.17 0
> 30 30 307 1420 37.12 0
> 31 31 307 1430 37.12 0
> 32 32 307 1440 37.17 0
> 33 33 307 1450 37.28 0
> 34 34 307 1500 37.28 0
> 35 35 307 1510 37.44 0
> 36 36 307 1520 37.51 0
> 37 37 307 1530 37.64 0
> 38 38 307 1540 37.51 0
> 39 39 307 1550 37.98 1
> 40 40 307 1600 38.02 1
> 41 41 307 1610 38.00 1
> 42 42 307 1620 38.24 1
> 43 43 307 1630 38.10 1
> 44 44 307 1640 38.24 1
> 45 45 307 1650 38.11 1
> 46 46 307 1700 38.02 1
> 47 47 307 1710 38.11 1
> 48 48 307 1720 38.01 1
> 49 49 307 1730 37.91 1
> 50 50 307 1740 37.96 1
> 51 51 307 1750 38.03 1
> 52 52 307 1800 38.17 1
> 53 53 307 1810 38.19 1
> 54 54 307 1820 38.18 1
> 55 55 307 1830 38.15 1
> 56 56 307 1840 38.04 1
> 57 57 307 1850 37.96 1
> 58 58 307 1900 37.84 1
> 59 59 307 1910 37.83 1
> 60 60 307 1920 37.84 1
> 61 61 307 1930 37.74 1
> 62 62 307 1940 37.76 1
> 63 63 307 1950 37.76 1
> 64 64 307 2000 37.64 1
> 65 65 307 2010 37.63 1
> 66 66 307 2020 38.06 1
> 67 67 307 2030 38.19 1
> 68 68 307 2040 38.35 1
> 69 69 307 2050 38.25 1
> 70 70 307 2100 37.86 1
> 71 71 307 2110 37.95 1
> 72 72 307 2120 37.95 1
> 73 73 307 2130 37.76 1
> 74 74 307 2140 37.60 1
> 75 75 307 2150 37.89 1
> 76 76 307 2200 37.86 1
> 77 77 307 2210 37.71 1
> 78 78 307 2220 37.78 1
> 79 79 307 2230 37.82 1
> 80 80 307 2240 37.76 1
> 81 81 307 2250 37.81 1
> 82 82 307 2300 37.84 1
> 83 83 307 2310 38.01 1
> 84 84 307 2320 38.10 1
> 85 85 307 2330 38.15 1
> 86 86 307 2340 37.92 1
> 87 87 307 2350 37.64 1
> 88 88 308 0 37.70 1
> 89 89 308 10 37.46 1
> 90 90 308 20 37.41 1
> 91 91 308 30 37.46 1
> 92 92 308 40 37.56 1
> 93 93 308 50 37.55 1
> 94 94 308 100 37.75 1
> 95 95 308 110 37.76 1
> 96 96 308 120 37.73 1
> 97 97 308 130 37.77 1
> 98 98 308 140 38.01 1
> 99 99 308 150 38.04 1
> 100 100 308 200 38.07 1
> > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
> V1 V2 V3 V4 V5
> 1 1 307 930 36.58 0
> 2 2 307 940 36.73 0
> 3 3 307 950 36.93 0
> 4 4 307 1000 37.15 0
> 5 5 307 1010 37.23 0
> 6 6 307 1020 37.24 0
> 7 7 307 1030 37.24 0
> 8 8 307 1040 36.90 0
> 9 9 307 1050 36.95 0
> 10 10 307 1100 36.89 0
> 11 11 307 1110 36.95 0
> 12 12 307 1120 37.00 0
> 13 13 307 1130 36.90 0
> 14 14 307 1140 36.99 0
> 15 15 307 1150 36.99 0
> 16 16 307 1200 37.01 0
> 17 17 307 1210 37.04 0
> 18 18 307 1220 37.04 0
> 19 19 307 1230 37.14 0
> 20 20 307 1240 37.07 0
> 21 21 307 1250 36.98 0
> 22 22 307 1300 37.01 0
> 23 23 307 1310 36.97 0
> 24 24 307 1320 36.97 0
> 25 25 307 1330 37.12 0
> 26 26 307 1340 37.13 0
> 27 27 307 1350 37.14 0
> 28 28 307 1400 37.15 0
> 29 29 307 1410 37.17 0
> 30 30 307 1420 37.12 0
> 31 31 307 1430 37.12 0
> 32 32 307 1440 37.17 0
> 33 33 307 1450 37.28 0
> 34 34 307 1500 37.28 0
> 35 35 307 1510 37.44 0
> 36 36 307 1520 37.51 0
> 37 37 307 1530 37.64 0
> 38 38 307 1540 37.51 0
> 39 39 307 1550 37.98 1
> 40 40 307 1600 38.02 1
> 41 41 307 1610 38.00 1
> 42 42 307 1620 38.24 1
> 43 43 307 1630 38.10 1
> 44 44 307 1640 38.24 1
> 45 45 307 1650 38.11 1
> 46 46 307 1700 38.02 1
> 47 47 307 1710 38.11 1
> 48 48 307 1720 38.01 1
> 49 49 307 1730 37.91 1
> 50 50 307 1740 37.96 1
> 51 51 307 1750 38.03 1
> 52 52 307 1800 38.17 1
> 53 53 307 1810 38.19 1
> 54 54 307 1820 38.18 1
> 55 55 307 1830 38.15 1
> 56 56 307 1840 38.04 1
> 57 57 307 1850 37.96 1
> 58 58 307 1900 37.84 1
> 59 59 307 1910 37.83 1
> 60 60 307 1920 37.84 1
