0s autopkgtest [01:04:16]: starting date and time: 2024-03-24 01:04:16+0000
  0s autopkgtest [01:04:16]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [01:04:16]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6w9y3mbb/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:r-base --apt-upgrade r-cran-survey --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-1.secgroup --name adt-noble-i386-r-cran-survey-20240324-010416-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
1067s autopkgtest [01:22:03]: testbed dpkg architecture: amd64
1067s autopkgtest [01:22:03]: testbed apt version: 2.7.12
1067s autopkgtest [01:22:03]: test architecture: i386
1067s autopkgtest [01:22:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup
1069s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
1069s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB]
1069s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3972 kB]
1069s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB]
1069s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
1069s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [725 kB]
1069s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [483 kB]
1069s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B]
1069s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB]
1069s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B]
1069s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B]
1069s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4417 kB]
1069s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1305 kB]
1069s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B]
1069s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [96.1 kB]
1069s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [27.1 kB]
1069s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B]
1072s Fetched 11.8 MB in 1s (7952 kB/s)
1072s Reading package lists...
1073s Reading package lists...
1074s Building dependency tree...
1074s Reading state information...
1074s Calculating upgrade...
1074s The following packages will be upgraded:
1074s   libc-bin libc6 locales
1074s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1074s Need to get 8176 kB of archives.
1074s After this operation, 2048 B of additional disk space will be used.
1074s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libc6 amd64 2.39-0ubuntu6 [3262 kB]
1074s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libc-bin amd64 2.39-0ubuntu6 [682 kB]
1074s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 locales all 2.39-0ubuntu6 [4232 kB]
1075s Preconfiguring packages ...
1075s Fetched 8176 kB in 0s (97.9 MB/s)
1075s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 71864 files and directories currently installed.)
1075s Preparing to unpack .../libc6_2.39-0ubuntu6_amd64.deb ...
1075s Unpacking libc6:amd64 (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
1075s Setting up libc6:amd64 (2.39-0ubuntu6) ...
1076s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 71864 files and directories currently installed.)
1076s Preparing to unpack .../libc-bin_2.39-0ubuntu6_amd64.deb ...
1076s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
1076s Setting up libc-bin (2.39-0ubuntu6) ...
1076s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 71864 files and directories currently installed.)
1076s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ...
1076s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
1076s Setting up locales (2.39-0ubuntu6) ...
1077s Generating locales (this might take a while)...
1078s   en_US.UTF-8... done
1078s Generation complete.
1078s Processing triggers for man-db (2.12.0-3) ...
1080s Reading package lists...
1080s Building dependency tree...
1080s Reading state information...
1080s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1081s sh: Attempting to set up Debian/Ubuntu apt sources automatically
1081s sh: Distribution appears to be Ubuntu
1081s Reading package lists...
1082s Building dependency tree...
1082s Reading state information...
1082s eatmydata is already the newest version (131-1).
1082s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1082s Reading package lists...
1082s Building dependency tree...
1082s Reading state information...
1083s dbus is already the newest version (1.14.10-4ubuntu1).
1083s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1083s Reading package lists...
1083s Building dependency tree...
1083s Reading state information...
1083s rng-tools-debian is already the newest version (2.4).
1083s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1083s Reading package lists...
1083s Building dependency tree...
1083s Reading state information...
1084s The following packages will be REMOVED:
1084s   cloud-init* python3-configobj* python3-debconf*
1084s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
1084s After this operation, 3256 kB disk space will be freed.
1084s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 71864 files and directories currently installed.)
1084s Removing cloud-init (24.1.2-0ubuntu1) ...
1085s Removing python3-configobj (5.0.8-3) ...
1085s Removing python3-debconf (1.5.86) ...
1085s Processing triggers for man-db (2.12.0-3) ...
1085s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 71475 files and directories currently installed.)
1085s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
1086s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
1086s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
1086s invoke-rc.d: policy-rc.d denied execution of try-restart.
1086s Reading package lists...
1086s Building dependency tree...
1086s Reading state information...
1086s linux-generic is already the newest version (6.8.0-11.11+1).
1086s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1087s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
1087s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
1087s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
1089s Reading package lists...
1089s Reading package lists...
1089s Building dependency tree...
1089s Reading state information...
1089s Calculating upgrade...
1089s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1090s Reading package lists...
1090s Building dependency tree...
1090s Reading state information...
1090s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1090s autopkgtest [01:22:26]: rebooting testbed after setup commands that affected boot
1242s autopkgtest [01:24:58]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024
1244s autopkgtest [01:25:00]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-survey
1245s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-survey 4.2-1-1 (dsc) [2212 B]
1245s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-survey 4.2-1-1 (tar) [2153 kB]
1245s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-survey 4.2-1-1 (diff) [4304 B]
1245s gpgv: Signature made Wed Jun 28 12:15:39 2023 UTC
1245s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
1245s gpgv:                issuer "tille@debian.org"
1245s gpgv: Can't check signature: No public key
1245s dpkg-source: warning: cannot verify inline signature for ./r-cran-survey_4.2-1-1.dsc: no acceptable signature found
1245s autopkgtest [01:25:01]: testing package r-cran-survey version 4.2-1-1
1246s autopkgtest [01:25:02]: build not needed
1248s autopkgtest [01:25:04]: test run-unit-test: preparing testbed
1252s Note, using file '/tmp/autopkgtest.fzci4f/1-autopkgtest-satdep.dsc' to get the build dependencies
1252s Reading package lists...
1252s Building dependency tree...
1252s Reading state information...
1252s Starting pkgProblemResolver with broken count: 0
1252s Starting 2 pkgProblemResolver with broken count: 0
1252s Done
1253s The following NEW packages will be installed:
1253s   build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu
1253s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
1253s   fonts-glyphicons-halflings fonts-mathjax g++ g++-13 g++-13-x86-64-linux-gnu
1253s   g++-x86-64-linux-gnu gcc gcc-13 gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu
1253s   libasan8 libatomic1 libblas3 libc-dev-bin libc6-dev libcairo2 libcc1-0
1253s   libcrypt-dev libdatrie1 libdeflate0 libfontconfig1 libgcc-13-dev
1253s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6
1253s   libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap
1253s   libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax
1253s   liblapack3 liblerc4 liblsan0 libmpc3 libnlopt0 libpango-1.0-0
1253s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
1253s   libquadmath0 libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6 libthai-data
1253s   libthai0 libtiff6 libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0
1253s   libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 linux-libc-dev littler
1253s   node-normalize.css r-base-core r-cran-abind r-cran-aer r-cran-backports
1253s   r-cran-bit r-cran-bit64 r-cran-blob r-cran-boot r-cran-brio r-cran-broom
1253s   r-cran-cachem r-cran-callr r-cran-car r-cran-cardata r-cran-caret
1253s   r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr r-cran-clock
1253s   r-cran-codetools r-cran-colorspace r-cran-conquer r-cran-cpp11 r-cran-crayon
1253s   r-cran-curl r-cran-data.table r-cran-dbi r-cran-desc r-cran-diagram
1253s   r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-e1071 r-cran-ellipsis
1253s   r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-forcats
1253s   r-cran-foreach r-cran-foreign r-cran-formula r-cran-fs r-cran-future
1253s   r-cran-future.apply r-cran-generics r-cran-ggplot2 r-cran-globals
1253s   r-cran-glue r-cran-gower r-cran-gtable r-cran-hardhat r-cran-haven
1253s   r-cran-highr r-cran-hms r-cran-ipred r-cran-isoband r-cran-iterators
1253s   r-cran-jsonlite r-cran-kernsmooth r-cran-knitr r-cran-labeling
1253s   r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv r-cran-littler
1253s   r-cran-lme4 r-cran-lmtest r-cran-lubridate r-cran-magrittr r-cran-maptools
1253s   r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats
1253s   r-cran-memoise r-cran-mgcv r-cran-minqa r-cran-mitools r-cran-modelmetrics
1253s   r-cran-munsell r-cran-nlme r-cran-nloptr r-cran-nnet r-cran-numderiv
1253s   r-cran-openxlsx r-cran-parallelly r-cran-pbkrtest r-cran-pillar
1253s   r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload
1253s   r-cran-plogr r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-proc
1253s   r-cran-processx r-cran-prodlim r-cran-progress r-cran-progressr r-cran-proxy
1253s   r-cran-ps r-cran-purrr r-cran-quantreg r-cran-r.methodss3 r-cran-r.oo
1253s   r-cran-r.utils r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp
1253s   r-cran-rcpparmadillo r-cran-rcppeigen r-cran-readr r-cran-readxl
1253s   r-cran-recipes r-cran-rematch r-cran-rematch2 r-cran-reshape2 r-cran-rio
1253s   r-cran-rlang r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-sandwich
1253s   r-cran-scales r-cran-shape r-cran-sp r-cran-sparsem r-cran-squarem
1253s   r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey r-cran-survival
1253s   r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect
1253s   r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs
1253s   r-cran-viridislite r-cran-vroom r-cran-waldo r-cran-withr r-cran-writexl
1253s   r-cran-xfun r-cran-yaml r-cran-zip r-cran-zoo rpcsvc-proto unzip x11-common
1253s   xdg-utils zip
1253s 0 upgraded, 240 newly installed, 0 to remove and 0 not upgraded.
1253s Need to get 228 MB of archives.
1253s After this operation, 571 MB of additional disk space will be used.
1253s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu6 [20.4 kB]
1253s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB]
1253s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB]
1253s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB]
1253s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu6 [2126 kB]
1253s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB]
1253s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB]
1253s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB]
1253s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B]
1253s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B]
1253s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB]
1253s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB]
1253s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB]
1253s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB]
1253s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB]
1253s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB]
1253s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB]
1253s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB]
1253s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB]
1253s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB]
1253s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB]
1253s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB]
1253s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB]
1253s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB]
1253s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B]
1253s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B]
1253s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB]
1253s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB]
1253s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB]
1253s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B]
1253s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B]
1253s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
1253s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
1253s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
1253s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB]
1253s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB]
1253s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB]
1253s Get:38 http://ftpmaster.internal/ubuntu noble/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
1253s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
1253s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB]
1253s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB]
1253s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB]
1253s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B]
1253s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB]
1253s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB]
1253s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB]
1253s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB]
1253s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB]
1253s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB]
1253s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB]
1253s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
1253s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB]
1253s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB]
1253s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
1253s Get:55 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
1253s Get:56 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
1253s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
1253s Get:58 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
1253s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB]
1253s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB]
1253s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB]
1253s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB]
1253s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB]
1253s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB]
1253s Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB]
1253s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB]
1253s Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B]
1253s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB]
1253s Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB]
1253s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB]
1253s Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB]
1253s Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB]
1253s Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB]
1253s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB]
1253s Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B]
1253s Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.14-1 [779 kB]
1253s Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6 amd64 1:1.2.1-1.1 [173 kB]
1253s Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB]
1253s Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB]
1253s Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
1253s Get:81 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.2-1build1 [27.0 MB]
1253s Get:82 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-littler amd64 0.3.19-1 [94.1 kB]
1253s Get:83 http://ftpmaster.internal/ubuntu noble/universe amd64 littler all 0.3.19-1 [2472 B]
1253s Get:84 http://ftpmaster.internal/ubuntu noble/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB]
1253s Get:85 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-abind all 1.4-5-2 [63.6 kB]
1253s Get:86 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cardata all 3.0.5-1 [1819 kB]
1253s Get:87 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mass amd64 7.3-60.0.1-1 [1119 kB]
1253s Get:88 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1 [1342 kB]
1253s Get:89 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-nlme amd64 3.1.164-1 [2260 kB]
1253s Get:90 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB]
1253s Get:91 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB]
1254s Get:92 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-nnet amd64 7.3-19-2 [112 kB]
1254s Get:93 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-boot all 1.3-30-1 [619 kB]
1254s Get:94 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB]
1254s Get:95 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcpp amd64 1.0.12-1 [1981 kB]
1254s Get:96 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-minqa amd64 1.2.6-1 [116 kB]
1254s Get:97 http://ftpmaster.internal/ubuntu noble/universe amd64 libnlopt0 amd64 2.7.1-5build2 [184 kB]
1254s Get:98 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-brio amd64 1.1.4-1 [37.9 kB]
1254s Get:99 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ps amd64 1.7.6-1 [313 kB]
1254s Get:100 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-r6 all 2.5.1-1 [99.0 kB]
1254s Get:101 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-processx amd64 3.8.3-1 [346 kB]
1254s Get:102 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-callr all 3.7.3-2 [425 kB]
1254s Get:103 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cli amd64 3.6.2-1 [1380 kB]
1254s Get:104 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-desc all 1.4.3-1 [359 kB]
1254s Get:105 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-digest amd64 0.6.34-1 [186 kB]
1254s Get:106 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-evaluate all 0.23-1 [90.2 kB]
1254s Get:107 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [441 kB]
1254s Get:108 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-glue amd64 1.7.0-1 [154 kB]
1254s Get:109 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rlang amd64 1.1.3-1 [1663 kB]
1254s Get:110 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
1254s Get:111 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
1254s Get:112 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-crayon all 1.5.2-1 [164 kB]
1254s Get:113 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fs amd64 1.6.3+dfsg-1 [229 kB]
1254s Get:114 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgbuild all 1.4.3-1 [209 kB]
1254s Get:115 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rprojroot all 2.0.4-1 [124 kB]
1254s Get:116 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-withr all 2.5.0-1 [225 kB]
1254s Get:117 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgload all 1.3.4-1 [207 kB]
1254s Get:118 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-praise all 1.0.0-4build1 [20.3 kB]
1254s Get:119 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-diffobj amd64 0.3.5-1 [1117 kB]
1254s Get:120 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB]
1254s Get:121 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB]
1254s Get:122 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
1254s Get:123 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB]
1254s Get:124 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
1254s Get:125 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [415 kB]
1254s Get:126 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB]
1254s Get:127 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-waldo all 0.5.2-1build1 [120 kB]
1254s Get:128 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-testthat amd64 3.2.1-1 [1684 kB]
1254s Get:129 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-nloptr amd64 2.0.3-1 [381 kB]
1254s Get:130 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcppeigen amd64 0.3.3.9.4-1 [1189 kB]
1254s Get:131 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB]
1254s Get:132 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lme4 amd64 1.1-35.1-4 [4138 kB]
1254s Get:133 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-backports amd64 1.4.1-1 [101 kB]
1254s Get:134 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB]
1254s Get:135 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [218 kB]
1254s Get:136 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dplyr amd64 1.1.4-1 [1515 kB]
1254s Get:137 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ellipsis amd64 0.3.2-2 [35.6 kB]
1254s Get:138 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-purrr amd64 1.0.2-1 [502 kB]
1254s Get:139 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-stringi amd64 1.8.3-1 [873 kB]
1254s Get:140 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB]
1254s Get:141 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cpp11 all 0.4.7-1 [266 kB]
1254s Get:142 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB]
1254s Get:143 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-broom all 1.0.5+dfsg-1 [1729 kB]
1254s Get:144 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB]
1254s Get:145 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xfun amd64 0.41+dfsg-1 [415 kB]
1254s Get:146 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-highr all 0.10+dfsg-1 [38.3 kB]
1254s Get:147 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-yaml amd64 2.3.8-1 [108 kB]
1254s Get:148 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
1254s Get:149 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-knitr all 1.45+dfsg-1 [917 kB]
1254s Get:150 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pbkrtest all 0.5.2-2 [182 kB]
1254s Get:151 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-sparsem amd64 1.81-1 [905 kB]
1254s Get:152 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrixmodels all 0.5-3-1 [361 kB]
1254s Get:153 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-survival amd64 3.5-8-1 [6120 kB]
1254s Get:154 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrixstats amd64 1.2.0-1 [488 kB]
1254s Get:155 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcpparmadillo amd64 0.12.8.0.0-1 [862 kB]
1254s Get:156 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB]
1254s Get:157 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB]
1254s Get:158 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-farver amd64 2.1.1-1 [1353 kB]
1254s Get:159 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB]
1254s Get:160 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1541 kB]
1254s Get:161 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-munsell all 0.5.0-2build1 [208 kB]
1254s Get:162 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
1254s Get:163 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB]
1254s Get:164 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-scales all 1.3.0-1 [603 kB]
1254s Get:165 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB]
1254s Get:166 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-class amd64 7.3-22-2 [88.3 kB]
1254s Get:167 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-proxy amd64 0.4-27-1 [182 kB]
1254s Get:168 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-e1071 amd64 1.7-14-1 [558 kB]
1254s Get:169 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-codetools all 0.2-19-1 [90.5 kB]
1254s Get:170 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-iterators all 1.0.14-1 [336 kB]
1254s Get:171 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-foreach all 1.5.2-1 [124 kB]
1254s Get:172 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-data.table amd64 1.14.10+dfsg-1 [1837 kB]
1254s Get:173 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-modelmetrics amd64 1.2.2.2-1build1 [128 kB]
1254s Get:174 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB]
1254s Get:175 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-proc amd64 1.18.5-1 [966 kB]
1254s Get:176 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tzdb amd64 0.4.0-2 [521 kB]
1254s Get:177 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-clock amd64 0.7.0-1.1 [1765 kB]
1254s Get:178 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-gower amd64 1.0.1-1 [207 kB]
1254s Get:179 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-hardhat all 1.3.1+dfsg-1 [554 kB]
1254s Get:180 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rpart amd64 4.1.23-1 [661 kB]
1254s Get:181 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-shape all 1.4.6-1 [770 kB]
1254s Get:182 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-diagram all 1.6.5-2 [656 kB]
1254s Get:183 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-kernsmooth amd64 2.23-22-1 [91.7 kB]
1254s Get:184 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-globals all 0.16.2-1 [117 kB]
1254s Get:185 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-listenv all 0.9.1+dfsg-1 [112 kB]
1254s Get:186 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-parallelly amd64 1.37.1-1 [365 kB]
1254s Get:187 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-future all 1.33.1+dfsg-1 [634 kB]
1254s Get:188 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-future.apply all 1.11.1+dfsg-1 [171 kB]
1254s Get:189 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-progressr all 0.14.0-1 [338 kB]
1254s Get:190 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-squarem all 2021.1-1 [179 kB]
1254s Get:191 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lava all 1.7.3+dfsg-1 [2166 kB]
1254s Get:192 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-prodlim amd64 2023.08.28-1 [408 kB]
1254s Get:193 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ipred amd64 0.9-14-1 [383 kB]
1254s Get:194 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-timechange amd64 0.3.0-1 [178 kB]
1254s Get:195 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lubridate amd64 1.9.3+dfsg-1 [1010 kB]
1254s Get:196 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-timedate amd64 4032.109-1 [1229 kB]
1254s Get:197 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-recipes all 1.0.9+dfsg-1 [1964 kB]
1254s Get:198 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-reshape2 amd64 1.4.4-2build1 [114 kB]
1254s Get:199 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-caret amd64 6.0-94+dfsg-1 [3434 kB]
1254s Get:200 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-conquer amd64 1.3.3-1 [499 kB]
1254s Get:201 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-quantreg amd64 5.97-1 [1533 kB]
1254s Get:202 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-sp amd64 1:2.1-2+dfsg-1 [1447 kB]
1254s Get:203 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-foreign amd64 0.8.86-1 [242 kB]
1254s Get:204 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-maptools amd64 1:1.1-8+dfsg-1 [1365 kB]
1254s Get:205 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-forcats all 1.0.0-1 [369 kB]
1254s Get:206 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-hms all 1.1.3-1 [96.5 kB]
1254s Get:207 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-clipr all 0.8.0-1 [53.5 kB]
1254s Get:208 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bit amd64 4.0.5-1 [1063 kB]
1254s Get:209 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bit64 amd64 4.0.5-1 [465 kB]
1254s Get:210 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-prettyunits all 1.2.0-1 [162 kB]
1254s Get:211 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-progress all 1.2.3-1 [91.9 kB]
1254s Get:212 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-vroom amd64 1.6.5-1 [848 kB]
1254s Get:213 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-readr amd64 2.1.5-1 [766 kB]
1254s Get:214 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-haven amd64 2.5.4-1 [346 kB]
1254s Get:215 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-curl amd64 5.2.0+dfsg-1 [188 kB]
1254s Get:216 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rematch all 2.0.0-1 [18.3 kB]
1254s Get:217 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cellranger all 1.1.0-3 [102 kB]
1254s Get:218 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-readxl amd64 1.4.3-1 [736 kB]
1254s Get:219 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-writexl amd64 1.5.0-1 [157 kB]
1254s Get:220 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB]
1254s Get:221 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-r.oo all 1.26.0-1 [955 kB]
1254s Get:222 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-r.utils all 2.12.3-1 [1386 kB]
1254s Get:223 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-zip amd64 2.3.1-1 [123 kB]
1254s Get:224 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-openxlsx amd64 4.2.5.2-1 [1943 kB]
1254s Get:225 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rio all 1.0.1-1 [529 kB]
1254s Get:226 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-car all 3.1-2-2 [1692 kB]
1254s Get:227 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-zoo amd64 1.8-12-2 [984 kB]
1254s Get:228 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lmtest amd64 0.9.40-1 [396 kB]
1254s Get:229 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-sandwich all 3.1-0-1 [1484 kB]
1254s Get:230 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-formula all 1.2-5-1 [158 kB]
1254s Get:231 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-aer all 1.2-12-1 [2582 kB]
1254s Get:232 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-blob all 1.2.4-1 [49.8 kB]
1254s Get:233 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fastmap amd64 1.1.1-1 [70.5 kB]
1254s Get:234 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cachem amd64 1.0.8-1 [72.1 kB]
1254s Get:235 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dbi all 1.2.2-1 [823 kB]
1254s Get:236 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB]
1254s Get:237 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mitools all 2.4-2build1 [265 kB]
1254s Get:238 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-plogr all 0.2.0-3build1 [15.1 kB]
1254s Get:239 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rsqlite amd64 2.3.4-1 [1364 kB]
1254s Get:240 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-survey all 4.2-1-1 [3189 kB]
1255s Preconfiguring packages ...
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1255s Selecting previously unselected package libc-dev-bin.
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1255s Preparing to unpack .../000-libc-dev-bin_2.39-0ubuntu6_amd64.deb ...
1255s Unpacking libc-dev-bin (2.39-0ubuntu6) ...
1255s Selecting previously unselected package linux-libc-dev:amd64.
1255s Preparing to unpack .../001-linux-libc-dev_6.8.0-11.11_amd64.deb ...
1255s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ...
1255s Selecting previously unselected package libcrypt-dev:amd64.
1255s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.36-4_amd64.deb ...
1256s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ...
1256s Selecting previously unselected package rpcsvc-proto.
1256s Preparing to unpack .../003-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ...
1256s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ...
1256s Selecting previously unselected package libc6-dev:amd64.
1256s Preparing to unpack .../004-libc6-dev_2.39-0ubuntu6_amd64.deb ...
1256s Unpacking libc6-dev:amd64 (2.39-0ubuntu6) ...
1256s Selecting previously unselected package libisl23:amd64.
1256s Preparing to unpack .../005-libisl23_0.26-3_amd64.deb ...
1256s Unpacking libisl23:amd64 (0.26-3) ...
1256s Selecting previously unselected package libmpc3:amd64.
1256s Preparing to unpack .../006-libmpc3_1.3.1-1_amd64.deb ...
1256s Unpacking libmpc3:amd64 (1.3.1-1) ...
1256s Selecting previously unselected package cpp-13-x86-64-linux-gnu.
1256s Preparing to unpack .../007-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
1256s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1256s Selecting previously unselected package cpp-13.
1256s Preparing to unpack .../008-cpp-13_13.2.0-17ubuntu2_amd64.deb ...
1256s Unpacking cpp-13 (13.2.0-17ubuntu2) ...
1256s Selecting previously unselected package cpp-x86-64-linux-gnu.
1256s Preparing to unpack .../009-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
1256s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1256s Selecting previously unselected package cpp.
1256s Preparing to unpack .../010-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ...
1256s Unpacking cpp (4:13.2.0-7ubuntu1) ...
1256s Selecting previously unselected package libcc1-0:amd64.
1256s Preparing to unpack .../011-libcc1-0_14-20240303-1ubuntu1_amd64.deb ...
1256s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ...
1256s Selecting previously unselected package libgomp1:amd64.
1256s Preparing to unpack .../012-libgomp1_14-20240303-1ubuntu1_amd64.deb ...
1256s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ...
1256s Selecting previously unselected package libitm1:amd64.
1256s Preparing to unpack .../013-libitm1_14-20240303-1ubuntu1_amd64.deb ...
1256s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ...
1256s Selecting previously unselected package libatomic1:amd64.
1256s Preparing to unpack .../014-libatomic1_14-20240303-1ubuntu1_amd64.deb ...
1256s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ...
1256s Selecting previously unselected package libasan8:amd64.
1256s Preparing to unpack .../015-libasan8_14-20240303-1ubuntu1_amd64.deb ...
1256s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ...
1256s Selecting previously unselected package liblsan0:amd64.
1256s Preparing to unpack .../016-liblsan0_14-20240303-1ubuntu1_amd64.deb ...
1256s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ...
1256s Selecting previously unselected package libtsan2:amd64.
1256s Preparing to unpack .../017-libtsan2_14-20240303-1ubuntu1_amd64.deb ...
1256s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ...
1256s Selecting previously unselected package libubsan1:amd64.
1256s Preparing to unpack .../018-libubsan1_14-20240303-1ubuntu1_amd64.deb ...
1256s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ...
1256s Selecting previously unselected package libhwasan0:amd64.
1256s Preparing to unpack .../019-libhwasan0_14-20240303-1ubuntu1_amd64.deb ...
1256s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ...
1256s Selecting previously unselected package libquadmath0:amd64.
1256s Preparing to unpack .../020-libquadmath0_14-20240303-1ubuntu1_amd64.deb ...
1256s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ...
1256s Selecting previously unselected package libgcc-13-dev:amd64.
1256s Preparing to unpack .../021-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ...
1256s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ...
1256s Selecting previously unselected package gcc-13-x86-64-linux-gnu.
1256s Preparing to unpack .../022-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
1256s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1257s Selecting previously unselected package gcc-13.
1257s Preparing to unpack .../023-gcc-13_13.2.0-17ubuntu2_amd64.deb ...
1257s Unpacking gcc-13 (13.2.0-17ubuntu2) ...
1257s Selecting previously unselected package gcc-x86-64-linux-gnu.
1257s Preparing to unpack .../024-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
1257s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1257s Selecting previously unselected package gcc.
1257s Preparing to unpack .../025-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ...
1257s Unpacking gcc (4:13.2.0-7ubuntu1) ...
1257s Selecting previously unselected package libstdc++-13-dev:amd64.
1257s Preparing to unpack .../026-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ...
1257s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ...
1257s Selecting previously unselected package g++-13-x86-64-linux-gnu.
1257s Preparing to unpack .../027-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
1257s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1257s Selecting previously unselected package g++-13.
1257s Preparing to unpack .../028-g++-13_13.2.0-17ubuntu2_amd64.deb ...
1257s Unpacking g++-13 (13.2.0-17ubuntu2) ...
1257s Selecting previously unselected package g++-x86-64-linux-gnu.
1257s Preparing to unpack .../029-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
1257s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1257s Selecting previously unselected package g++.
1257s Preparing to unpack .../030-g++_4%3a13.2.0-7ubuntu1_amd64.deb ...
1257s Unpacking g++ (4:13.2.0-7ubuntu1) ...
1257s Selecting previously unselected package build-essential.
1257s Preparing to unpack .../031-build-essential_12.10ubuntu1_amd64.deb ...
1257s Unpacking build-essential (12.10ubuntu1) ...
1257s Selecting previously unselected package fonts-dejavu-mono.
1257s Preparing to unpack .../032-fonts-dejavu-mono_2.37-8_all.deb ...
1257s Unpacking fonts-dejavu-mono (2.37-8) ...
1257s Selecting previously unselected package fonts-dejavu-core.
1257s Preparing to unpack .../033-fonts-dejavu-core_2.37-8_all.deb ...
1257s Unpacking fonts-dejavu-core (2.37-8) ...
1257s Selecting previously unselected package fontconfig-config.
1257s Preparing to unpack .../034-fontconfig-config_2.15.0-1ubuntu1_amd64.deb ...
1258s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
1258s Selecting previously unselected package libfontconfig1:amd64.
1258s Preparing to unpack .../035-libfontconfig1_2.15.0-1ubuntu1_amd64.deb ...
1258s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ...
1258s Selecting previously unselected package fontconfig.
1258s Preparing to unpack .../036-fontconfig_2.15.0-1ubuntu1_amd64.deb ...
1258s Unpacking fontconfig (2.15.0-1ubuntu1) ...
1258s Selecting previously unselected package fonts-glyphicons-halflings.
1258s Preparing to unpack .../037-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ...
1258s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
1258s Selecting previously unselected package fonts-mathjax.
1258s Preparing to unpack .../038-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
1258s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
1258s Selecting previously unselected package libblas3:amd64.
1258s Preparing to unpack .../039-libblas3_3.12.0-3_amd64.deb ...
1258s Unpacking libblas3:amd64 (3.12.0-3) ...
1258s Selecting previously unselected package libpixman-1-0:amd64.
1258s Preparing to unpack .../040-libpixman-1-0_0.42.2-1_amd64.deb ...
1258s Unpacking libpixman-1-0:amd64 (0.42.2-1) ...
1258s Selecting previously unselected package libxcb-render0:amd64.
1258s Preparing to unpack .../041-libxcb-render0_1.15-1_amd64.deb ...
1258s Unpacking libxcb-render0:amd64 (1.15-1) ...
1258s Selecting previously unselected package libxcb-shm0:amd64.
1258s Preparing to unpack .../042-libxcb-shm0_1.15-1_amd64.deb ...
1258s Unpacking libxcb-shm0:amd64 (1.15-1) ...
1258s Selecting previously unselected package libxrender1:amd64.
1258s Preparing to unpack .../043-libxrender1_1%3a0.9.10-1.1_amd64.deb ...
1258s Unpacking libxrender1:amd64 (1:0.9.10-1.1) ...
1258s Selecting previously unselected package libcairo2:amd64.
1258s Preparing to unpack .../044-libcairo2_1.18.0-1_amd64.deb ...
1258s Unpacking libcairo2:amd64 (1.18.0-1) ...
1258s Selecting previously unselected package libdatrie1:amd64.
1258s Preparing to unpack .../045-libdatrie1_0.2.13-3_amd64.deb ...
1258s Unpacking libdatrie1:amd64 (0.2.13-3) ...
1258s Selecting previously unselected package libdeflate0:amd64.
1258s Preparing to unpack .../046-libdeflate0_1.19-1_amd64.deb ...
1258s Unpacking libdeflate0:amd64 (1.19-1) ...
1258s Selecting previously unselected package libgfortran5:amd64.
1258s Preparing to unpack .../047-libgfortran5_14-20240303-1ubuntu1_amd64.deb ...
1258s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ...
1258s Selecting previously unselected package libgraphite2-3:amd64.
1258s Preparing to unpack .../048-libgraphite2-3_1.3.14-2_amd64.deb ...
1258s Unpacking libgraphite2-3:amd64 (1.3.14-2) ...
1258s Selecting previously unselected package libharfbuzz0b:amd64.
1258s Preparing to unpack .../049-libharfbuzz0b_8.3.0-2_amd64.deb ...
1258s Unpacking libharfbuzz0b:amd64 (8.3.0-2) ...
1258s Selecting previously unselected package x11-common.
1258s Preparing to unpack .../050-x11-common_1%3a7.7+23ubuntu2_all.deb ...
1258s Unpacking x11-common (1:7.7+23ubuntu2) ...
1258s Selecting previously unselected package libice6:amd64.
1258s Preparing to unpack .../051-libice6_2%3a1.0.10-1build2_amd64.deb ...
1258s Unpacking libice6:amd64 (2:1.0.10-1build2) ...
1258s Selecting previously unselected package libjpeg-turbo8:amd64.
1258s Preparing to unpack .../052-libjpeg-turbo8_2.1.5-2ubuntu1_amd64.deb ...
1258s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ...
1258s Selecting previously unselected package libjpeg8:amd64.
1258s Preparing to unpack .../053-libjpeg8_8c-2ubuntu11_amd64.deb ...
1258s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ...
1258s Selecting previously unselected package libjs-bootstrap.
1258s Preparing to unpack .../054-libjs-bootstrap_3.4.1+dfsg-3_all.deb ...
1258s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ...
1258s Selecting previously unselected package libjs-highlight.js.
1258s Preparing to unpack .../055-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ...
1258s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ...
1258s Selecting previously unselected package libjs-jquery.
1258s Preparing to unpack .../056-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
1258s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
1258s Selecting previously unselected package libjs-jquery-datatables.
1258s Preparing to unpack .../057-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ...
1258s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ...
1258s Selecting previously unselected package liblapack3:amd64.
1258s Preparing to unpack .../058-liblapack3_3.12.0-3_amd64.deb ...
1258s Unpacking liblapack3:amd64 (3.12.0-3) ...
1259s Selecting previously unselected package liblerc4:amd64.
1259s Preparing to unpack .../059-liblerc4_4.0.0+ds-4ubuntu1_amd64.deb ...
1259s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu1) ...
1259s Selecting previously unselected package libthai-data.
1259s Preparing to unpack .../060-libthai-data_0.1.29-2_all.deb ...
1259s Unpacking libthai-data (0.1.29-2) ...
1259s Selecting previously unselected package libthai0:amd64.
1259s Preparing to unpack .../061-libthai0_0.1.29-2_amd64.deb ...
1259s Unpacking libthai0:amd64 (0.1.29-2) ...
1259s Selecting previously unselected package libpango-1.0-0:amd64.
1259s Preparing to unpack .../062-libpango-1.0-0_1.51.0+ds-4_amd64.deb ...
1259s Unpacking libpango-1.0-0:amd64 (1.51.0+ds-4) ...
1259s Selecting previously unselected package libpangoft2-1.0-0:amd64.
1259s Preparing to unpack .../063-libpangoft2-1.0-0_1.51.0+ds-4_amd64.deb ...
1259s Unpacking libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ...
1259s Selecting previously unselected package libpangocairo-1.0-0:amd64.
1259s Preparing to unpack .../064-libpangocairo-1.0-0_1.51.0+ds-4_amd64.deb ...
1259s Unpacking libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ...
1259s Selecting previously unselected package libpaper1:amd64.
1259s Preparing to unpack .../065-libpaper1_1.1.29_amd64.deb ...
1259s Unpacking libpaper1:amd64 (1.1.29) ...
1259s Selecting previously unselected package libpaper-utils.
1259s Preparing to unpack .../066-libpaper-utils_1.1.29_amd64.deb ...
1259s Unpacking libpaper-utils (1.1.29) ...
1259s Selecting previously unselected package libsharpyuv0:amd64.
1259s Preparing to unpack .../067-libsharpyuv0_1.3.2-0.4_amd64.deb ...
1259s Unpacking libsharpyuv0:amd64 (1.3.2-0.4) ...
1259s Selecting previously unselected package libsm6:amd64.
1259s Preparing to unpack .../068-libsm6_2%3a1.2.3-1build2_amd64.deb ...
1259s Unpacking libsm6:amd64 (2:1.2.3-1build2) ...
1259s Selecting previously unselected package libtcl8.6:amd64.
1259s Preparing to unpack .../069-libtcl8.6_8.6.13+dfsg-2_amd64.deb ...
1259s Unpacking libtcl8.6:amd64 (8.6.13+dfsg-2) ...
1259s Selecting previously unselected package libjbig0:amd64.
1259s Preparing to unpack .../070-libjbig0_2.1-6.1ubuntu1_amd64.deb ...
1259s Unpacking libjbig0:amd64 (2.1-6.1ubuntu1) ...
1259s Selecting previously unselected package libwebp7:amd64.
1259s Preparing to unpack .../071-libwebp7_1.3.2-0.4_amd64.deb ...
1259s Unpacking libwebp7:amd64 (1.3.2-0.4) ...
1259s Selecting previously unselected package libtiff6:amd64.
1259s Preparing to unpack .../072-libtiff6_4.5.1+git230720-3ubuntu1_amd64.deb ...
1259s Unpacking libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ...
1259s Selecting previously unselected package libxft2:amd64.
1259s Preparing to unpack .../073-libxft2_2.3.6-1_amd64.deb ...
1259s Unpacking libxft2:amd64 (2.3.6-1) ...
1259s Selecting previously unselected package libxss1:amd64.
1259s Preparing to unpack .../074-libxss1_1%3a1.2.3-1build2_amd64.deb ...
1259s Unpacking libxss1:amd64 (1:1.2.3-1build2) ...
1259s Selecting previously unselected package libtk8.6:amd64.
1259s Preparing to unpack .../075-libtk8.6_8.6.14-1_amd64.deb ...