> 61 61 307 1930 37.74 1
> 62 62 307 1940 37.76 1
> 63 63 307 1950 37.76 1
> 64 64 307 2000 37.64 1
> 65 65 307 2010 37.63 1
> 66 66 307 2020 38.06 1
> 67 67 307 2030 38.19 1
> 68 68 307 2040 38.35 1
> 69 69 307 2050 38.25 1
> 70 70 307 2100 37.86 1
> 71 71 307 2110 37.95 1
> 72 72 307 2120 37.95 1
> 73 73 307 2130 37.76 1
> 74 74 307 2140 37.60 1
> 75 75 307 2150 37.89 1
> 76 76 307 2200 37.86 1
> 77 77 307 2210 37.71 1
> 78 78 307 2220 37.78 1
> 79 79 307 2230 37.82 1
> 80 80 307 2240 37.76 1
> 81 81 307 2250 37.81 1
> 82 82 307 2300 37.84 1
> 83 83 307 2310 38.01 1
> 84 84 307 2320 38.10 1
> 85 85 307 2330 38.15 1
> 86 86 307 2340 37.92 1
> 87 87 307 2350 37.64 1
> 88 88 308 0 37.70 1
> 89 89 308 10 37.46 1
> 90 90 308 20 37.41 1
> 91 91 308 30 37.46 1
> 92 92 308 40 37.56 1
> 93 93 308 50 37.55 1
> 94 94 308 100 37.75 1
> 95 95 308 110 37.76 1
> 96 96 308 120 37.73 1
> 97 97 308 130 37.77 1
> 98 98 308 140 38.01 1
> 99 99 308 150 38.04 1
> 100 100 308 200 38.07 1
> >
> > ## everything from here on is directly over sockets
> > if(!capabilities("sockets")) stop("no socket capabilities")
> >
> > # do the same thing via sockets (cut-down httpclient)
> > httpget <- function (url, port = 80)
> + {
> + urlel <- strsplit(url, "/")[[1]]
> + if (urlel[1] != "http:") stop("Not an http:// URL")
> + host <- urlel[3]
> + rurl <- paste(c("", urlel[-(1:3)]), collapse = "/")
> + a <- make.socket(host, port = port)
> + on.exit(close.socket(a))
> + headreq <- paste("HEAD", rurl, "HTTP/1.0\r\nConnection: Keep-Alive\r\nAccept: text/plain\r\n\r\n")
> + write.socket(a, headreq)
> + head <- read.socket(a, maxlen = 8000)
> + b <- strsplit(head, "\n")[[1]]
> + if (length(grep("200 OK", b[1])) == 0) stop(b[1])
> + len <- as.numeric(strsplit(grep("Content-Length", b, value = TRUE),
> + ":")[[1]][2])
> + getreq <- paste("GET", rurl, "HTTP/1.0\r\nConnection: Keep-Alive\r\nAccept: text/plain\r\n\r\n")
> + write.socket(a, getreq)
> + junk <- read.socket(a, maxlen = nchar(head))
> + data <- ""
> + b <- strsplit(c(head, junk), "\n")
> + nn <- length(b[[1]])
> + if (length(b[[2]]) > nn)
> + data <- paste(b[[2]][-(1:nn)], collapse = "\n")
> + while (nchar(data) < len) {
> + data <- paste(data, read.socket(a, maxlen = len - nchar(data)),
> + sep = "")
> + }
> + strsplit(data, "\n")[[1]]
> + }
> >
> > if(nzchar(Sys.getenv("http_proxy")) || nzchar(Sys.getenv("HTTP_PROXY"))) {
> + cat("http proxy is set, so skip test of http over sockets\n")
> + } else {
> + httpget("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
> + }
> [1] "001 307 0930 36.58 0" "002 307 0940 36.73 0" "003 307 0950 36.93 0"
> [4] "004 307 1000 37.15 0" "005 307 1010 37.23 0" "006 307 1020 37.24 0"
> [7] "007 307 1030 37.24 0" "008 307 1040 36.90 0" "009 307 1050 36.95 0"
> [10] "010 307 1100 36.89 0" "011 307 1110 36.95 0" "012 307 1120 37.00 0"
> [13] "013 307 1130 36.90 0" "014 307 1140 36.99 0" "015 307 1150 36.99 0"
> [16] "016 307 1200 37.01 0" "017 307 1210 37.04 0" "018 307 1220 37.04 0"
> [19] "019 307 1230 37.14 0" "020 307 1240 37.07 0" "021 307 1250 36.98 0"
> [22] "022 307 1300 37.01 0" "023 307 1310 36.97 0" "024 307 1320 36.97 0"
> [25] "025 307 1330 37.12 0" "026 307 1340 37.13 0" "027 307 1350 37.14 0"
> [28] "028 307 1400 37.15 0" "029 307 1410 37.17 0" "030 307 1420 37.12 0"