1259s Unpacking libtk8.6:amd64 (8.6.14-1) ...
1259s Selecting previously unselected package libxt6:amd64.
1259s Preparing to unpack .../076-libxt6_1%3a1.2.1-1.1_amd64.deb ...
1259s Unpacking libxt6:amd64 (1:1.2.1-1.1) ...
1259s Selecting previously unselected package zip.
1259s Preparing to unpack .../077-zip_3.0-13_amd64.deb ...
1259s Unpacking zip (3.0-13) ...
1259s Selecting previously unselected package unzip.
1259s Preparing to unpack .../078-unzip_6.0-28ubuntu3_amd64.deb ...
1259s Unpacking unzip (6.0-28ubuntu3) ...
1259s Selecting previously unselected package xdg-utils.
1259s Preparing to unpack .../079-xdg-utils_1.1.3-4.1ubuntu3_all.deb ...
1259s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ...
1259s Selecting previously unselected package r-base-core.
1259s Preparing to unpack .../080-r-base-core_4.3.2-1build1_amd64.deb ...
1259s Unpacking r-base-core (4.3.2-1build1) ...
1259s Selecting previously unselected package r-cran-littler.
1259s Preparing to unpack .../081-r-cran-littler_0.3.19-1_amd64.deb ...
1259s Unpacking r-cran-littler (0.3.19-1) ...
1260s Selecting previously unselected package littler.
1260s Preparing to unpack .../082-littler_0.3.19-1_all.deb ...
1260s Unpacking littler (0.3.19-1) ...
1260s Selecting previously unselected package node-normalize.css.
1260s Preparing to unpack .../083-node-normalize.css_8.0.1-5_all.deb ...
1260s Unpacking node-normalize.css (8.0.1-5) ...
1260s Selecting previously unselected package r-cran-abind.
1260s Preparing to unpack .../084-r-cran-abind_1.4-5-2_all.deb ...
1260s Unpacking r-cran-abind (1.4-5-2) ...
1260s Selecting previously unselected package r-cran-cardata.
1260s Preparing to unpack .../085-r-cran-cardata_3.0.5-1_all.deb ...
1260s Unpacking r-cran-cardata (3.0.5-1) ...
1260s Selecting previously unselected package r-cran-mass.
1260s Preparing to unpack .../086-r-cran-mass_7.3-60.0.1-1_amd64.deb ...
1260s Unpacking r-cran-mass (7.3-60.0.1-1) ...
1260s Selecting previously unselected package r-cran-lattice.
1260s Preparing to unpack .../087-r-cran-lattice_0.22-5-1_amd64.deb ...
1260s Unpacking r-cran-lattice (0.22-5-1) ...
1260s Selecting previously unselected package r-cran-nlme.
1260s Preparing to unpack .../088-r-cran-nlme_3.1.164-1_amd64.deb ...
1260s Unpacking r-cran-nlme (3.1.164-1) ...
1260s Selecting previously unselected package r-cran-matrix.
1260s Preparing to unpack .../089-r-cran-matrix_1.6-5-1_amd64.deb ...
1260s Unpacking r-cran-matrix (1.6-5-1) ...
1260s Selecting previously unselected package r-cran-mgcv.
1260s Preparing to unpack .../090-r-cran-mgcv_1.9-1-1_amd64.deb ...
1260s Unpacking r-cran-mgcv (1.9-1-1) ...
1260s Selecting previously unselected package r-cran-nnet.
1260s Preparing to unpack .../091-r-cran-nnet_7.3-19-2_amd64.deb ...
1260s Unpacking r-cran-nnet (7.3-19-2) ...
1260s Selecting previously unselected package r-cran-boot.
1260s Preparing to unpack .../092-r-cran-boot_1.3-30-1_all.deb ...
1260s Unpacking r-cran-boot (1.3-30-1) ...
1260s Selecting previously unselected package r-cran-pkgkitten.
1260s Preparing to unpack .../093-r-cran-pkgkitten_0.2.3-1_all.deb ...
1260s Unpacking r-cran-pkgkitten (0.2.3-1) ...
1260s Selecting previously unselected package r-cran-rcpp.
1260s Preparing to unpack .../094-r-cran-rcpp_1.0.12-1_amd64.deb ...
1260s Unpacking r-cran-rcpp (1.0.12-1) ...
1260s Selecting previously unselected package r-cran-minqa.
1260s Preparing to unpack .../095-r-cran-minqa_1.2.6-1_amd64.deb ...
1260s Unpacking r-cran-minqa (1.2.6-1) ...
1260s Selecting previously unselected package libnlopt0:amd64.
1260s Preparing to unpack .../096-libnlopt0_2.7.1-5build2_amd64.deb ...
1260s Unpacking libnlopt0:amd64 (2.7.1-5build2) ...
1260s Selecting previously unselected package r-cran-brio.
1260s Preparing to unpack .../097-r-cran-brio_1.1.4-1_amd64.deb ...
1260s Unpacking r-cran-brio (1.1.4-1) ...
1260s Selecting previously unselected package r-cran-ps.
1260s Preparing to unpack .../098-r-cran-ps_1.7.6-1_amd64.deb ...
1260s Unpacking r-cran-ps (1.7.6-1) ...
1260s Selecting previously unselected package r-cran-r6.
1260s Preparing to unpack .../099-r-cran-r6_2.5.1-1_all.deb ...
1260s Unpacking r-cran-r6 (2.5.1-1) ...
1260s Selecting previously unselected package r-cran-processx.
1260s Preparing to unpack .../100-r-cran-processx_3.8.3-1_amd64.deb ...
1260s Unpacking r-cran-processx (3.8.3-1) ...
1260s Selecting previously unselected package r-cran-callr.
1260s Preparing to unpack .../101-r-cran-callr_3.7.3-2_all.deb ...
1260s Unpacking r-cran-callr (3.7.3-2) ...
1260s Selecting previously unselected package r-cran-cli.
1260s Preparing to unpack .../102-r-cran-cli_3.6.2-1_amd64.deb ...
1260s Unpacking r-cran-cli (3.6.2-1) ...
1260s Selecting previously unselected package r-cran-desc.
1260s Preparing to unpack .../103-r-cran-desc_1.4.3-1_all.deb ...
1260s Unpacking r-cran-desc (1.4.3-1) ...
1260s Selecting previously unselected package r-cran-digest.
1260s Preparing to unpack .../104-r-cran-digest_0.6.34-1_amd64.deb ...
1260s Unpacking r-cran-digest (0.6.34-1) ...
1260s Selecting previously unselected package r-cran-evaluate.
1260s Preparing to unpack .../105-r-cran-evaluate_0.23-1_all.deb ...
1260s Unpacking r-cran-evaluate (0.23-1) ...
1261s Selecting previously unselected package r-cran-jsonlite.
1261s Preparing to unpack .../106-r-cran-jsonlite_1.8.8+dfsg-1_amd64.deb ...
1261s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ...
1261s Selecting previously unselected package r-cran-glue.
1261s Preparing to unpack .../107-r-cran-glue_1.7.0-1_amd64.deb ...
1261s Unpacking r-cran-glue (1.7.0-1) ...
1261s Selecting previously unselected package r-cran-rlang.
1261s Preparing to unpack .../108-r-cran-rlang_1.1.3-1_amd64.deb ...
1261s Unpacking r-cran-rlang (1.1.3-1) ...
1261s Selecting previously unselected package r-cran-lifecycle.
1261s Preparing to unpack .../109-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ...
1261s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ...
1261s Selecting previously unselected package r-cran-magrittr.
1261s Preparing to unpack .../110-r-cran-magrittr_2.0.3-1_amd64.deb ...
1261s Unpacking r-cran-magrittr (2.0.3-1) ...
1261s Selecting previously unselected package r-cran-crayon.
1261s Preparing to unpack .../111-r-cran-crayon_1.5.2-1_all.deb ...
1261s Unpacking r-cran-crayon (1.5.2-1) ...
1261s Selecting previously unselected package r-cran-fs.
1261s Preparing to unpack .../112-r-cran-fs_1.6.3+dfsg-1_amd64.deb ...
1261s Unpacking r-cran-fs (1.6.3+dfsg-1) ...
1261s Selecting previously unselected package r-cran-pkgbuild.
1261s Preparing to unpack .../113-r-cran-pkgbuild_1.4.3-1_all.deb ...
1261s Unpacking r-cran-pkgbuild (1.4.3-1) ...
1261s Selecting previously unselected package r-cran-rprojroot.
1261s Preparing to unpack .../114-r-cran-rprojroot_2.0.4-1_all.deb ...
1261s Unpacking r-cran-rprojroot (2.0.4-1) ...
1261s Selecting previously unselected package r-cran-withr.
1261s Preparing to unpack .../115-r-cran-withr_2.5.0-1_all.deb ...
1261s Unpacking r-cran-withr (2.5.0-1) ...
1261s Selecting previously unselected package r-cran-pkgload.
1261s Preparing to unpack .../116-r-cran-pkgload_1.3.4-1_all.deb ...
1261s Unpacking r-cran-pkgload (1.3.4-1) ...
1261s Selecting previously unselected package r-cran-praise.
1261s Preparing to unpack .../117-r-cran-praise_1.0.0-4build1_all.deb ...
1261s Unpacking r-cran-praise (1.0.0-4build1) ...
1261s Selecting previously unselected package r-cran-diffobj.
1261s Preparing to unpack .../118-r-cran-diffobj_0.3.5-1_amd64.deb ...
1261s Unpacking r-cran-diffobj (0.3.5-1) ...
1261s Selecting previously unselected package r-cran-fansi.
1261s Preparing to unpack .../119-r-cran-fansi_1.0.5-1_amd64.deb ...
1261s Unpacking r-cran-fansi (1.0.5-1) ...
1261s Selecting previously unselected package r-cran-utf8.
1261s Preparing to unpack .../120-r-cran-utf8_1.2.4-1_amd64.deb ...
1261s Unpacking r-cran-utf8 (1.2.4-1) ...
1261s Selecting previously unselected package r-cran-vctrs.
1261s Preparing to unpack .../121-r-cran-vctrs_0.6.5-1_amd64.deb ...
1261s Unpacking r-cran-vctrs (0.6.5-1) ...
1261s Selecting previously unselected package r-cran-pillar.
1261s Preparing to unpack .../122-r-cran-pillar_1.9.0+dfsg-1_all.deb ...
1261s Unpacking r-cran-pillar (1.9.0+dfsg-1) ...
1261s Selecting previously unselected package r-cran-pkgconfig.
1261s Preparing to unpack .../123-r-cran-pkgconfig_2.0.3-2build1_all.deb ...
1261s Unpacking r-cran-pkgconfig (2.0.3-2build1) ...
1261s Selecting previously unselected package r-cran-tibble.
1261s Preparing to unpack .../124-r-cran-tibble_3.2.1+dfsg-2_amd64.deb ...
1261s Unpacking r-cran-tibble (3.2.1+dfsg-2) ...
1261s Selecting previously unselected package r-cran-rematch2.
1261s Preparing to unpack .../125-r-cran-rematch2_2.1.2-2build1_all.deb ...
1261s Unpacking r-cran-rematch2 (2.1.2-2build1) ...
1261s Selecting previously unselected package r-cran-waldo.
1261s Preparing to unpack .../126-r-cran-waldo_0.5.2-1build1_all.deb ...
1261s Unpacking r-cran-waldo (0.5.2-1build1) ...
1261s Selecting previously unselected package r-cran-testthat.
1261s Preparing to unpack .../127-r-cran-testthat_3.2.1-1_amd64.deb ...
1261s Unpacking r-cran-testthat (3.2.1-1) ...
1261s Selecting previously unselected package r-cran-nloptr.
1261s Preparing to unpack .../128-r-cran-nloptr_2.0.3-1_amd64.deb ...
1261s Unpacking r-cran-nloptr (2.0.3-1) ...
1261s Selecting previously unselected package r-cran-rcppeigen.
1261s Preparing to unpack .../129-r-cran-rcppeigen_0.3.3.9.4-1_amd64.deb ...
1261s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ...
1261s Selecting previously unselected package r-cran-statmod.
1262s Preparing to unpack .../130-r-cran-statmod_1.5.0-1_amd64.deb ...
1262s Unpacking r-cran-statmod (1.5.0-1) ...
1262s Selecting previously unselected package r-cran-lme4.
1262s Preparing to unpack .../131-r-cran-lme4_1.1-35.1-4_amd64.deb ...
1262s Unpacking r-cran-lme4 (1.1-35.1-4) ...
1262s Selecting previously unselected package r-cran-backports.
1262s Preparing to unpack .../132-r-cran-backports_1.4.1-1_amd64.deb ...
1262s Unpacking r-cran-backports (1.4.1-1) ...
1262s Selecting previously unselected package r-cran-generics.
1262s Preparing to unpack .../133-r-cran-generics_0.1.3-1_all.deb ...
1262s Unpacking r-cran-generics (0.1.3-1) ...
1262s Selecting previously unselected package r-cran-tidyselect.
1262s Preparing to unpack .../134-r-cran-tidyselect_1.2.0+dfsg-1_amd64.deb ...
1262s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ...
1262s Selecting previously unselected package r-cran-dplyr.
1262s Preparing to unpack .../135-r-cran-dplyr_1.1.4-1_amd64.deb ...
1262s Unpacking r-cran-dplyr (1.1.4-1) ...
1262s Selecting previously unselected package r-cran-ellipsis.
1262s Preparing to unpack .../136-r-cran-ellipsis_0.3.2-2_amd64.deb ...
1262s Unpacking r-cran-ellipsis (0.3.2-2) ...
1262s Selecting previously unselected package r-cran-purrr.
1262s Preparing to unpack .../137-r-cran-purrr_1.0.2-1_amd64.deb ...
1262s Unpacking r-cran-purrr (1.0.2-1) ...
1262s Selecting previously unselected package r-cran-stringi.
1262s Preparing to unpack .../138-r-cran-stringi_1.8.3-1_amd64.deb ...
1262s Unpacking r-cran-stringi (1.8.3-1) ...
1262s Selecting previously unselected package r-cran-stringr.
1262s Preparing to unpack .../139-r-cran-stringr_1.5.1-1_all.deb ...
1262s Unpacking r-cran-stringr (1.5.1-1) ...
1262s Selecting previously unselected package r-cran-cpp11.
1262s Preparing to unpack .../140-r-cran-cpp11_0.4.7-1_all.deb ...
1262s Unpacking r-cran-cpp11 (0.4.7-1) ...
1262s Selecting previously unselected package r-cran-tidyr.
1262s Preparing to unpack .../141-r-cran-tidyr_1.3.1-1_amd64.deb ...
1262s Unpacking r-cran-tidyr (1.3.1-1) ...
1262s Selecting previously unselected package r-cran-broom.
1262s Preparing to unpack .../142-r-cran-broom_1.0.5+dfsg-1_all.deb ...
1262s Unpacking r-cran-broom (1.0.5+dfsg-1) ...
1262s Selecting previously unselected package r-cran-numderiv.
1262s Preparing to unpack .../143-r-cran-numderiv_2016.8-1.1-3_all.deb ...
1262s Unpacking r-cran-numderiv (2016.8-1.1-3) ...
1262s Selecting previously unselected package r-cran-xfun.
1262s Preparing to unpack .../144-r-cran-xfun_0.41+dfsg-1_amd64.deb ...
1262s Unpacking r-cran-xfun (0.41+dfsg-1) ...
1262s Selecting previously unselected package r-cran-highr.
1262s Preparing to unpack .../145-r-cran-highr_0.10+dfsg-1_all.deb ...
1262s Unpacking r-cran-highr (0.10+dfsg-1) ...
1262s Selecting previously unselected package r-cran-yaml.
1262s Preparing to unpack .../146-r-cran-yaml_2.3.8-1_amd64.deb ...
1262s Unpacking r-cran-yaml (2.3.8-1) ...
1262s Selecting previously unselected package libjs-mathjax.
1262s Preparing to unpack .../147-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
1262s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
1263s Selecting previously unselected package r-cran-knitr.
1263s Preparing to unpack .../148-r-cran-knitr_1.45+dfsg-1_all.deb ...
1263s Unpacking r-cran-knitr (1.45+dfsg-1) ...
1263s Selecting previously unselected package r-cran-pbkrtest.
1263s Preparing to unpack .../149-r-cran-pbkrtest_0.5.2-2_all.deb ...
1263s Unpacking r-cran-pbkrtest (0.5.2-2) ...
1263s Selecting previously unselected package r-cran-sparsem.
1263s Preparing to unpack .../150-r-cran-sparsem_1.81-1_amd64.deb ...
1263s Unpacking r-cran-sparsem (1.81-1) ...
1263s Selecting previously unselected package r-cran-matrixmodels.
1263s Preparing to unpack .../151-r-cran-matrixmodels_0.5-3-1_all.deb ...
1263s Unpacking r-cran-matrixmodels (0.5-3-1) ...
1263s Selecting previously unselected package r-cran-survival.
1263s Preparing to unpack .../152-r-cran-survival_3.5-8-1_amd64.deb ...
1263s Unpacking r-cran-survival (3.5-8-1) ...
1263s Selecting previously unselected package r-cran-matrixstats.
1263s Preparing to unpack .../153-r-cran-matrixstats_1.2.0-1_amd64.deb ...
1263s Unpacking r-cran-matrixstats (1.2.0-1) ...
1263s Selecting previously unselected package r-cran-rcpparmadillo.
1263s Preparing to unpack .../154-r-cran-rcpparmadillo_0.12.8.0.0-1_amd64.deb ...
1263s Unpacking r-cran-rcpparmadillo (0.12.8.0.0-1) ...
1263s Selecting previously unselected package r-cran-gtable.
1263s Preparing to unpack .../155-r-cran-gtable_0.3.4+dfsg-1_all.deb ...
1263s Unpacking r-cran-gtable (0.3.4+dfsg-1) ...
1263s Selecting previously unselected package r-cran-isoband.
1263s Preparing to unpack .../156-r-cran-isoband_0.2.7-1_amd64.deb ...
1263s Unpacking r-cran-isoband (0.2.7-1) ...
1264s Selecting previously unselected package r-cran-farver.
1264s Preparing to unpack .../157-r-cran-farver_2.1.1-1_amd64.deb ...
1264s Unpacking r-cran-farver (2.1.1-1) ...
1264s Selecting previously unselected package r-cran-labeling.
1264s Preparing to unpack .../158-r-cran-labeling_0.4.3-1_all.deb ...