> [31] "031 307 1430 37.12 0" "032 307 1440 37.17 0" "033 307 1450 37.28 0"
> [34] "034 307 1500 37.28 0" "035 307 1510 37.44 0" "036 307 1520 37.51 0"
> [37] "037 307 1530 37.64 0" "038 307 1540 37.51 0" "039 307 1550 37.98 1"
> [40] "040 307 1600 38.02 1" "041 307 1610 38.00 1 " "042 307 1620 38.24 1 "
> [43] "043 307 1630 38.10 1" "044 307 1640 38.24 1" "045 307 1650 38.11 1"
> [46] "046 307 1700 38.02 1" "047 307 1710 38.11 1" "048 307 1720 38.01 1"
> [49] "049 307 1730 37.91 1" "050 307 1740 37.96 1" "051 307 1750 38.03 1"
> [52] "052 307 1800 38.17 1" "053 307 1810 38.19 1" "054 307 1820 38.18 1"
> [55] "055 307 1830 38.15 1" "056 307 1840 38.04 1" "057 307 1850 37.96 1"
> [58] "058 307 1900 37.84 1" "059 307 1910 37.83 1" "060 307 1920 37.84 1"
> [61] "061 307 1930 37.74 1" "062 307 1940 37.76 1" "063 307 1950 37.76 1"
> [64] "064 307 2000 37.64 1" "065 307 2010 37.63 1" "066 307 2020 38.06 1"
> [67] "067 307 2030 38.19 1" "068 307 2040 38.35 1" "069 307 2050 38.25 1"
> [70] "070 307 2100 37.86 1" "071 307 2110 37.95 1" "072 307 2120 37.95 1"
> [73] "073 307 2130 37.76 1" "074 307 2140 37.60 1" "075 307 2150 37.89 1"
> [76] "076 307 2200 37.86 1" "077 307 2210 37.71 1" "078 307 2220 37.78 1"
> [79] "079 307 2230 37.82 1" "080 307 2240 37.76 1" "081 307 2250 37.81 1"
> [82] "082 307 2300 37.84 1" "083 307 2310 38.01 1" "084 307 2320 38.10 1"
> [85] "085 307 2330 38.15 1" "086 307 2340 37.92 1" "087 307 2350 37.64 1"
> [88] "088 308 0000 37.70 1" "089 308 0010 37.46 1" "090 308 0020 37.41 1"
> [91] "091 308 0030 37.46 1" "092 308 0040 37.56 1" "093 308 0050 37.55 1"
> [94] "094 308 0100 37.75 1" "095 308 0110 37.76 1" "096 308 0120 37.73 1"
> [97] "097 308 0130 37.77 1" "098 308 0140 38.01 1" "099 308 0150 38.04 1"
> [100] "100 308 0200 38.07 1"
> >
> > finger <- function(user, host = "localhost", port = 79, print = TRUE)
> + {
> + if (!is.character(user))
> + stop("user name must be a string")
> + user <- paste(user,"\r\n")
> + socket <- make.socket(host, port)
> + on.exit(close.socket(socket))
> + write.socket(socket, user)
> + output <- character(0)
> + repeat{
> + ss <- read.socket(socket)
> + if (ss == "") break
> + output <- paste(output, ss)
> + }
> + close.socket(socket)
> + if (print) cat(output)
> + invisible(output)
> + }
> > try(finger("root")) ## only works if your site provides a finger daemon
> socket error: Connection refused
> Error in make.socket(host, port) : socket not established
> >
OK
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2'
+ exit 0
Processing files: R-base-3.1.2-alt1.1
Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.59333
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.1.2
+ DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ export DOCDIR
+ rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ exit 0
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warning: File listed twice: /usr/lib64/R/library/utils/html/setRepositories.html
warning: File listed twice: /usr/lib64/R/library/utils/html/sourceutils.html
warning: File listed twice: /usr/lib64/R/library/utils/html/stack.html
warning: File listed twice: /usr/lib64/R/library/utils/html/str.html
warning: File listed twice: /usr/lib64/R/library/utils/html/summaryRprof.html
warning: File listed twice: /usr/lib64/R/library/utils/html/tar.html
warning: File listed twice: /usr/lib64/R/library/utils/html/toLatex.html