1264s Unpacking r-cran-labeling (0.4.3-1) ...
1264s Selecting previously unselected package r-cran-colorspace.
1264s Preparing to unpack .../159-r-cran-colorspace_2.1-0+dfsg-1_amd64.deb ...
1264s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ...
1264s Selecting previously unselected package r-cran-munsell.
1264s Preparing to unpack .../160-r-cran-munsell_0.5.0-2build1_all.deb ...
1264s Unpacking r-cran-munsell (0.5.0-2build1) ...
1264s Selecting previously unselected package r-cran-rcolorbrewer.
1264s Preparing to unpack .../161-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ...
1264s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ...
1264s Selecting previously unselected package r-cran-viridislite.
1264s Preparing to unpack .../162-r-cran-viridislite_0.4.2-2_all.deb ...
1264s Unpacking r-cran-viridislite (0.4.2-2) ...
1264s Selecting previously unselected package r-cran-scales.
1264s Preparing to unpack .../163-r-cran-scales_1.3.0-1_all.deb ...
1264s Unpacking r-cran-scales (1.3.0-1) ...
1264s Selecting previously unselected package r-cran-ggplot2.
1264s Preparing to unpack .../164-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ...
1264s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ...
1264s Selecting previously unselected package r-cran-class.
1264s Preparing to unpack .../165-r-cran-class_7.3-22-2_amd64.deb ...
1264s Unpacking r-cran-class (7.3-22-2) ...
1264s Selecting previously unselected package r-cran-proxy.
1264s Preparing to unpack .../166-r-cran-proxy_0.4-27-1_amd64.deb ...
1264s Unpacking r-cran-proxy (0.4-27-1) ...
1264s Selecting previously unselected package r-cran-e1071.
1264s Preparing to unpack .../167-r-cran-e1071_1.7-14-1_amd64.deb ...
1264s Unpacking r-cran-e1071 (1.7-14-1) ...
1264s Selecting previously unselected package r-cran-codetools.
1264s Preparing to unpack .../168-r-cran-codetools_0.2-19-1_all.deb ...
1264s Unpacking r-cran-codetools (0.2-19-1) ...
1264s Selecting previously unselected package r-cran-iterators.
1264s Preparing to unpack .../169-r-cran-iterators_1.0.14-1_all.deb ...
1264s Unpacking r-cran-iterators (1.0.14-1) ...
1264s Selecting previously unselected package r-cran-foreach.
1264s Preparing to unpack .../170-r-cran-foreach_1.5.2-1_all.deb ...
1264s Unpacking r-cran-foreach (1.5.2-1) ...
1264s Selecting previously unselected package r-cran-data.table.
1264s Preparing to unpack .../171-r-cran-data.table_1.14.10+dfsg-1_amd64.deb ...
1264s Unpacking r-cran-data.table (1.14.10+dfsg-1) ...
1264s Selecting previously unselected package r-cran-modelmetrics.
1264s Preparing to unpack .../172-r-cran-modelmetrics_1.2.2.2-1build1_amd64.deb ...
1264s Unpacking r-cran-modelmetrics (1.2.2.2-1build1) ...
1264s Selecting previously unselected package r-cran-plyr.
1264s Preparing to unpack .../173-r-cran-plyr_1.8.9-1_amd64.deb ...
1264s Unpacking r-cran-plyr (1.8.9-1) ...
1264s Selecting previously unselected package r-cran-proc.
1264s Preparing to unpack .../174-r-cran-proc_1.18.5-1_amd64.deb ...
1264s Unpacking r-cran-proc (1.18.5-1) ...
1264s Selecting previously unselected package r-cran-tzdb.
1264s Preparing to unpack .../175-r-cran-tzdb_0.4.0-2_amd64.deb ...
1264s Unpacking r-cran-tzdb (0.4.0-2) ...
1264s Selecting previously unselected package r-cran-clock.
1264s Preparing to unpack .../176-r-cran-clock_0.7.0-1.1_amd64.deb ...
1264s Unpacking r-cran-clock (0.7.0-1.1) ...
1264s Selecting previously unselected package r-cran-gower.
1264s Preparing to unpack .../177-r-cran-gower_1.0.1-1_amd64.deb ...
1264s Unpacking r-cran-gower (1.0.1-1) ...
1264s Selecting previously unselected package r-cran-hardhat.
1264s Preparing to unpack .../178-r-cran-hardhat_1.3.1+dfsg-1_all.deb ...
1264s Unpacking r-cran-hardhat (1.3.1+dfsg-1) ...
1264s Selecting previously unselected package r-cran-rpart.
1264s Preparing to unpack .../179-r-cran-rpart_4.1.23-1_amd64.deb ...
1264s Unpacking r-cran-rpart (4.1.23-1) ...
1264s Selecting previously unselected package r-cran-shape.
1264s Preparing to unpack .../180-r-cran-shape_1.4.6-1_all.deb ...
1264s Unpacking r-cran-shape (1.4.6-1) ...
1264s Selecting previously unselected package r-cran-diagram.
1264s Preparing to unpack .../181-r-cran-diagram_1.6.5-2_all.deb ...
1264s Unpacking r-cran-diagram (1.6.5-2) ...
1265s Selecting previously unselected package r-cran-kernsmooth.
1265s Preparing to unpack .../182-r-cran-kernsmooth_2.23-22-1_amd64.deb ...
1265s Unpacking r-cran-kernsmooth (2.23-22-1) ...
1265s Selecting previously unselected package r-cran-globals.
1265s Preparing to unpack .../183-r-cran-globals_0.16.2-1_all.deb ...
1265s Unpacking r-cran-globals (0.16.2-1) ...
1265s Selecting previously unselected package r-cran-listenv.
1265s Preparing to unpack .../184-r-cran-listenv_0.9.1+dfsg-1_all.deb ...
1265s Unpacking r-cran-listenv (0.9.1+dfsg-1) ...
1265s Selecting previously unselected package r-cran-parallelly.
1265s Preparing to unpack .../185-r-cran-parallelly_1.37.1-1_amd64.deb ...
1265s Unpacking r-cran-parallelly (1.37.1-1) ...
1265s Selecting previously unselected package r-cran-future.
1265s Preparing to unpack .../186-r-cran-future_1.33.1+dfsg-1_all.deb ...
1265s Unpacking r-cran-future (1.33.1+dfsg-1) ...
1265s Selecting previously unselected package r-cran-future.apply.
1265s Preparing to unpack .../187-r-cran-future.apply_1.11.1+dfsg-1_all.deb ...
1265s Unpacking r-cran-future.apply (1.11.1+dfsg-1) ...
1265s Selecting previously unselected package r-cran-progressr.
1265s Preparing to unpack .../188-r-cran-progressr_0.14.0-1_all.deb ...
1265s Unpacking r-cran-progressr (0.14.0-1) ...
1265s Selecting previously unselected package r-cran-squarem.
1265s Preparing to unpack .../189-r-cran-squarem_2021.1-1_all.deb ...
1265s Unpacking r-cran-squarem (2021.1-1) ...
1265s Selecting previously unselected package r-cran-lava.
1265s Preparing to unpack .../190-r-cran-lava_1.7.3+dfsg-1_all.deb ...
1265s Unpacking r-cran-lava (1.7.3+dfsg-1) ...
1265s Selecting previously unselected package r-cran-prodlim.
1265s Preparing to unpack .../191-r-cran-prodlim_2023.08.28-1_amd64.deb ...
1265s Unpacking r-cran-prodlim (2023.08.28-1) ...
1265s Selecting previously unselected package r-cran-ipred.
1265s Preparing to unpack .../192-r-cran-ipred_0.9-14-1_amd64.deb ...
1265s Unpacking r-cran-ipred (0.9-14-1) ...
1265s Selecting previously unselected package r-cran-timechange.
1265s Preparing to unpack .../193-r-cran-timechange_0.3.0-1_amd64.deb ...
1265s Unpacking r-cran-timechange (0.3.0-1) ...
1265s Selecting previously unselected package r-cran-lubridate.
1265s Preparing to unpack .../194-r-cran-lubridate_1.9.3+dfsg-1_amd64.deb ...
1265s Unpacking r-cran-lubridate (1.9.3+dfsg-1) ...
1265s Selecting previously unselected package r-cran-timedate.
1265s Preparing to unpack .../195-r-cran-timedate_4032.109-1_amd64.deb ...
1265s Unpacking r-cran-timedate (4032.109-1) ...
1265s Selecting previously unselected package r-cran-recipes.
1265s Preparing to unpack .../196-r-cran-recipes_1.0.9+dfsg-1_all.deb ...
1265s Unpacking r-cran-recipes (1.0.9+dfsg-1) ...
1265s Selecting previously unselected package r-cran-reshape2.
1265s Preparing to unpack .../197-r-cran-reshape2_1.4.4-2build1_amd64.deb ...
1265s Unpacking r-cran-reshape2 (1.4.4-2build1) ...
1265s Selecting previously unselected package r-cran-caret.
1265s Preparing to unpack .../198-r-cran-caret_6.0-94+dfsg-1_amd64.deb ...
1265s Unpacking r-cran-caret (6.0-94+dfsg-1) ...
1265s Selecting previously unselected package r-cran-conquer.
1265s Preparing to unpack .../199-r-cran-conquer_1.3.3-1_amd64.deb ...
1265s Unpacking r-cran-conquer (1.3.3-1) ...
1265s Selecting previously unselected package r-cran-quantreg.
1265s Preparing to unpack .../200-r-cran-quantreg_5.97-1_amd64.deb ...
1265s Unpacking r-cran-quantreg (5.97-1) ...
1265s Selecting previously unselected package r-cran-sp.
1265s Preparing to unpack .../201-r-cran-sp_1%3a2.1-2+dfsg-1_amd64.deb ...
1265s Unpacking r-cran-sp (1:2.1-2+dfsg-1) ...
1265s Selecting previously unselected package r-cran-foreign.
1265s Preparing to unpack .../202-r-cran-foreign_0.8.86-1_amd64.deb ...
1265s Unpacking r-cran-foreign (0.8.86-1) ...
1265s Selecting previously unselected package r-cran-maptools.
1265s Preparing to unpack .../203-r-cran-maptools_1%3a1.1-8+dfsg-1_amd64.deb ...
1265s Unpacking r-cran-maptools (1:1.1-8+dfsg-1) ...
1265s Selecting previously unselected package r-cran-forcats.
1265s Preparing to unpack .../204-r-cran-forcats_1.0.0-1_all.deb ...
1265s Unpacking r-cran-forcats (1.0.0-1) ...
1265s Selecting previously unselected package r-cran-hms.
1265s Preparing to unpack .../205-r-cran-hms_1.1.3-1_all.deb ...
1265s Unpacking r-cran-hms (1.1.3-1) ...
1265s Selecting previously unselected package r-cran-clipr.
1265s Preparing to unpack .../206-r-cran-clipr_0.8.0-1_all.deb ...
1265s Unpacking r-cran-clipr (0.8.0-1) ...
1265s Selecting previously unselected package r-cran-bit.
1265s Preparing to unpack .../207-r-cran-bit_4.0.5-1_amd64.deb ...
1265s Unpacking r-cran-bit (4.0.5-1) ...
1266s Selecting previously unselected package r-cran-bit64.
1266s Preparing to unpack .../208-r-cran-bit64_4.0.5-1_amd64.deb ...
1266s Unpacking r-cran-bit64 (4.0.5-1) ...
1266s Selecting previously unselected package r-cran-prettyunits.
1266s Preparing to unpack .../209-r-cran-prettyunits_1.2.0-1_all.deb ...
1266s Unpacking r-cran-prettyunits (1.2.0-1) ...
1266s Selecting previously unselected package r-cran-progress.
1266s Preparing to unpack .../210-r-cran-progress_1.2.3-1_all.deb ...
1266s Unpacking r-cran-progress (1.2.3-1) ...
1266s Selecting previously unselected package r-cran-vroom.
1266s Preparing to unpack .../211-r-cran-vroom_1.6.5-1_amd64.deb ...
1266s Unpacking r-cran-vroom (1.6.5-1) ...
1266s Selecting previously unselected package r-cran-readr.
1266s Preparing to unpack .../212-r-cran-readr_2.1.5-1_amd64.deb ...
1266s Unpacking r-cran-readr (2.1.5-1) ...
1266s Selecting previously unselected package r-cran-haven.
1266s Preparing to unpack .../213-r-cran-haven_2.5.4-1_amd64.deb ...
1266s Unpacking r-cran-haven (2.5.4-1) ...
1266s Selecting previously unselected package r-cran-curl.
1266s Preparing to unpack .../214-r-cran-curl_5.2.0+dfsg-1_amd64.deb ...
1266s Unpacking r-cran-curl (5.2.0+dfsg-1) ...
1266s Selecting previously unselected package r-cran-rematch.
1266s Preparing to unpack .../215-r-cran-rematch_2.0.0-1_all.deb ...
1266s Unpacking r-cran-rematch (2.0.0-1) ...
1266s Selecting previously unselected package r-cran-cellranger.
1266s Preparing to unpack .../216-r-cran-cellranger_1.1.0-3_all.deb ...
1266s Unpacking r-cran-cellranger (1.1.0-3) ...
1266s Selecting previously unselected package r-cran-readxl.
1266s Preparing to unpack .../217-r-cran-readxl_1.4.3-1_amd64.deb ...
1266s Unpacking r-cran-readxl (1.4.3-1) ...
1266s Selecting previously unselected package r-cran-writexl.
1266s Preparing to unpack .../218-r-cran-writexl_1.5.0-1_amd64.deb ...
1266s Unpacking r-cran-writexl (1.5.0-1) ...
1266s Selecting previously unselected package r-cran-r.methodss3.
1266s Preparing to unpack .../219-r-cran-r.methodss3_1.8.2-1_all.deb ...
1266s Unpacking r-cran-r.methodss3 (1.8.2-1) ...
1266s Selecting previously unselected package r-cran-r.oo.
1266s Preparing to unpack .../220-r-cran-r.oo_1.26.0-1_all.deb ...
1266s Unpacking r-cran-r.oo (1.26.0-1) ...
1266s Selecting previously unselected package r-cran-r.utils.
1266s Preparing to unpack .../221-r-cran-r.utils_2.12.3-1_all.deb ...
1266s Unpacking r-cran-r.utils (2.12.3-1) ...
1266s Selecting previously unselected package r-cran-zip.
1266s Preparing to unpack .../222-r-cran-zip_2.3.1-1_amd64.deb ...
1266s Unpacking r-cran-zip (2.3.1-1) ...
1266s Selecting previously unselected package r-cran-openxlsx.
1266s Preparing to unpack .../223-r-cran-openxlsx_4.2.5.2-1_amd64.deb ...
1266s Unpacking r-cran-openxlsx (4.2.5.2-1) ...
1266s Selecting previously unselected package r-cran-rio.
1266s Preparing to unpack .../224-r-cran-rio_1.0.1-1_all.deb ...
1266s Unpacking r-cran-rio (1.0.1-1) ...
1266s Selecting previously unselected package r-cran-car.
1266s Preparing to unpack .../225-r-cran-car_3.1-2-2_all.deb ...
1266s Unpacking r-cran-car (3.1-2-2) ...
1266s Selecting previously unselected package r-cran-zoo.
1266s Preparing to unpack .../226-r-cran-zoo_1.8-12-2_amd64.deb ...
1266s Unpacking r-cran-zoo (1.8-12-2) ...
1266s Selecting previously unselected package r-cran-lmtest.
1266s Preparing to unpack .../227-r-cran-lmtest_0.9.40-1_amd64.deb ...
1266s Unpacking r-cran-lmtest (0.9.40-1) ...
1266s Selecting previously unselected package r-cran-sandwich.
1266s Preparing to unpack .../228-r-cran-sandwich_3.1-0-1_all.deb ...
1266s Unpacking r-cran-sandwich (3.1-0-1) ...
1266s Selecting previously unselected package r-cran-formula.
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1266s Unpacking r-cran-formula (1.2-5-1) ...
1266s Selecting previously unselected package r-cran-aer.
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1266s Unpacking r-cran-aer (1.2-12-1) ...
1266s Selecting previously unselected package r-cran-blob.
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1266s Unpacking r-cran-blob (1.2.4-1) ...
1266s Selecting previously unselected package r-cran-fastmap.
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1266s Unpacking r-cran-fastmap (1.1.1-1) ...
1266s Selecting previously unselected package r-cran-cachem.
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1266s Unpacking r-cran-cachem (1.0.8-1) ...
1266s Selecting previously unselected package r-cran-dbi.
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1267s Selecting previously unselected package r-cran-memoise.
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1267s Selecting previously unselected package r-cran-mitools.
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1267s Selecting previously unselected package r-cran-plogr.
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1267s Selecting previously unselected package r-cran-rsqlite.
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1267s Selecting previously unselected package r-cran-survey.
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1267s Setting up libgraphite2-3:amd64 (1.3.14-2) ...
1267s Setting up libpixman-1-0:amd64 (0.42.2-1) ...
1267s Setting up libsharpyuv0:amd64 (1.3.2-0.4) ...
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1267s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu1) ...
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1267s Setting up unzip (6.0-28ubuntu3) ...
1267s Setting up x11-common (1:7.7+23ubuntu2) ...
1267s Setting up libdeflate0:amd64 (1.19-1) ...
1267s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ...
1267s Setting up libnlopt0:amd64 (2.7.1-5build2) ...
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1267s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
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1267s Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ...
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1267s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ...
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1267s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
1267s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
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1270s Setting up libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ...
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1270s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1270s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1270s Setting up gcc (4:13.2.0-7ubuntu1) ...
1270s Setting up r-base-core (4.3.2-1build1) ...
1270s 
1270s Creating config file /etc/R/Renviron with new version
1270s Setting up r-cran-crayon (1.5.2-1) ...
1270s Setting up r-cran-squarem (2021.1-1) ...
1270s Setting up r-cran-labeling (0.4.3-1) ...
1270s Setting up r-cran-lattice (0.22-5-1) ...
1270s Setting up r-cran-ps (1.7.6-1) ...
1270s Setting up r-cran-nlme (3.1.164-1) ...
1270s Setting up r-cran-farver (2.1.1-1) ...
1270s Setting up r-cran-formula (1.2-5-1) ...
1270s Setting up r-cran-zip (2.3.1-1) ...
1270s Setting up r-cran-viridislite (0.4.2-2) ...
1270s Setting up r-cran-sparsem (1.81-1) ...
1270s Setting up r-cran-statmod (1.5.0-1) ...
1270s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1270s Setting up r-cran-nnet (7.3-19-2) ...
1270s Setting up r-cran-clipr (0.8.0-1) ...
1270s Setting up r-cran-proxy (0.4-27-1) ...
1270s Setting up r-cran-r6 (2.5.1-1) ...
1270s Setting up r-cran-pkgkitten (0.2.3-1) ...
1270s Setting up r-cran-numderiv (2016.8-1.1-3) ...
1270s Setting up r-cran-magrittr (2.0.3-1) ...
1270s Setting up r-cran-littler (0.3.19-1) ...
1270s Setting up r-cran-fs (1.6.3+dfsg-1) ...
1270s Setting up r-cran-rcpp (1.0.12-1) ...
1270s Setting up r-cran-curl (5.2.0+dfsg-1) ...
1270s Setting up r-cran-codetools (0.2-19-1) ...
1270s Setting up g++-13 (13.2.0-17ubuntu2) ...
1270s Setting up r-cran-brio (1.1.4-1) ...
1270s Setting up r-cran-boot (1.3-30-1) ...
1270s Setting up r-cran-diffobj (0.3.5-1) ...
1270s Setting up r-cran-rematch (2.0.0-1) ...
1270s Setting up r-cran-rlang (1.1.3-1) ...
1270s Setting up r-cran-matrixstats (1.2.0-1) ...
1270s Setting up r-cran-listenv (0.9.1+dfsg-1) ...
1270s Setting up littler (0.3.19-1) ...
1270s Setting up r-cran-xfun (0.41+dfsg-1) ...
1270s Setting up r-cran-plogr (0.2.0-3build1) ...
1270s Setting up r-cran-withr (2.5.0-1) ...
1270s Setting up r-cran-backports (1.4.1-1) ...
1270s Setting up r-cran-processx (3.8.3-1) ...
1270s Setting up r-cran-praise (1.0.0-4build1) ...
1270s Setting up r-cran-generics (0.1.3-1) ...
1270s Setting up r-cran-iterators (1.0.14-1) ...
1270s Setting up r-cran-abind (1.4-5-2) ...
1270s Setting up r-cran-digest (0.6.34-1) ...
1270s Setting up r-cran-yaml (2.3.8-1) ...
1270s Setting up r-cran-gower (1.0.1-1) ...
1270s Setting up r-cran-evaluate (0.23-1) ...
1270s Setting up r-cran-dbi (1.2.2-1) ...
1270s Setting up r-cran-timedate (4032.109-1) ...
1270s Setting up r-cran-highr (0.10+dfsg-1) ...
1270s Setting up r-cran-foreach (1.5.2-1) ...
1270s Setting up r-cran-prettyunits (1.2.0-1) ...
1270s Setting up r-cran-fansi (1.0.5-1) ...
1270s Setting up r-cran-cardata (3.0.5-1) ...
1270s Setting up r-cran-mass (7.3-60.0.1-1) ...
1270s Setting up r-cran-data.table (1.14.10+dfsg-1) ...
1270s Setting up r-cran-glue (1.7.0-1) ...
1270s Setting up r-cran-foreign (0.8.86-1) ...
1270s Setting up r-cran-writexl (1.5.0-1) ...
1270s Setting up r-cran-bit (4.0.5-1) ...
1270s Setting up r-cran-cli (3.6.2-1) ...
1270s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
1270s Setting up r-cran-rprojroot (2.0.4-1) ...
1270s Setting up r-cran-bit64 (4.0.5-1) ...
1270s Setting up r-cran-progressr (0.14.0-1) ...
1270s Setting up r-cran-shape (1.4.6-1) ...
1270s Setting up r-cran-fastmap (1.1.1-1) ...
1270s Setting up r-cran-r.methodss3 (1.8.2-1) ...
1270s Setting up r-cran-jsonlite (1.8.8+dfsg-1) ...
1270s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
1270s Setting up r-cran-sp (1:2.1-2+dfsg-1) ...
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1270s Setting up r-cran-gtable (0.3.4+dfsg-1) ...
1270s Setting up r-cran-zoo (1.8-12-2) ...
1270s Setting up r-cran-matrix (1.6-5-1) ...
1270s Setting up r-cran-kernsmooth (2.23-22-1) ...
1270s Setting up r-cran-knitr (1.45+dfsg-1) ...
1270s Setting up r-cran-mgcv (1.9-1-1) ...
1270s Setting up g++ (4:13.2.0-7ubuntu1) ...
1270s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
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1270s Setting up r-cran-rcpparmadillo (0.12.8.0.0-1) ...
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1270s Setting up r-cran-pillar (1.9.0+dfsg-1) ...
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1270s Setting up r-cran-stringr (1.5.1-1) ...
1270s Setting up r-cran-class (7.3-22-2) ...
1270s Setting up r-cran-modelmetrics (1.2.2.2-1build1) ...
1270s Setting up r-cran-callr (3.7.3-2) ...
1270s Setting up r-cran-openxlsx (4.2.5.2-1) ...
1270s Setting up r-cran-matrixmodels (0.5-3-1) ...
1270s Setting up r-cran-desc (1.4.3-1) ...
1270s Setting up r-cran-munsell (0.5.0-2build1) ...
1270s Setting up r-cran-tibble (3.2.1+dfsg-2) ...
1270s Setting up r-cran-clock (0.7.0-1.1) ...
1270s Setting up r-cran-sandwich (3.1-0-1) ...
1270s Setting up r-cran-proc (1.18.5-1) ...
1270s Setting up r-cran-survival (3.5-8-1) ...
1270s Setting up r-cran-survey (4.2-1-1) ...
1270s Setting up r-cran-r.oo (1.26.0-1) ...
1270s Setting up r-cran-future (1.33.1+dfsg-1) ...
1270s Setting up r-cran-forcats (1.0.0-1) ...
1270s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ...
1270s Setting up r-cran-reshape2 (1.4.4-2build1) ...
1270s Setting up r-cran-future.apply (1.11.1+dfsg-1) ...
1270s Setting up r-cran-timechange (0.3.0-1) ...
1270s Setting up r-cran-hms (1.1.3-1) ...
1270s Setting up r-cran-scales (1.3.0-1) ...
1270s Setting up r-cran-memoise (2.0.1-1) ...
1270s Setting up r-cran-lava (1.7.3+dfsg-1) ...
1270s Setting up r-cran-purrr (1.0.2-1) ...
1270s Setting up r-cran-e1071 (1.7-14-1) ...
1270s Setting up r-cran-blob (1.2.4-1) ...
1270s Setting up r-cran-pkgbuild (1.4.3-1) ...
1270s Setting up r-cran-hardhat (1.3.1+dfsg-1) ...
1270s Setting up r-cran-dplyr (1.1.4-1) ...
1270s Setting up r-cran-rsqlite (2.3.4-1) ...
1270s Setting up r-cran-progress (1.2.3-1) ...
1270s Setting up r-cran-lubridate (1.9.3+dfsg-1) ...
1270s Setting up r-cran-pkgload (1.3.4-1) ...
1270s Setting up r-cran-r.utils (2.12.3-1) ...
1270s Setting up r-cran-vroom (1.6.5-1) ...
1270s Setting up r-cran-prodlim (2023.08.28-1) ...
1270s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ...
1270s Setting up r-cran-cellranger (1.1.0-3) ...
1270s Setting up r-cran-rematch2 (2.1.2-2build1) ...
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1270s Setting up r-cran-recipes (1.0.9+dfsg-1) ...
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1270s Setting up r-cran-nloptr (2.0.3-1) ...
1270s Setting up r-cran-quantreg (5.97-1) ...
1270s Setting up r-cran-lme4 (1.1-35.1-4) ...
1270s Setting up r-cran-pbkrtest (0.5.2-2) ...
1270s Setting up r-cran-car (3.1-2-2) ...
1270s Setting up r-cran-aer (1.2-12-1) ...
1270s Processing triggers for libc-bin (2.39-0ubuntu6) ...
1270s Processing triggers for man-db (2.12.0-3) ...
1271s Processing triggers for install-info (7.1-3) ...
1278s Reading package lists...
1279s Building dependency tree...
1279s Reading state information...
1279s Starting pkgProblemResolver with broken count: 0
1279s Starting 2 pkgProblemResolver with broken count: 0
1279s Done
1279s The following NEW packages will be installed:
1279s   autopkgtest-satdep
1279s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
1279s Need to get 0 B/696 B of archives.
1279s After this operation, 0 B of additional disk space will be used.
1279s Get:1 /tmp/autopkgtest.fzci4f/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B]
1280s Selecting previously unselected package autopkgtest-satdep.
1280s (Reading database ... 
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1280s Unpacking autopkgtest-satdep (0) ...
1280s Setting up autopkgtest-satdep (0) ...
1281s (Reading database ... 95550 files and directories currently installed.)
1281s Removing autopkgtest-satdep (0) ...
1281s autopkgtest [01:25:37]: test run-unit-test: [-----------------------
1281s BEGIN TEST 3stage2phase.R
1281s 
1281s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1281s Copyright (C) 2023 The R Foundation for Statistical Computing
1281s Platform: x86_64-pc-linux-gnu (64-bit)
1281s 
1281s R is free software and comes with ABSOLUTELY NO WARRANTY.
1281s You are welcome to redistribute it under certain conditions.
1281s Type 'license()' or 'licence()' for distribution details.
1281s 
1281s R is a collaborative project with many contributors.
1281s Type 'contributors()' for more information and
1281s 'citation()' on how to cite R or R packages in publications.
1281s 
1281s Type 'demo()' for some demos, 'help()' for on-line help, or
1281s 'help.start()' for an HTML browser interface to help.
1281s Type 'q()' to quit R.
1281s 
1281s > ## simulated data with three-stage sample at phase 1, SRS at phase 2
1281s > ## motivated by dietary biomarker substudy in HCHS
1281s > 
1281s > library(survey)
1281s Loading required package: grid
1281s Loading required package: Matrix
1282s Loading required package: survival
1282s 
1282s Attaching package: 'survey'
1282s 
1282s > 
1282s > load("simdata1.RData")
1282s The following object is masked from 'package:graphics':
1282s 
1282s     dotchart
1282s 
1282s > 
1282s > twophase.full = twophase(id=list(~block+house+ind,~1),
1282s +                          strata=list(~strat,NULL),
1282s +                          probs=list(~P.block+P.house+P.ind,NULL),
1282s +                          subset=~phase2,
1282s +                          data=simdata1,method='full')
1283s > 
1283s > twophase.approx = twophase(id=list(~block+house+ind,~1),
1283s +                          strata=list(~strat,NULL),
1283s +                          probs=list(~P.block+P.house+P.ind,NULL),
1283s +                          subset=~phase2,
1283s +                          data=simdata1,method='approx')
1283s > 
1283s > twophase.rep = twophase(id=list(~block,~1),
1283s +                          strata=list(~strat,NULL),
1283s +                          probs=list(~I(P.block*P.house*P.ind),NULL),
1283s +                          subset=~phase2,
1283s +                          data=simdata1,method='full')
1283s > 
1283s > 
1283s > twophase.repapprox = twophase(id=list(~block,~1),
1283s +                          strata=list(~strat,NULL),
1283s +                          probs=list(~I(P.block*P.house*P.ind),NULL),
1283s +                          subset=~phase2,
1283s +                          data=simdata1,method='approx')
1283s > 
1283s > 
1283s > svymean(~age, twophase.full)
1283s       mean     SE
1283s age 41.116 0.8114
1283s > svymean(~age, twophase.approx)
1283s       mean     SE
1283s age 41.116 0.6693
1283s > svymean(~age, twophase.rep)
1283s       mean    SE
1283s age 41.116 0.784
1283s > svymean(~age, twophase.repapprox)
1283s       mean     SE
1283s age 41.116 0.6592
1283s > 
1283s BEGIN TEST DBIcheck.R
1283s 
1283s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1283s Copyright (C) 2023 The R Foundation for Statistical Computing
1283s Platform: x86_64-pc-linux-gnu (64-bit)
1283s 
1283s R is free software and comes with ABSOLUTELY NO WARRANTY.
1283s You are welcome to redistribute it under certain conditions.
1283s Type 'license()' or 'licence()' for distribution details.
1283s 
1283s R is a collaborative project with many contributors.
1283s Type 'contributors()' for more information and
1283s 'citation()' on how to cite R or R packages in publications.
1283s 
1283s Type 'demo()' for some demos, 'help()' for on-line help, or
1283s 'help.start()' for an HTML browser interface to help.
1283s Type 'q()' to quit R.
1283s 
1283s > 
1283s > library(survey)
1283s Loading required package: grid
1283s Loading required package: Matrix
1284s Loading required package: survival
1284s 
1284s Attaching package: 'survey'
1284s 
1284s The following object is masked from 'package:graphics':
1284s 
1284s     dotchart
1284s 
1284s > library(RSQLite)
1284s > 
1284s > data(api)
1284s > apiclus1$api_stu<-apiclus1$api.stu
1284s > apiclus1$comp_imp<-apiclus1$comp.imp
1284s > dclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,data=apiclus1)
1284s > dbclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,
1284s + data="apiclus1",dbtype="SQLite", dbname=system.file("api.db",package="survey"))
1285s > 
1285s > m<-svymean(~api00+stype,dclus1)
1285s > m.db<-svymean(~api00+stype, dbclus1)
1285s > all.equal(coef(m),coef(m.db))
1285s [1] TRUE
1285s > all.equal(vcov(m), vcov(m.db))
1285s [1] TRUE
1285s > 
1285s > r<-svyratio(~api_stu, ~enroll, design=dclus1)
1285s > r.db<-svyratio(~api_stu, ~enroll, design=dbclus1)
1285s > all.equal(coef(r), coef(r.db))
1285s [1] TRUE
1285s > all.equal(SE(r), SE(r.db))
1285s [1] TRUE
1285s > 
1285s > b<-svyby(~api99+api00,~stype, design=dclus1, svymean, deff=TRUE)
1285s > b.db<-svyby(~api99+api00,~stype, design=dbclus1,svymean, deff=TRUE)
1285s > all.equal(coef(b), coef(b.db))
1285s [1] TRUE
1285s > all.equal(SE(b), SE(b.db))
1285s [1] TRUE
1285s > all.equal(deff(b), deff(b.db))
1285s [1] TRUE
1285s > 
1285s > l<-svyglm(api00~api99+mobility, design=dclus1)
1285s > l.db<-svyglm(api00~api99+mobility, design=dbclus1)
1285s > all.equal(coef(l),coef(l.db))
1285s [1] TRUE
1285s > all.equal(vcov(l), vcov(l.db))
1285s [1] TRUE
1285s > 
1285s > dclus1<-update(dclus1, apidiff=api00-api99)
1285s > dclus1<-update(dclus1, apipct= apidiff/api99)
1285s > dbclus1<-update(dbclus1, apidiff=api00-api99)
1285s > dbclus1<-update(dbclus1, apipct= apidiff/api99)
1285s > 
1285s > u<-svymean(~api00+apidiff+apipct, dclus1)
1285s > u.db<-svymean(~api00+apidiff+apipct, dbclus1)
1285s > all.equal(u, u.db)
1285s [1] TRUE
1285s > 
1285s > all.equal(nrow(dclus1),nrow(dbclus1))
1285s [1] TRUE
1285s > all.equal(nrow(subset(dclus1,stype=="E")),
1285s +           nrow(subset(dbclus1,stype=="E")))
1285s [1] "Mean relative difference: 0.2708333"
1285s > 
1285s > ## replicate weights
1285s > rclus1<-as.svrepdesign(dclus1)
1285s > db_rclus1<-svrepdesign(weights=~pw, repweights="wt[1-9]+", type="JK1", scale=(1-15/757)*14/15,
1285s + data="apiclus1rep",dbtype="SQLite", dbname=system.file("api.db",package="survey"),combined.weights=FALSE)
1285s > m<-svymean(~api00+api99,rclus1)
1285s > m.db<-svymean(~api00+api99,db_rclus1)
1285s > all.equal(m,m.db)
1285s [1] TRUE
1285s > 
1285s > summary(db_rclus1)
1285s DB-backed replicate weight design
1285s Call: svrepdesign(weights = ~pw, repweights = "wt[1-9]+", type = "JK1", 
1285s     scale = (1 - 15/757) * 14/15, data = "apiclus1rep", dbtype = "SQLite", 
1285s     dbname = system.file("api.db", package = "survey"), combined.weights = FALSE)
1285s Unstratified cluster jacknife (JK1) with 15 replicates.
1285s Variables: 
1285s  [1] "row_names"   "cds"         "stype"       "name"        "sname"      
1285s  [6] "snum"        "dname"       "dnum"        "cname"       "cnum"       
1285s [11] "flag"        "pcttest"     "api00"       "api99"       "target"     
1285s [16] "growth"      "sch_wide"    "comp_imp"    "both"        "awards"     
1285s [21] "meals"       "ell"         "yr_rnd"      "mobility"    "acs_k3"     
1285s [26] "acs_46"      "acs_core"    "pct_resp"    "not_hsg"     "hsg"        
1285s [31] "some_col"    "col_grad"    "grad_sch"    "avg_ed"      "full__1"    
1285s [36] "emer"        "enroll"      "api_stu"     "fpc"         "pw"         
1285s [41] "row_names:1" "wt1"         "wt2"         "wt3"         "wt4"        
1285s [46] "wt5"         "wt6"         "wt7"         "wt8"         "wt9"        
1285s [51] "wt10"        "wt11"        "wt12"        "wt13"        "wt14"       
1285s [56] "wt15"       
1285s > 
1285s > s<-svymean(~api00, subset(rclus1, comp_imp=="Yes"))
1285s > s.db<-svymean(~api00, subset(db_rclus1, comp_imp=="Yes"))
1285s > all.equal(s,s.db)
1285s [1] TRUE
1285s > 
1285s BEGIN TEST anova-svycoxph.R
1285s 
1285s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1285s Copyright (C) 2023 The R Foundation for Statistical Computing
1285s Platform: x86_64-pc-linux-gnu (64-bit)
1285s 
1285s R is free software and comes with ABSOLUTELY NO WARRANTY.
1285s You are welcome to redistribute it under certain conditions.
1285s Type 'license()' or 'licence()' for distribution details.
1285s 
1285s R is a collaborative project with many contributors.
1285s Type 'contributors()' for more information and
1285s 'citation()' on how to cite R or R packages in publications.