warning: File listed twice: /usr/lib64/R/library/utils/html/txtProgressBar.html
warning: File listed twice: /usr/lib64/R/library/utils/html/type.convert.html
warning: File listed twice: /usr/lib64/R/library/utils/html/untar.html
warning: File listed twice: /usr/lib64/R/library/utils/html/unzip.html
warning: File listed twice: /usr/lib64/R/library/utils/html/update.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/url.show.html
warning: File listed twice: /usr/lib64/R/library/utils/html/utils-defunct.html
warning: File listed twice: /usr/lib64/R/library/utils/html/utils-deprecated.html
warning: File listed twice: /usr/lib64/R/library/utils/html/utils-package.html
warning: File listed twice: /usr/lib64/R/library/utils/html/vignette.html
warning: File listed twice: /usr/lib64/R/library/utils/html/write.table.html
warning: File listed twice: /usr/lib64/R/library/utils/html/zip.html
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.aZijxB
find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,shell,tcl,typelib)
++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}'
--- find-provides-deps 2015-12-11 12:41:49.784974777 +0000
+++ filter-provides-deps 2015-12-11 12:41:49.788974776 +0000
@@ -1 +1,2 @@
libR.so()(64bit) = set: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
+libR-2.11.so()(64bit) = set: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
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.oYN8Bw
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,tcl,typelib)
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/MASS/libs/MASS.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/foreign/libs/foreign.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grDevices/libs/grDevices.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/graphics/libs/graphics.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grid/libs/grid.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/lattice/libs/lattice.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/nnet/libs/nnet.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/rpart/libs/rpart.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/spatial/libs/spatial.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/survival/libs/survival.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/utils/libs/utils.so: underlinked libraries: /lib64/liblzma.so.5 /lib64/libm.so.6
shebang.req.files: executable script /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/sh/echo.sh is not executable
find-requires: FINDPACKAGE-COMMANDS: cat grep sh
Provides: libR.so()(64bit) = set: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, libR-2.11.so()(64bit) = set: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
Requires: /bin/sh, /lib64/ld-linux-x86-64.so.2, coreutils, grep, ld-linux-x86-64.so.2()(64bit) >= set:ihbW3, ld-linux-x86-64.so.2(GLIBC_2.2.5)(64bit), libX11.so.6()(64bit) >= set:ohpSxBZ85GUbjr3ZiTS4Op7MNvybxvVcEOfOqXEF1qAwZs71CCJnKVDCNaOeQuhN2XiwdPdDviaX7NJgyWjw426Dgj994wsONU8RZq4ZjETw6Fhp3zWVUZw5ciXODiTumQluRVpoa1IvTZLG17jMAL3ACpj6Ac4oFudXhDSHmmi88f5kj4Wr9Vnm0e7EI25u1z9ZgUcSd8uJBSFYSNRimTAoZrh3ZBnylGc5tzA2LuNkPBBiUQUU6ywg3U8ZhexsVJ8zR8RTyGBSx6p5JwQZtURAFElDl8totXyLZkjPS80tH2, libXmu.so.6()(64bit) >= set:ljat5WdZ0, libXt.so.6()(64bit) >= set:miBmG8bmWeKY1r3A0IpjGJmzcnuk4L1fZ82d, libbz2.so.1()(64bit) >= set:ieU4cq8R9SL02Pd7T6CQAbuVPJL2, libc.so.6(GLIBC_2.11)(64bit), libc.so.6(GLIBC_2.14)(64bit), libc.so.6(GLIBC_2.15)(64bit), libc.so.6(GLIBC_2.16)(64bit), libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.4)(64bit), libc.so.6(GLIBC_2.6)(64bit), libc.so.6(GLIBC_2.7)(64bit), libc.so.6(GLIBC_2.8)(64bit), libcairo.so.2()(64bit) >= set:mgBeCp25NOIyrlQHFS7nAegwnSqIIeytSyjemApNcNsUClh1Z3fji718UL5HMxPMkimVZpVN9h6QFUdKO6OFjNsjitz641ARaZ5HZAmxdD86kgBnSaNq3ZAVlemZpcoP0tsFeDiZfuQuf3, libdl.so.2(GLIBC_2.2.5)(64bit), libgobject-2.0.so.0()(64bit) >= set:ml6W90, libicui18n.so.50()(64bit) >= set:qnzoOwLhMIix4mUiJaHPcrq7, libicuuc.so.50()(64bit) >= set:pnTfJo5ss, libjpeg.so.62()(64bit) >= set:jfgjDuQy7g6kiGvkp5kR7Bd0, liblapack.so.4()(64bit) >= set:ohd6FWZC9Z0w5c4a9UukCXhjBhYH4Y4FFzzOsPQ6Ly73P71OXgQjXcEVpBpZdQN0du6bEemIGcwvkRUyfGzE7kPRWTAeHIPYhIl5W1Y695GSMOChpvZBbtwQPBftLjrj750B9wOLQMqCw2WsWFYAb4WY6oiJ3rgT0C7giNl5FM20Ezc0060tUk1, liblzma.so.5()(64bit) >= set:kgIy0DJFZFQ2NtZsOqIUpfV9l2, libm.so.6(GLIBC_2.2.5)(64bit), libopenblas.so.0()(64bit) >= set:rme9dGe009CqZyeEKu0c959bA01WKVsu0KL3f0MzHG9G3SAPMCzdZ2ZyhPe7xLi5vYvWeHEOFls8vqO9WfXluFSG02, libpango-1.0.so.0()(64bit) >= set:miPmiaRgNQ6cD75j31i4ky6SMMCoRQ1, libpangocairo-1.0.so.0()(64bit) >= set:jhWzZgd5, libpcre.so.3()(64bit) >= set:jgZdsEZ2sgNXHHLwc1, libpng15.so.15()(64bit) >= set:lhHMixNA5RSP1K7ShG9w7fCPfx2bPUEiWED20, libpng15.so.15(PNG15_0)(64bit), libreadline.so.6()(64bit) >= set:nioSWGipM22fZzwThmVscM35BWrboE0sZwI3SqZmoz0XZu0BVGKnVqw4lr, librt.so.1()(64bit) >= set:jiq20, librt.so.1(GLIBC_2.2.5)(64bit), libtiff.so.5()(64bit) >= set:lihRIYpxQTgnDIeRTSwCs2, libz.so.1()(64bit) >= set:kgb6dgbWdAhpAO8J7FmJCZm37ST4, rtld(GNU_HASH), sh
Requires(rpmlib): rpmlib(SetVersions)
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.GoSVO4
Creating R-base-debuginfo package
Processing files: R-devel-3.1.2-alt1.1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.9JygaI
find-provides: broken symbolic link /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool -> ../../../bin/libtool is not going to provide anything
find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,shell,tcl,typelib)
++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}'
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.TJYkgp
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,tcl,typelib)
/usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:39:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header
# error R_ext/GraphicsEngine.h must be included first, and includes this header
^
cpp.req: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed, trying c++ mode
/usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:39:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header
# error R_ext/GraphicsEngine.h must be included first, and includes this header
^
cpp.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed
find-requires: FINDPACKAGE-COMMANDS: chmod mkdir rm rmdir
Provides: pkgconfig(libR) = 3.1.2
PreReq: R-base = 3.1.2-alt1.1
Requires: /bin/sh, /usr/bin/libtool, /usr/lib64/libR.so, /usr/lib64/pkgconfig, coreutils
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.X3pGRd
Processing files: R-tcltk-3.1.2-alt1.1
warning: File listed twice: /usr/lib64/R/library/tcltk/html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/R.css