1285s 
1285s Type 'demo()' for some demos, 'help()' for on-line help, or
1285s 'help.start()' for an HTML browser interface to help.
1285s Type 'q()' to quit R.
1285s 
1285s > 
1285s >  library(survey)
1285s Loading required package: grid
1285s Loading required package: Matrix
1286s Loading required package: survival
1286s 
1286s Attaching package: 'survey'
1286s 
1286s The following object is masked from 'package:graphics':
1286s 
1286s     dotchart
1286s 
1286s > example(svycoxph, ask=FALSE)
1286s 
1286s svycxp> ## Somewhat unrealistic example of nonresponse bias.
1286s svycxp> data(pbc, package="survival")
1286s 
1286s svycxp> pbc$randomized<-with(pbc, !is.na(trt) & trt>0)
1286s 
1286s svycxp> biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial)
1286s 
1286s svycxp> pbc$randprob<-fitted(biasmodel)
1286s 
1286s svycxp> if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0
1286s 
1286s svycxp> dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized))
1286s 
1286s svycxp> rpbc<-as.svrepdesign(dpbc)
1286s 
1286s svycxp> (model<-svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=dpbc))
1286s Call:
1286s svycoxph(formula = Surv(time, status > 0) ~ log(bili) + protime + 
1286s     albumin, design = dpbc)
1286s 
1286s               coef exp(coef) se(coef) robust se      z        p
1286s log(bili)  0.88592   2.42522  0.09140   0.09048  9.791  < 2e-16
1286s protime    0.24487   1.27745  0.07825   0.08122  3.015  0.00257
1286s albumin   -1.04298   0.35240  0.21211   0.20454 -5.099 3.41e-07
1286s 
1286s Likelihood ratio test=  on 3 df, p=
1286s n= 312, number of events= 144 
1286s 
1286s svycxp> svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=rpbc)
1286s Call:
1286s svycoxph.svyrep.design(formula = Surv(time, status > 0) ~ log(bili) + 
1286s     protime + albumin, design = rpbc)
1286s 
1286s               coef exp(coef) se(coef)      z        p
1286s log(bili)  0.88592   2.42522  0.09838  9.005  < 2e-16
1286s protime    0.24487   1.27745  0.09373  2.612  0.00899
1286s albumin   -1.04298   0.35240  0.21966 -4.748 2.05e-06
1286s 
1286s Likelihood ratio test=NA  on 3 df, p=NA
1286s n= 312, number of events= 144 
1286s 
1286s svycxp> s<-predict(model,se=TRUE, type="curve",
1286s svycxp+      newdata=data.frame(bili=c(3,9), protime=c(10,10), albumin=c(3.5,3.5)))
1286s 
1286s svycxp> plot(s[[1]],ci=TRUE,col="sienna")
1286s 
1286s svycxp> lines(s[[2]], ci=TRUE,col="royalblue")
1286s 
1286s svycxp> quantile(s[[1]], ci=TRUE)
1286s 0.75  0.5 0.25 
1286s 1435 2503 3574 
1286s attr(,"ci")
1286s      0.025 0.975
1286s 0.75  1217  1786
1286s 0.5   2256  3170
1286s 0.25  3222   Inf
1286s 
1286s svycxp> confint(s[[2]], parm=365*(1:5))
1286s          0.025     0.975
1286s 365  0.8375139 0.9453781
1286s 730  0.7382750 0.8999016
1286s 1095 0.4784105 0.7478460
1286s 1460 0.3192009 0.6206764
1286s 1825 0.2149475 0.5292978
1286s > m<-update(model, .~.+I(protime^2))
1286s > a<-anova(m,model)
1286s > b<-anova(m, model,force=TRUE)
1286s > stopifnot(isTRUE(all.equal(b[2:6],a[c(3,4,6,7,8)])))
1286s > 
1286s BEGIN TEST api.R
1286s 
1286s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1286s Copyright (C) 2023 The R Foundation for Statistical Computing
1286s Platform: x86_64-pc-linux-gnu (64-bit)
1286s 
1286s R is free software and comes with ABSOLUTELY NO WARRANTY.
1286s You are welcome to redistribute it under certain conditions.
1286s Type 'license()' or 'licence()' for distribution details.
1286s 
1286s R is a collaborative project with many contributors.
1286s Type 'contributors()' for more information and
1286s 'citation()' on how to cite R or R packages in publications.
1286s 
1286s Type 'demo()' for some demos, 'help()' for on-line help, or
1286s 'help.start()' for an HTML browser interface to help.
1286s Type 'q()' to quit R.
1286s 
1286s > library(survey)
1286s Loading required package: grid
1286s Loading required package: Matrix
1287s Loading required package: survival
1287s > options(survey.replicates.mse=TRUE)
1287s > example(api)
1287s 
1287s Attaching package: 'survey'
1287s 
1287s The following object is masked from 'package:graphics':
1287s 
1287s     dotchart
1287s 
1287s 
1287s api> library(survey)
1287s 
1287s api> data(api)
1288s 
1288s api> mean(apipop$api00)
1288s [1] 664.7126
1288s 
1288s api> sum(apipop$enroll, na.rm=TRUE)
1288s [1] 3811472
1288s 
1288s api> #stratified sample
1288s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
1288s 
1288s api> summary(dstrat)
1288s Stratified Independent Sampling design
1288s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
1288s Probabilities:
1288s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1288s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 
1288s Stratum Sizes: 
1288s              E  H  M
1288s obs        100 50 50
1288s design.PSU 100 50 50
1288s actual.PSU 100 50 50
1288s Population stratum sizes (PSUs): 
1288s    E    H    M 
1288s 4421  755 1018 
1288s Data variables:
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "pw"       "fpc"     
1288s 
1288s api> svymean(~api00, dstrat)
1288s         mean     SE
1288s api00 662.29 9.4089
1288s 
1288s api> svytotal(~enroll, dstrat, na.rm=TRUE)
1288s          total     SE
1288s enroll 3687178 114642
1288s 
1288s api> # one-stage cluster sample
1288s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1288s 
1288s api> summary(dclus1)
1288s 1 - level Cluster Sampling design
1288s With (15) clusters.
1288s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1288s Probabilities:
1288s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1288s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
1288s Population size (PSUs): 757 
1288s Data variables:
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "fpc"      "pw"      
1288s 
1288s api> svymean(~api00, dclus1)
1288s         mean     SE
1288s api00 644.17 23.542
1288s 
1288s api> svytotal(~enroll, dclus1, na.rm=TRUE)
1288s          total     SE
1288s enroll 3404940 932235
1288s 
1288s api> # two-stage cluster sample
1288s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
1288s 
1288s api> summary(dclus2)
1288s 2 - level Cluster Sampling design
1288s With (40, 126) clusters.
1288s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
1288s Probabilities:
1288s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
1288s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
1288s Population size (PSUs): 757 
1288s Data variables:
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
1288s 
1288s api> svymean(~api00, dclus2)
1288s         mean     SE
1288s api00 670.81 30.099
1288s 
1288s api> svytotal(~enroll, dclus2, na.rm=TRUE)
1288s          total     SE
1288s enroll 2639273 799638
1288s 
1288s api> # two-stage `with replacement'
1288s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
1288s 
1288s api> summary(dclus2wr)
1288s 2 - level Cluster Sampling design (with replacement)
1288s With (40, 126) clusters.
1288s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
1288s Probabilities:
1288s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
1288s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
1288s Data variables:
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
1288s 
1288s api> svymean(~api00, dclus2wr)
1288s         mean     SE
1288s api00 670.81 30.712
1288s 
1288s api> svytotal(~enroll, dclus2wr, na.rm=TRUE)
1288s          total     SE
1288s enroll 2639273 820261
1288s 
1288s api> # convert to replicate weights
1288s api> rclus1<-as.svrepdesign(dclus1)
1288s 
1288s api> summary(rclus1)
1288s Call: as.svrepdesign.default(dclus1)
1288s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances.
1288s Variables: 
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "fpc"      "pw"      
1288s 
1288s api> svymean(~api00, rclus1)
1288s         mean     SE
1288s api00 644.17 26.335
1288s 
1288s api> svytotal(~enroll, rclus1, na.rm=TRUE)
1288s          total     SE
1288s enroll 3404940 932235
1288s 
1288s api> # post-stratify on school type
1288s api> pop.types<-xtabs(~stype, data=apipop)
1288s 
1288s api> rclus1p<-postStratify(rclus1, ~stype, pop.types)
1288s 
1288s api> dclus1p<-postStratify(dclus1, ~stype, pop.types)
1288s 
1288s api> summary(dclus1p)
1288s 1 - level Cluster Sampling design
1288s With (15) clusters.
1288s dclus1p<-postStratify(dclus1, ~stype, pop.types)
1288s Probabilities:
1288s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1288s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 
1288s Population size (PSUs): 757 
1288s Data variables:
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "fpc"      "pw"      
1288s 
1288s api> summary(rclus1p)
1288s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types)
1288s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances.
1288s Variables: 
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "fpc"      "pw"      
1288s 
1288s api> svymean(~api00, dclus1p)
1288s         mean     SE
1288s api00 642.31 23.921
1288s 
1288s api> svytotal(~enroll, dclus1p, na.rm=TRUE)
1288s          total     SE
1288s enroll 3680893 406293
1288s 
1288s api> svymean(~api00, rclus1p)
1288s         mean     SE
1288s api00 642.31 26.936
1288s 
1288s api> svytotal(~enroll, rclus1p, na.rm=TRUE)
1288s          total     SE
1288s enroll 3680893 473434
1288s > 
1288s > options(survey.replicates.mse=FALSE)
1288s > example(api)
1288s 
1288s api> library(survey)
1288s 
1288s api> data(api)
1288s 
1288s api> mean(apipop$api00)
1288s [1] 664.7126
1288s 
1288s api> sum(apipop$enroll, na.rm=TRUE)
1288s [1] 3811472
1288s 
1288s api> #stratified sample
1288s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
1288s 
1288s api> summary(dstrat)
1288s Stratified Independent Sampling design
1288s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
1288s Probabilities:
1288s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1288s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 
1288s Stratum Sizes: 
1288s              E  H  M
1288s obs        100 50 50
1288s design.PSU 100 50 50
1288s actual.PSU 100 50 50
1288s Population stratum sizes (PSUs): 
1288s    E    H    M 
1288s 4421  755 1018 
1288s Data variables:
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "pw"       "fpc"     
1288s 
1288s api> svymean(~api00, dstrat)
1288s         mean     SE
1288s api00 662.29 9.4089
1288s 
1288s api> svytotal(~enroll, dstrat, na.rm=TRUE)
1288s          total     SE
1288s enroll 3687178 114642
1288s 
1288s api> # one-stage cluster sample
1288s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1288s 
1288s api> summary(dclus1)
1288s 1 - level Cluster Sampling design
1288s With (15) clusters.
1288s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1288s Probabilities:
1288s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1288s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
1288s Population size (PSUs): 757 
1288s Data variables:
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "fpc"      "pw"      
1288s 
1288s api> svymean(~api00, dclus1)
1288s         mean     SE
1288s api00 644.17 23.542
1288s 
1288s api> svytotal(~enroll, dclus1, na.rm=TRUE)
1288s          total     SE
1288s enroll 3404940 932235
1288s 
1288s api> # two-stage cluster sample
1288s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
1288s 
1288s api> summary(dclus2)
1288s 2 - level Cluster Sampling design
1288s With (40, 126) clusters.
1288s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
1288s Probabilities:
1288s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
1288s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
1288s Population size (PSUs): 757 
1288s Data variables:
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
1288s 
1288s api> svymean(~api00, dclus2)
1288s         mean     SE
1288s api00 670.81 30.099
1288s 
1288s api> svytotal(~enroll, dclus2, na.rm=TRUE)
1288s          total     SE
1288s enroll 2639273 799638
1288s 
1288s api> # two-stage `with replacement'
1288s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
1288s 
1288s api> summary(dclus2wr)
1288s 2 - level Cluster Sampling design (with replacement)
1288s With (40, 126) clusters.
1288s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
1288s Probabilities:
1288s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
1288s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
1288s Data variables:
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
1288s 
1288s api> svymean(~api00, dclus2wr)
1288s         mean     SE
1288s api00 670.81 30.712
1288s 
1288s api> svytotal(~enroll, dclus2wr, na.rm=TRUE)
1288s          total     SE
1288s enroll 2639273 820261
1288s 
1288s api> # convert to replicate weights
1288s api> rclus1<-as.svrepdesign(dclus1)
1288s 
1288s api> summary(rclus1)
1288s Call: as.svrepdesign.default(dclus1)
1288s Unstratified cluster jacknife (JK1) with 15 replicates.
1288s Variables: 
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "fpc"      "pw"      
1288s 
1288s api> svymean(~api00, rclus1)
1288s         mean     SE
1288s api00 644.17 26.329
1288s 
1288s api> svytotal(~enroll, rclus1, na.rm=TRUE)
1288s          total     SE
1288s enroll 3404940 932235
1288s 
1288s api> # post-stratify on school type
1288s api> pop.types<-xtabs(~stype, data=apipop)
1288s 
1288s api> rclus1p<-postStratify(rclus1, ~stype, pop.types)
1288s 
1288s api> dclus1p<-postStratify(dclus1, ~stype, pop.types)
1288s 
1288s api> summary(dclus1p)
1288s 1 - level Cluster Sampling design
1288s With (15) clusters.
1288s dclus1p<-postStratify(dclus1, ~stype, pop.types)
1288s Probabilities:
1288s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1288s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 
1288s Population size (PSUs): 757 
1288s Data variables:
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "fpc"      "pw"      
1288s 
1288s api> summary(rclus1p)
1288s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types)
1288s Unstratified cluster jacknife (JK1) with 15 replicates.
1288s Variables: 
1288s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1288s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1288s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1288s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1288s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1288s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1288s [37] "api.stu"  "fpc"      "pw"      
1288s 
1288s api> svymean(~api00, dclus1p)
1288s         mean     SE
1288s api00 642.31 23.921
1288s 
1288s api> svytotal(~enroll, dclus1p, na.rm=TRUE)
1288s          total     SE
1288s enroll 3680893 406293
1288s 
1288s api> svymean(~api00, rclus1p)
1288s         mean     SE
1288s api00 642.31 26.934
1288s 
1288s api> svytotal(~enroll, rclus1p, na.rm=TRUE)
1288s          total     SE
1288s enroll 3680893 473431
1288s > 
1288s BEGIN TEST badcal.R
1288s 
1288s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1288s Copyright (C) 2023 The R Foundation for Statistical Computing
1288s Platform: x86_64-pc-linux-gnu (64-bit)
1288s 
1288s R is free software and comes with ABSOLUTELY NO WARRANTY.
1288s You are welcome to redistribute it under certain conditions.
1288s Type 'license()' or 'licence()' for distribution details.
1288s 
1288s R is a collaborative project with many contributors.
1288s Type 'contributors()' for more information and
1288s 'citation()' on how to cite R or R packages in publications.
1288s 
1288s Type 'demo()' for some demos, 'help()' for on-line help, or
1288s 'help.start()' for an HTML browser interface to help.
1288s Type 'q()' to quit R.
1288s 
1288s > ##
1288s > ## Calibration with badly-scaled initial weights (bug report by Takahiro Tsuchiya)
1288s > ##
1288s > library(survey)
1288s Loading required package: grid
1288s Loading required package: Matrix
1289s Loading required package: survival
1289s 
1289s Attaching package: 'survey'
1289s 
1289s > data <- data.frame(x=c(1,1,1,1,2,2,2,2,2,2), w=rep(10,10))
1289s The following object is masked from 'package:graphics':
1289s 
1289s     dotchart
1289s 
1289s > des <- svydesign(ids=~1, weights=~w, data=data)
1289s > des.c <- calibrate(des, ~factor(x), c(10000, 5000))
1289s > des.r <- calibrate(des, ~factor(x), c(10000, 5000), calfun='raking')
1289s > stopifnot(all.equal(svytotal(~factor(x), des.c), svytotal(~factor(x), des.r)))
1289s > 
1289s BEGIN TEST bycovmat.R
1289s 
1289s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1289s Copyright (C) 2023 The R Foundation for Statistical Computing
1289s Platform: x86_64-pc-linux-gnu (64-bit)
1289s 
1289s R is free software and comes with ABSOLUTELY NO WARRANTY.
1289s You are welcome to redistribute it under certain conditions.
1289s Type 'license()' or 'licence()' for distribution details.
1289s 
1289s R is a collaborative project with many contributors.
1289s Type 'contributors()' for more information and
1289s 'citation()' on how to cite R or R packages in publications.
1289s 
1289s Type 'demo()' for some demos, 'help()' for on-line help, or
1289s 'help.start()' for an HTML browser interface to help.
1289s Type 'q()' to quit R.
1289s 
1289s > 
1289s > library(survey)
1289s Loading required package: grid
1289s Loading required package: Matrix
1290s Loading required package: survival
1290s > data(api)
1290s 
1290s Attaching package: 'survey'
1290s 
1290s The following object is masked from 'package:graphics':
1290s 
1290s     dotchart
1290s 
1290s > options(survey.replicates.mse=TRUE)
1290s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1290s > rclus1<-as.svrepdesign(dclus1)
1290s > 
1290s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
1290s +          covmat=TRUE,drop.empty.groups=FALSE)
1290s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
1290s +          covmat=TRUE,drop.empty.groups=TRUE)
1290s > 
1290s > stopifnot(all.equal(
1290s +               as.vector(as.matrix(SE(a))),as.vector(sqrt(diag(vcov(a))))
1290s + ))
1290s > stopifnot(all.equal(
1290s +               as.vector(as.matrix(SE(b))),as.vector(sqrt(diag(vcov(b))))
1290s +               ))
1290s > 
1290s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE)
1290s > all <- svytotal(~ell+mobility+meals, dclus1)
1290s > 
1290s > stopifnot(all(abs(vcov(svycontrast(all,
1290s +                                    list(quote(ell/mobility),
1290s +                                         quote(mobility/mobility),
1290s +                                         quote(ell/meals),quote(mobility/meals))))
1290s +                   -vcov(rat))<1e-10))
1290s > 
1290s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10))
1290s > 
1290s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE)
1290s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE)
1290s > 
1290s > con<-svycontrast(all,
1290s +                  list(quote(ell/mobility),
1290s +                       quote(mobility/mobility),
1290s +                       quote(ell/meals),quote(mobility/meals)))
1290s > 
1290s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10))
1290s > 
1290s > options(survey.replicates.mse=FALSE)
1290s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1290s > rclus1<-as.svrepdesign(dclus1)
1290s > 
1290s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
1290s +          covmat=TRUE,drop.empty.groups=FALSE)
1290s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
1290s +          covmat=TRUE,drop.empty.groups=TRUE)
1290s > 
1290s > stopifnot(all.equal(
1290s +               as.vector(as.matrix(SE(a))), as.vector(sqrt(diag(vcov(a))))
1290s + ))
1290s > stopifnot(all.equal(
1290s +               as.vector(as.matrix(SE(b))), as.vector(sqrt(diag(vcov(b))))
1290s +               ))
1290s > 
1290s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE)
1290s > all <- svytotal(~ell+mobility+meals, dclus1)
1290s > 
1290s > stopifnot(all(abs(vcov(svycontrast(all,
1290s +                                    list(quote(ell/mobility),
1290s +                                         quote(mobility/mobility),
1290s +                                         quote(ell/meals),quote(mobility/meals))))
1290s +                   -vcov(rat))<1e-10))
1290s > 
1290s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10))
1290s > 
1290s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE)
1290s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE)
1290s > 
1290s > con<-svycontrast(all,
1290s +                  list(quote(ell/mobility),
1290s +                       quote(mobility/mobility),
1290s +                       quote(ell/meals),quote(mobility/meals)))
1290s > 
1290s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10))
1290s > 
1290s > 
1290s > 
1290s BEGIN TEST caleg.R
1291s 
1291s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1291s Copyright (C) 2023 The R Foundation for Statistical Computing
1291s Platform: x86_64-pc-linux-gnu (64-bit)
1291s 
1291s R is free software and comes with ABSOLUTELY NO WARRANTY.