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TclInterface.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkCommands.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgetcmds.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgets.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tclServiceMode.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-defunct.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-package.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkProgressBar.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkStartGUI.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.dir.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.files.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_messageBox.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_select.list.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkpager.html
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.zcdve6
find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,shell,tcl,typelib)
++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}'
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.faeMl2
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,tcl,typelib)
Provides: tcl(::Utility) = 1.0, tcl(::Utility::dump) = 1.0, tcl(::Utility::expand) = 1.0, tcl(::Utility::number) = 1.0, tcl(::Utility::string) = 1.0, tcl(::Utility::tk) = 1.0, tcl(Hierarchy) = 2.0, tcl(PBar) = 1.0, tcl(Widget) = 2.0
Requires: R-base = 3.1.2-alt1.1, libR.so()(64bit) >= set:ng3YhoVZ7zG1yRZ5FTWvS3cZe7GN2bQlckaUP3hGPQZ9ZDUD4rZrfNE7wbgoIdtiz5VnwW3HABLzZbEsM4Ch8s6gQMWD7416FVYn9zdqood7g7fgCwK9Giw5JBqEyOof0MFnhEpT9X5JupXdGI6VXZGYdo0iIJYXNsqzxXD0veJIrUzULDPywvN1, libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.4)(64bit), libtcl8.5.so()(64bit) >= set:nhgjl7axi5LXwZCwtKzEgR46OGPDdUhperIBMUpAQNxfXAzzCME2ZC3VjYspFcvGIvhP7CaHXaui690CwrRamfbKeqMwV4FNim2oZ0Yf9OWVxM1, libtk8.5.so()(64bit) >= set:mkluxApv1, rtld(GNU_HASH), tcl(Tk)
Requires(rpmlib): rpmlib(SetVersions)
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.P4t8c2
Creating R-tcltk-debuginfo package
Processing files: R-doc-html-3.1.2-alt1.1
error: File not found by glob: /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual/*.html
RPM build errors:
File listed twice: /usr/lib64/R/library/KernSmooth/html
File listed twice: /usr/lib64/R/library/KernSmooth/html/00Index.html
File listed twice: /usr/lib64/R/library/KernSmooth/html/R.css
File listed twice: /usr/lib64/R/library/KernSmooth/html/bkde.html
File listed twice: /usr/lib64/R/library/KernSmooth/html/bkde2D.html
File listed twice: /usr/lib64/R/library/KernSmooth/html/bkfe.html
File listed twice: /usr/lib64/R/library/KernSmooth/html/dpih.html
File listed twice: /usr/lib64/R/library/KernSmooth/html/dpik.html
File listed twice: /usr/lib64/R/library/KernSmooth/html/dpill.html
File listed twice: /usr/lib64/R/library/KernSmooth/html/locpoly.html
File listed twice: /usr/lib64/R/library/MASS/html
File listed twice: /usr/lib64/R/library/MASS/html/00Index.html
File listed twice: /usr/lib64/R/library/MASS/html/Aids2.html
File listed twice: /usr/lib64/R/library/MASS/html/Animals.html
File listed twice: /usr/lib64/R/library/MASS/html/Boston.html
File listed twice: /usr/lib64/R/library/MASS/html/Cars93.html
File listed twice: /usr/lib64/R/library/MASS/html/Cushings.html
File listed twice: /usr/lib64/R/library/MASS/html/DDT.html
File listed twice: /usr/lib64/R/library/MASS/html/GAGurine.html
File listed twice: /usr/lib64/R/library/MASS/html/Insurance.html
File listed twice: /usr/lib64/R/library/MASS/html/MASS-internal.html
File listed twice: /usr/lib64/R/library/MASS/html/Melanoma.html
File listed twice: /usr/lib64/R/library/MASS/html/Null.html
File listed twice: /usr/lib64/R/library/MASS/html/OME.html
File listed twice: /usr/lib64/R/library/MASS/html/Pima.tr.html
File listed twice: /usr/lib64/R/library/MASS/html/R.css
File listed twice: /usr/lib64/R/library/MASS/html/Rabbit.html
File listed twice: /usr/lib64/R/library/MASS/html/Rubber.html
File listed twice: /usr/lib64/R/library/MASS/html/SP500.html
File listed twice: /usr/lib64/R/library/MASS/html/Sitka.html
File listed twice: /usr/lib64/R/library/MASS/html/Sitka89.html
File listed twice: /usr/lib64/R/library/MASS/html/Skye.html
File listed twice: /usr/lib64/R/library/MASS/html/Traffic.html
File listed twice: /usr/lib64/R/library/MASS/html/UScereal.html
File listed twice: /usr/lib64/R/library/MASS/html/UScrime.html
File listed twice: /usr/lib64/R/library/MASS/html/VA.html
File listed twice: /usr/lib64/R/library/MASS/html/abbey.html
File listed twice: /usr/lib64/R/library/MASS/html/accdeaths.html
File listed twice: /usr/lib64/R/library/MASS/html/addterm.html
File listed twice: /usr/lib64/R/library/MASS/html/anorexia.html
File listed twice: /usr/lib64/R/library/MASS/html/anova.negbin.html
File listed twice: /usr/lib64/R/library/MASS/html/area.html
File listed twice: /usr/lib64/R/library/MASS/html/bacteria.html
File listed twice: /usr/lib64/R/library/MASS/html/bandwidth.nrd.html
File listed twice: /usr/lib64/R/library/MASS/html/bcv.html
File listed twice: /usr/lib64/R/library/MASS/html/beav1.html
File listed twice: /usr/lib64/R/library/MASS/html/beav2.html
File listed twice: /usr/lib64/R/library/MASS/html/biopsy.html
File listed twice: /usr/lib64/R/library/MASS/html/birthwt.html
File listed twice: /usr/lib64/R/library/MASS/html/boxcox.html
File listed twice: /usr/lib64/R/library/MASS/html/cabbages.html
File listed twice: /usr/lib64/R/library/MASS/html/caith.html
File listed twice: /usr/lib64/R/library/MASS/html/cats.html
File listed twice: /usr/lib64/R/library/MASS/html/cement.html
File listed twice: /usr/lib64/R/library/MASS/html/chem.html
File listed twice: /usr/lib64/R/library/MASS/html/con2tr.html
File listed twice: /usr/lib64/R/library/MASS/html/confint.html
File listed twice: /usr/lib64/R/library/MASS/html/contr.sdif.html
File listed twice: /usr/lib64/R/library/MASS/html/coop.html
File listed twice: /usr/lib64/R/library/MASS/html/corresp.html
File listed twice: /usr/lib64/R/library/MASS/html/cov.rob.html
File listed twice: /usr/lib64/R/library/MASS/html/cov.trob.html
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File not found by glob: /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual/*.html
Command exited with non-zero status 1
784.99user 51.56system 18:39.43elapsed 74%CPU (0avgtext+0avgdata 163556maxresident)k
0inputs+0outputs (0major+21736500minor)pagefaults 0swaps
hsh-rebuild: rebuild of `pkg.tar' failed.
ERROR: build failed for R-base
^ permalink raw reply [flat|nested] 11+ messages in thread