1291s You are welcome to redistribute it under certain conditions.
1291s Type 'license()' or 'licence()' for distribution details.
1291s 
1291s R is a collaborative project with many contributors.
1291s Type 'contributors()' for more information and
1291s 'citation()' on how to cite R or R packages in publications.
1291s 
1291s Type 'demo()' for some demos, 'help()' for on-line help, or
1291s 'help.start()' for an HTML browser interface to help.
1291s Type 'q()' to quit R.
1291s 
1291s > ##
1291s > ## Calibration examples
1291s > ##
1291s > 
1291s > 
1291s > ## Example of calibration to first-stage clusters
1291s > library(survey)
1291s Loading required package: grid
1291s Loading required package: Matrix
1291s Loading required package: survival
1292s 
1292s Attaching package: 'survey'
1292s 
1292s > data(api)
1292s The following object is masked from 'package:graphics':
1292s 
1292s     dotchart
1292s 
1292s > 
1292s > clusters<-table(apiclus2$dnum)
1292s > clusters<-clusters[clusters>1 & names(clusters)!="639"]
1292s > apiclus2a<-subset(apiclus2, dnum %in% as.numeric(names(clusters)))
1292s > 
1292s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2a)
1292s > 
1292s > popclusters<-subset(apipop, dnum %in% as.numeric(names(clusters)))
1292s > 
1292s > pop<-lapply(as.numeric(names(clusters)), function(cluster) {
1292s +   colSums(model.matrix(~api99, model.frame(~api99, subset(popclusters, dnum %in% cluster))))})
1292s > 
1292s > names(pop)<-names(clusters)
1292s > 
1292s > dclus2g<-calibrate(dclus2, ~api99, pop,stage=1)
1292s > 
1292s > svymean(~api99, dclus2)
1292s         mean     SE
1292s api99 642.14 31.434
1292s > svymean(~api99, dclus2g)
1292s         mean    SE
1292s api99 654.49 29.82
1292s > 
1292s > round(svyby(~api99, ~dnum, design=dclus2, svymean),4)
1292s     dnum    api99      se
1292s 83    83 694.3333  0.0000
1292s 132  132 505.0000  0.0000
1292s 152  152 574.0000  0.0000
1292s 173  173 894.7500  0.0000
1292s 198  198 533.7500  0.0000
1292s 200  200 589.8000  6.8335
1292s 228  228 477.0000  0.0000
1292s 295  295 646.4000  0.0000
1292s 302  302 903.5000  0.0000
1292s 403  403 852.4000  0.0000
1292s 452  452 533.0000  0.0000
1292s 480  480 614.2000  0.0000
1292s 523  523 580.5000  0.0000
1292s 534  534 564.6000  0.0000
1292s 549  549 896.2000  0.0000
1292s 552  552 730.0000  0.0000
1292s 570  570 518.4000  7.5478
1292s 575  575 800.8000  4.2513
1292s 596  596 785.6000  2.4155
1292s 620  620 591.6000 10.5869
1292s 638  638 560.2000  4.0954
1292s 674  674 760.0000  0.0000
1292s 679  679 610.2500  0.0000
1292s 687  687 718.6667  0.0000
1292s 701  701 651.5000  0.0000
1292s 711  711 690.5000  0.0000
1292s 731  731 702.0000  2.1744
1292s 768  768 562.5000  0.0000
1292s 781  781 854.4000  0.7456
1292s > 
1292s > round(svyby(~api99, ~dnum, design=dclus2g, svymean),4)
1292s     dnum    api99 se
1292s 83    83 694.3333  0
1292s 132  132 505.0000  0
1292s 152  152 574.0000  0
1292s 173  173 894.7500  0
1292s 198  198 533.7500  0
1292s 200  200 567.5455  0
1292s 228  228 477.0000  0
1292s 295  295 646.4000  0
1292s 302  302 903.5000  0
1292s 403  403 852.4000  0
1292s 452  452 533.0000  0
1292s 480  480 614.2000  0
1292s 523  523 580.5000  0
1292s 534  534 564.6000  0
1292s 549  549 896.2000  0
1292s 552  552 730.0000  0
1292s 570  570 548.9444  0
1292s 575  575 824.5357  0
1292s 596  596 787.5714  0
1292s 620  620 609.3750  0
1292s 638  638 585.6429  0
1292s 674  674 760.0000  0
1292s 679  679 610.2500  0
1292s 687  687 718.6667  0
1292s 701  701 651.5000  0
1292s 711  711 690.5000  0
1292s 731  731 700.6667  0
1292s 768  768 562.5000  0
1292s 781  781 851.0000  0
1292s > 
1292s > ## Averaging to first stage
1292s > 
1292s > dclus1<- svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc)
1292s > pop<-colSums(cbind(1,apipop$enroll),na.rm=TRUE)
1292s > 
1292s > dclus1g<-calibrate(dclus1, ~enroll, pop, aggregate=1)
1292s > 
1292s > svytotal(~enroll,dclus1g)
1292s          total SE
1292s enroll 3811472  0
1292s > svytotal(~api.stu,dclus1g)
1292s           total    SE
1292s api.stu 3242857 38967
1292s > 
1292s > #variation within clusters should be zero
1292s > all.equal(0, max(ave(weights(dclus1g),dclus1g$cluster,FUN=var),na.rm=TRUE))
1292s [1] TRUE
1292s > 
1292s > ##bounded weights
1292s >  dclus1g<-calibrate(dclus1, ~enroll, pop)
1292s >  range(weights(dclus1g)/weights(dclus1))
1292s [1] 0.7906782 1.7891164
1292s >  dclus1gb<-calibrate(dclus1, ~enroll, pop, bounds=c(.6,1.5))
1292s >  range(weights(dclus1gb)/weights(dclus1))
1292s [1] 0.7198751 1.5000000
1292s > 
1292s > ## Ratio estimators
1292s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
1292s > svytotal(~api.stu,dstrat)
1292s           total    SE
1292s api.stu 3086009 99477
1292s > common<-svyratio(~api.stu, ~enroll, dstrat, separate=FALSE)
1292s > total.enroll<-sum(apipop$enroll,na.rm=TRUE)
1292s > predict(common, total=total.enroll)
1292s $total
1292s          enroll
1292s api.stu 3190038
1292s 
1292s $se
1292s           enroll
1292s api.stu 29565.98
1292s 
1292s > dstratg<-calibrate(dstrat,~enroll-1, total.enroll, variance=1)
1292s > svytotal(~api.stu, dstratg)
1292s           total    SE
1292s api.stu 3190038 29566
1292s > 
1292s > ## postStratify vs calibrate in stratified sample (Ben French)
1292s > set.seed(17)
1292s > dat<-data.frame(y=rep(0:1,each=100),x=rnorm(200)+2*rep(0:1,each=100),
1292s +                 z=rbinom(200,1,.2), fpc=rep(c(100,10000),each=100))
1292s > dat$w<-ifelse(dat$y,dat$z,1-dat$z)
1292s > popw<-data.frame(w=c("0","1"), Freq=c(2000,8000))
1292s >  des<-svydesign(id=~1,fpc=~fpc, data=dat,strata=~y)
1292s > postStratify(des,~w,popw)->dps
1292s > dcal<-calibrate(des,~factor(w), pop=c(10000,8000))
1292s > 
1292s > all.equal(SE(svymean(~x,dcal)),SE(svymean(~x,dps)))
1292s [1] TRUE
1292s > 
1292s > ## missing data in calibrated design
1292s > dps$variables$z[1]<-NA
1292s > summary(svyglm(y~z+x,design=dps,family=quasibinomial))
1292s 
1292s Call:
1292s svyglm(formula = y ~ z + x, design = dps, family = quasibinomial)
1292s 
1292s Survey design:
1292s postStratify(des, ~w, popw)
1292s 
1292s Coefficients:
1292s             Estimate Std. Error t value Pr(>|t|)    
1292s (Intercept)  -0.1203     0.3380  -0.356    0.722    
1292s z             6.2118     0.6451   9.630   <2e-16 ***
1292s x             2.2602     0.2514   8.992   <2e-16 ***
1292s ---
1292s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1292s 
1292s (Dispersion parameter for quasibinomial family taken to be 1.919987)
1292s 
1292s Number of Fisher Scoring iterations: 9
1292s 
1292s > 
1292s > ## Ratio estimator using the heteroskedasticity parameter (Daniel Oehm)
1292s > # should match the ratio estmate above
1292s > dstratgh <- calibrate(dstrat,~enroll-1, total.enroll, variance=apistrat$enroll)
1292s > svytotal(~api.stu, dstratgh)
1292s           total    SE
1292s api.stu 3190038 29566
1292s > 
1292s > ## individual boundary constraints as multiplicative values (Daniel Oehm)
1292s > bnds <- list(
1292s +   lower = c(1, 1, rep(-Inf, nrow(apistrat)-2)), 
1292s +   upper = c(1, 1, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged the others are free to move
1292s > lapply(bnds, head)
1292s $lower
1292s [1]    1    1 -Inf -Inf -Inf -Inf
1292s 
1292s $upper
1292s [1]   1   1 Inf Inf Inf Inf
1292s 
1292s > dstratg1<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, variance=apistrat$enroll)
1292s > svytotal(~api.stu, dstratg1)
1292s           total    SE
1292s api.stu 3190133 29561
1292s > head(weights(dstrat))
1292s     1     2     3     4     5     6 
1292s 44.21 44.21 44.21 44.21 44.21 44.21 
1292s > head(weights(dstratg1))
1292s        1        2        3        4        5        6 
1292s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 
1292s > all.equal(weights(dstrat)[1:2], weights(dstratg1)[1:2])
1292s [1] TRUE
1292s > 
1292s > ## individual boundary constraints as constant values (Daniel Oehm)
1292s > bnds <- list(
1292s +   lower = c(44.21, 44.21, rep(-Inf, nrow(apistrat)-2)), 
1292s +   upper = c(44.21, 44.21, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged
1292s > lapply(bnds, head)
1292s $lower
1292s [1] 44.21 44.21  -Inf  -Inf  -Inf  -Inf
1292s 
1292s $upper
1292s [1] 44.21 44.21   Inf   Inf   Inf   Inf
1292s 
1292s > dstratg2<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, bounds.const = TRUE, variance=apistrat$enroll)
1292s > svytotal(~api.stu, dstratg2)
1292s           total    SE
1292s api.stu 3190133 29561
1292s > head(weights(dstrat))
1292s     1     2     3     4     5     6 
1292s 44.21 44.21 44.21 44.21 44.21 44.21 
1292s > head(weights(dstratg2))
1292s        1        2        3        4        5        6 
1292s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 
1292s > all.equal(round(weights(dstrat)[1:2], 8), round(weights(dstratg2)[1:2]), 8) # minor rounding error but all good
1292s [1] TRUE
1292s > 
1292s > # sparse matrix support (Daniel Oehm)
1292s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1292s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
1292s > dclus1g<-calibrate(dclus1, ~stype, pop.totals)
1292s > svymean(~api00, dclus1g)
1292s         mean     SE
1292s api00 642.31 23.921
1292s > svytotal(~enroll, dclus1g)
1292s          total     SE
1292s enroll 3680893 406293
1292s > 
1292s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
1292s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE)
1292s > svymean(~api00, dclus1g)
1292s         mean     SE
1292s api00 642.31 23.921
1292s > svytotal(~enroll, dclus1g)
1292s          total     SE
1292s enroll 3680893 406293
1292s > 
1292s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
1292s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE, calfun = "raking")
1292s > svymean(~api00, dclus1g)
1292s         mean     SE
1292s api00 642.31 23.921
1292s > svytotal(~enroll, dclus1g)
1292s          total     SE
1292s enroll 3680893 406293
1292s > 
1293s BEGIN TEST check.R
1293s 
1293s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1293s Copyright (C) 2023 The R Foundation for Statistical Computing
1293s Platform: x86_64-pc-linux-gnu (64-bit)
1293s 
1293s R is free software and comes with ABSOLUTELY NO WARRANTY.
1293s You are welcome to redistribute it under certain conditions.
1293s Type 'license()' or 'licence()' for distribution details.
1293s 
1293s R is a collaborative project with many contributors.
1293s Type 'contributors()' for more information and
1293s 'citation()' on how to cite R or R packages in publications.
1293s 
1293s Type 'demo()' for some demos, 'help()' for on-line help, or
1293s 'help.start()' for an HTML browser interface to help.
1293s Type 'q()' to quit R.
1293s 
1293s > library(survey)
1293s Loading required package: grid
1293s Loading required package: Matrix
1293s Loading required package: survival
1294s 
1294s Attaching package: 'survey'
1294s 
1294s The following object is masked from 'package:graphics':
1294s 
1294s     dotchart
1294s 
1294s > data(fpc)
1294s > ## test various possibilities for svydesign
1294s > a<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
1294s > a
1294s Stratified Independent Sampling design (with replacement)
1294s svydesign(weights = ~weight, ids = ~psuid, strata = ~stratid, 
1294s     variables = ~x, data = fpc, nest = TRUE)
1294s > svymean(~x,a)
1294s     mean     SE
1294s x 5.4481 0.7413
1294s > a<-svydesign(weights=~weight, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
1294s > a
1294s Stratified Independent Sampling design (with replacement)
1294s svydesign(weights = ~weight, ids = ~0, strata = ~stratid, variables = ~x, 
1294s     data = fpc, nest = TRUE)
1294s > svymean(~x,a)
1294s     mean     SE
1294s x 5.4481 0.7413
1294s > a<-svydesign(weights=1, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
1294s > a
1294s Stratified Independent Sampling design (with replacement)
1294s svydesign(weights = 1, ids = ~0, strata = ~stratid, variables = ~x, 
1294s     data = fpc, nest = TRUE)
1294s > svymean(~x,a)
1294s   mean    SE
1294s x 44.2 6.237
1294s > a<-svydesign(ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
1294s Warning message:
1294s In svydesign.default(ids = ~0, strata = ~stratid, variables = ~x,  :
1294s   No weights or probabilities supplied, assuming equal probability
1294s > a
1294s Stratified Independent Sampling design (with replacement)
1294s svydesign(ids = ~0, strata = ~stratid, variables = ~x, data = fpc, 
1294s     nest = TRUE)
1294s > svymean(~x,a)
1294s    mean     SE
1294s x 5.525 0.7796
1294s > a<-svydesign(ids=~0, strata=~stratid, prob=~I(1/weight),variables=~x, data=fpc, nest=TRUE)
1294s > a
1294s Stratified Independent Sampling design (with replacement)
1294s svydesign(ids = ~0, strata = ~stratid, prob = ~I(1/weight), variables = ~x, 
1294s     data = fpc, nest = TRUE)
1294s > svymean(~x,a)
1294s     mean     SE
1294s x 5.4481 0.7413
1294s > a<-svydesign(ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
1294s > a
1294s Stratified Independent Sampling designWarning message:
1294s In svydesign.default(ids = ~psuid, strata = ~stratid, variables = ~x,  :
1294s   No weights or probabilities supplied, assuming equal probability
1294s  (with replacement)
1294s svydesign(ids = ~psuid, strata = ~stratid, variables = ~x, data = fpc, 
1294s     nest = TRUE)
1294s > svymean(~x,a)
1294s    mean     SE
1294s x 5.525 0.7796
1294s > a<-svydesign(ids=~psuid, variables=~x, data=fpc, nest=TRUE)
1294s Warning message:
1294s In svydesign.default(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) :> a
1294s 1 - level Cluster Sampling design (with replacement)
1294s 
1294s   No weights or probabilities supplied, assuming equal probability
1294s With (5) clusters.
1294s svydesign(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE)
1294s > svymean(~x,a)
1294s    mean    SE
1294s x 5.525 0.838
1294s > a<-svydesign(ids=~psuid, weights=~weight, variables=~x, data=fpc, nest=TRUE)
1294s > a
1294s 1 - level Cluster Sampling design (with replacement)
1294s With (5) clusters.
1294s svydesign(ids = ~psuid, weights = ~weight, variables = ~x, data = fpc, 
1294s     nest = TRUE)
1294s > svymean(~x,a)
1294s     mean     SE
1294s x 5.4481 0.7938
1294s > a<-svydesign(ids=~stratid+psuid, weights=~weight, variables=~x, data=fpc)
1294s > a
1294s 2 - level Cluster Sampling design (with replacement)
1294s With (2, 8) clusters.
1294s svydesign(ids = ~stratid + psuid, weights = ~weight, variables = ~x, 
1294s     data = fpc)
1294s > svymean(~x,a)
1294s     mean     SE
1294s x 5.4481 0.5465
1294s > a<-svydesign(ids=~stratid+psuid, variables=~x, data=fpc)
1294s > a
1294s 2 - level Cluster Sampling design (with replacement)
1294s Warning message:
1294s In svydesign.default(ids = ~stratid + psuid, variables = ~x, data = fpc) :
1294s   No weights or probabilities supplied, assuming equal probability
1294s With (2, 8) clusters.
1294s svydesign(ids = ~stratid + psuid, variables = ~x, data = fpc)
1294s > svymean(~x,a)
1294s    mean     SE
1294s x 5.525 0.5188
1294s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,"x",drop=FALSE],  nest=TRUE)
1294s > a
1294s Stratified Independent Sampling design (with replacement)
1294s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 
1294s     variables = fpc[, "x", drop = FALSE], nest = TRUE)
1294s > svymean(~x,a)
1294s     mean     SE
1294s x 5.4481 0.7413
1294s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,4:6],  nest=TRUE)
1294s > a
1294s Stratified Independent Sampling design (with replacement)
1294s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 
1294s     variables = fpc[, 4:6], nest = TRUE)
1294s > svymean(~x,a)
1294s     mean     SE
1294s x 5.4481 0.7413
1294s > 
1294s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid,  variables=fpc[,4:6], fpc=rep(27,8))
1294s > a
1294s 1 - level Cluster Sampling design
1294s With (5) clusters.
1294s svydesign(weights = fpc$weight, ids = fpc$psuid, variables = fpc[, 
1294s     4:6], fpc = rep(27, 8))
1294s > svymean(~x,a)
1294s     mean     SE
1294s x 5.4481 0.7165
1294s > 
1294s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid,  strata=fpc$stratid, nest=TRUE, variables=fpc[,4:6], fpc=fpc$Nh)
1294s > a
1294s Stratified Independent Sampling design
1294s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 
1294s     nest = TRUE, variables = fpc[, 4:6], fpc = fpc$Nh)
1294s > svymean(~x,a)
1294s     mean    SE
1294s x 5.4481 0.616
1294s > 
1294s BEGIN TEST contrast-replicates.R
1294s 
1294s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1294s Copyright (C) 2023 The R Foundation for Statistical Computing
1294s Platform: x86_64-pc-linux-gnu (64-bit)
1294s 
1294s R is free software and comes with ABSOLUTELY NO WARRANTY.
1294s You are welcome to redistribute it under certain conditions.
1294s Type 'license()' or 'licence()' for distribution details.
1294s 
1294s R is a collaborative project with many contributors.
1294s Type 'contributors()' for more information and
1294s 'citation()' on how to cite R or R packages in publications.
1294s 
1294s Type 'demo()' for some demos, 'help()' for on-line help, or
1294s 'help.start()' for an HTML browser interface to help.
1294s Type 'q()' to quit R.
1294s 
1294s > ## test use of replicates in svyby, svycontrast
1294s > library(survey)
1294s Loading required package: grid
1294s Loading required package: Matrix
1295s Loading required package: survival
1295s 
1295s Attaching package: 'survey'
1295s 
1295s > 
1295s > data(api)
1295s The following object is masked from 'package:graphics':
1295s 
1295s     dotchart
1295s 
1295s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1295s > rclus1<-as.svrepdesign(dclus1)
1295s > 
1295s > meanlogs_without<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE)
1295s > c_without<-svycontrast(meanlogs_without, quote(exp(E-H)))
1295s > vcov(c_without)
1295s            contrast
1295s contrast 0.06862947
1295s > 
1295s > meanlogs_with<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE,return.replicates=TRUE)
1295s > 
1295s > c_with<-svycontrast(meanlogs_with, quote(exp(E-H)))
1295s > 
1295s > v_with<- vcov(rclus1, c_with$replicates)
1295s > 
1295s > r<- attr(meanlogs_with, "replicates")
1295s > vr_with<-vcov(rclus1,exp(r[,1]-r[,2]))
1295s > 
1295s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vr_with)))
1295s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vcov(c_with))))
1295s > 
1295s BEGIN TEST coxph-termtest.R
1295s 
1295s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1295s Copyright (C) 2023 The R Foundation for Statistical Computing
1295s Platform: x86_64-pc-linux-gnu (64-bit)
1295s 
1295s R is free software and comes with ABSOLUTELY NO WARRANTY.
1295s You are welcome to redistribute it under certain conditions.
1295s Type 'license()' or 'licence()' for distribution details.
1295s 
1295s R is a collaborative project with many contributors.
1295s Type 'contributors()' for more information and
1295s 'citation()' on how to cite R or R packages in publications.
1295s 
1295s Type 'demo()' for some demos, 'help()' for on-line help, or
1295s 'help.start()' for an HTML browser interface to help.
1295s Type 'q()' to quit R.
1295s 
1295s > library(survey)
1295s Loading required package: grid
1295s Loading required package: Matrix
1296s Loading required package: survival
1296s 
1296s Attaching package: 'survey'
1296s 
1296s The following object is masked from 'package:graphics':
1296s 
1296s     dotchart
1296s 
1296s > library(survival)
1296s > set.seed(2021-6-25)
1296s > test1 <- list(time=c(4,3,1,1,2,2,3),
1296s +               status=c(1,1,1,0,1,1,0),
1296s +               x1=as.factor(rbinom(7, 2, 0.5)),
1296s +               x=c(0,2,1,1,1,0,0))
1296s > # Fit a stratified model
1296s > mod_c <- coxph(Surv(time, status) ~ x1 + x, test1)
1296s > mod_d <- coxph(Surv(time, status) ~ x + x1, test1)
1296s > stopifnot(all.equal(regTermTest(mod_c, ~x1, df = Inf)[c("chisq","df","test.terms","p")],
1296s + regTermTest(mod_d, ~x1, df = Inf)[c("chisq","df","test.terms","p")]))
1296s > 
1296s > data(pbc, package="survival")
1296s > 
1296s > pbc$randomized<-with(pbc, !is.na(trt) & trt>0)
1296s > biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial)
1296s > pbc$randprob<-fitted(biasmodel)
1296s > if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0
1296s > 
1296s > dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized))
1296s > library(splines)
1296s > model<-svycoxph(formula = Surv(time, status > 0) ~ bili + protime + albumin+ns(bili,4)[,1:3], design = dpbc)
1296s > test<-regTermTest(model, ~ns(bili,4)[,1:3],method="LRT")
1296s > stopifnot(all.equal(test$chisq, 47.314, tolerance=1e-4))
1296s > stopifnot(all.equal(test$lambda, c(1.4764260, 1.0109836, 0.6923415),tolerance=1e-4))
1296s > 
1296s BEGIN TEST deff.R
1296s 
1296s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1296s Copyright (C) 2023 The R Foundation for Statistical Computing
1296s Platform: x86_64-pc-linux-gnu (64-bit)
1296s 
1296s R is free software and comes with ABSOLUTELY NO WARRANTY.
1296s You are welcome to redistribute it under certain conditions.
1296s Type 'license()' or 'licence()' for distribution details.
1296s 
1296s R is a collaborative project with many contributors.
1296s Type 'contributors()' for more information and
1296s 'citation()' on how to cite R or R packages in publications.
1296s 
1296s Type 'demo()' for some demos, 'help()' for on-line help, or
1296s 'help.start()' for an HTML browser interface to help.
1296s Type 'q()' to quit R.
1296s 
1296s > ## from Takahiro Tsuchiya
1296s > library(survey)
1296s Loading required package: grid
1296s Loading required package: Matrix
1297s Loading required package: survival
1297s 
1297s Attaching package: 'survey'
1297s 
1297s The following object is masked from 'package:graphics':
1297s 
1297s     dotchart
1297s 
1297s > kigyo<-read.table(tmp<-textConnection("  obs uriage srs.w pps.w
1297s + 1    1     15   100    20
1297s + 2    2    143   100   200
1297s + 3    3     21   100    11
1297s + 4    4     51   100    25
1297s + 5    5    337   100   550
1297s + 6    6     50   100    30
1297s + 7    7    274   100   250
1297s + 8    8    145   100   100
1297s + 9    9     15   100    10
1297s + 10  10     86   100    55
1297s + ",open="r"),header=TRUE)
1297s > close(tmp)
1297s > des.srs <- svydesign(ids=~1, weights=~srs.w, data=kigyo)
1297s > (res.srs <- svymean(~uriage, des.srs, deff=TRUE))
1297s           mean      SE   DEff
1297s uriage 113.700  35.626 1.0101
1297s > (SE(res.srs)^2) / ((1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10)
1297s          uriage
1297s uriage 1.010101
1297s > 
1297s > (tres.srs <- svytotal(~uriage, des.srs, deff=TRUE))
1297s         total     SE   DEff
1297s uriage 113700  35626 1.0101
1297s > (SE(tres.srs)^2) / (1000^2 * (1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10)
1297s          uriage
1297s uriage 1.010101
1297s > 
1297s > 
1297s > des.pps <- svydesign(ids=~1, weights=~pps.w, data=kigyo)
1297s > (res.pps <- svymean(~uriage, des.pps, deff='replace'))
1298s           mean      SE   DEff
1298s uriage 243.914  48.752 1.9741
1298s > (SE(res.pps)^2) / (coef(svyvar(~uriage, des.pps)) / 10)
1298s          uriage
1298s uriage 1.974067
1298s > (tres.pps <- svytotal(~uriage, des.pps, deff='replace'))
1298s         total     SE   DEff
1298s uriage 305136 184965 18.157
1298s > (N.hat <- sum(weights(des.pps)))
1298s [1] 1251
1298s > (SE(tres.pps)^2) / (N.hat^2 * coef(svyvar(~uriage, des.pps)) / 10)
1298s          uriage
1298s uriage 18.15669
1298s > 
1298s BEGIN TEST defftest.R
1298s 
1298s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1298s Copyright (C) 2023 The R Foundation for Statistical Computing
1298s Platform: x86_64-pc-linux-gnu (64-bit)
1298s 
1298s R is free software and comes with ABSOLUTELY NO WARRANTY.
1298s You are welcome to redistribute it under certain conditions.
1298s Type 'license()' or 'licence()' for distribution details.
1298s 
1298s R is a collaborative project with many contributors.
1298s Type 'contributors()' for more information and
1298s 'citation()' on how to cite R or R packages in publications.
1298s 
1298s Type 'demo()' for some demos, 'help()' for on-line help, or
1298s 'help.start()' for an HTML browser interface to help.
1298s Type 'q()' to quit R.
1298s 
1298s > library(survey)
1298s Loading required package: grid
1298s Loading required package: Matrix
1299s Loading required package: survival
1299s 
1299s Attaching package: 'survey'
1299s 
1299s The following object is masked from 'package:graphics':
1299s 
1299s     dotchart
1299s 
1299s > 
1299s > data(api)
1299s > 
1299s > ## one-stage cluster sample
1299s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1299s > 
1299s > # svyglm model
1299s > mod <- svyglm(api99 ~ enroll + api.stu, design = dclus1, deff = TRUE)
1299s > 
1299s > #deffs returned from svyglm model - implausibly high
1299s > deff(mod)
1299s (Intercept)      enroll     api.stu 
1299s    1.919945    2.500983    2.686102 
1299s > #> (Intercept)      enroll     api.stu 
1299s > #>    351.3500    457.6799    491.5567
1299s > 
1299s > # run mod with same data and glm()
1299s > srs_mod <- glm(api99 ~ enroll + api.stu, data = apiclus1)
1299s > 
1299s > # manually calculate deffs
1299s > 
1299s > clust_se <- summary(mod)$coefficients[,2]
1299s > srs_se <- summary(srs_mod)$coefficients[,2]
1299s > 
1299s > deffs <- clust_se^2 / srs_se^2
1299s > stopifnot(all.equal(deffs, deff(mod)))
1299s > 
1299s > 
1299s BEGIN TEST domain.R
1299s 
1299s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1299s Copyright (C) 2023 The R Foundation for Statistical Computing
1299s Platform: x86_64-pc-linux-gnu (64-bit)
1299s 
1299s R is free software and comes with ABSOLUTELY NO WARRANTY.
1299s You are welcome to redistribute it under certain conditions.
1299s Type 'license()' or 'licence()' for distribution details.
1299s 
1299s R is a collaborative project with many contributors.
1299s Type 'contributors()' for more information and
1299s 'citation()' on how to cite R or R packages in publications.
1299s 
1299s Type 'demo()' for some demos, 'help()' for on-line help, or
1299s 'help.start()' for an HTML browser interface to help.
1299s Type 'q()' to quit R.
1299s 
1299s > ##
1299s > ## Domain means can be written as ratio estimators or as regression coefficients
1299s > ##
1299s > ## This code checks that subsetting the design object gives the same results as
1299s > ## these approaches.
1299s > ##
1299s > 
1299s > 
1299s > library(survey)
1299s Loading required package: grid
1299s Loading required package: Matrix
1300s Loading required package: survival
1300s 
1300s Attaching package: 'survey'
1300s 
1300s The following object is masked from 'package:graphics':
1300s 
1300s     dotchart
1300s 
1300s > data(fpc)
1300s > dfpc<-svydesign(id=~psuid,strat=~stratid,weight=~weight,data=fpc,nest=TRUE)
1300s > dsub<-subset(dfpc,x>4)
1300s > (m1<-svymean(~x,design=dsub))
1300s    mean     SE
1300s x 6.195 0.7555
1300s > 
1300s > ## These should give the same domain estimates and standard errors
1300s > (m2<-svyby(~x,~I(x>4),design=dfpc, svymean,keep.var=TRUE))
1300s       I(x > 4)        x        se
1300s FALSE    FALSE 3.314286 0.3117042
1300s TRUE      TRUE 6.195000 0.7555129
1300s > m3<-svyglm(x~I(x>4)+0,design=dfpc)
1300s > summary(m3)
1300s 
1300s Call:
1300s svyglm(formula = x ~ I(x > 4) + 0, design = dfpc)
1300s 
1300s Survey design:
1300s svydesign(id = ~psuid, strat = ~stratid, weight = ~weight, data = fpc, 
1300s     nest = TRUE)
1300s 
1300s Coefficients:
1300s               Estimate Std. Error t value Pr(>|t|)    
1300s I(x > 4)FALSE   3.3143     0.3117   10.63 0.000127 ***
1300s I(x > 4)TRUE    6.1950     0.7555    8.20 0.000439 ***
1300s ---
1300s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1300s 
1300s (Dispersion parameter for gaussian family taken to be 2.557379)
1300s 
1300s Number of Fisher Scoring iterations: 2
1300s 
1300s > (m4<-svyratio(~I(x*(x>4)),~as.numeric(x>4), dfpc))
1300s Ratio estimator: svyratio.survey.design2(~I(x * (x > 4)), ~as.numeric(x > 4), 
1300s     dfpc)
1300s Ratios=
1300s                as.numeric(x > 4)
1300s I(x * (x > 4))             6.195
1300s SEs=
1300s                as.numeric(x > 4)
1300s I(x * (x > 4))         0.7555129
1300s > stopifnot(isTRUE(all.equal(SE(m2), as.vector(SE(m3)))))
1300s > stopifnot(isTRUE(all.equal(SE(m2)[2], as.vector(SE(m4)))))
1300s > 
1300s > ## with strata
1300s > data(api)
1300s > dstrat<-svydesign(id=~1, strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
1300s > m1<-svymean(~enroll, subset(dstrat, comp.imp=="Yes"))
1300s > m2<-svyglm(enroll~comp.imp-1, dstrat)
1300s > m3<- svyratio(~I(enroll*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dstrat)
1300s > stopifnot(isTRUE(all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1)))))
1300s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3))))))
1300s > 
1300s > ## with calibration
1300s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1300s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
1300s > (dclus1g3 <- calibrate(dclus1, ~stype+api99, c(pop.totals, api99=3914069)))
1300s 1 - level Cluster Sampling design
1300s With (15) clusters.
1300s calibrate(dclus1, ~stype + api99, c(pop.totals, api99 = 3914069))
1300s > 
1300s > m1<-svymean(~api00, subset(dclus1g3, comp.imp=="Yes"))
1300s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1g3)
1300s > m2<-svyglm(api00~comp.imp-1, dclus1g3)
1300s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1)))))
1300s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3))))))
1300s > 
1300s > ## with raking
1300s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018))
1300s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122))
1300s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
1300s > m1<-svymean(~api00, subset(dclus1r, comp.imp=="Yes"))
1300s > m2<-svyglm(api00~comp.imp-1, dclus1r)
1300s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1r)
1300s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1)))))
1300s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3))))))
1300s > 
1300s > 
1300s > 
1300s > ##
1300s > ## based on bug report from Takahiro Tsuchiya for version 3.4
1300s > ## 
1300s > rei<-read.table(tmp<-textConnection(
1300s + "  id   N n.a h n.ah n.h   sub  y
1300s + 1   1 300  20 1   12   5  TRUE  1
1300s + 2   2 300  20 1   12   5  TRUE  2
1300s + 3   3 300  20 1   12   5  TRUE  3
1300s + 4   4 300  20 1   12   5  TRUE  4
1300s + 5   5 300  20 1   12   5  TRUE  5
1300s + 6   6 300  20 1   12   5 FALSE NA
1300s + 7   7 300  20 1   12   5 FALSE NA
1300s + 8   8 300  20 1   12   5 FALSE NA
1300s + 9   9 300  20 1   12   5 FALSE NA
1300s + 10 10 300  20 1   12   5 FALSE NA
1300s + 11 11 300  20 1   12   5 FALSE NA
1300s + 12 12 300  20 1   12   5 FALSE NA
1300s + 13 13 300  20 2    8   3  TRUE  6
1300s + 14 14 300  20 2    8   3  TRUE  7
1300s + 15 15 300  20 2    8   3  TRUE  8
1300s + 16 16 300  20 2    8   3 FALSE NA
1300s + 17 17 300  20 2    8   3 FALSE NA
1300s + 18 18 300  20 2    8   3 FALSE NA
1300s + 19 19 300  20 2    8   3 FALSE NA
1300s + 20 20 300  20 2    8   3 FALSE NA
1300s + "), header=TRUE)
1300s > close(tmp)
1300s > 
1300s > 
1300s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h),
1300s +                     fpc=list(~N,NULL), subset=~sub, data=rei, method="full")
1300s > tot2<- svytotal(~y, subset(des.rei2, y>3))
1300s > 
1300s > rei$y<-rei$y*(rei$y>3)
1300s > ## based on Sarndal et al (9.4.14)
1300s > rei$w.ah <- rei$n.ah / rei$n.a
1300s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE)
1300s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE)
1300s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y)
1300s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h))
1300s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1)))
1300s > 
1300s > a.rei$f.h<-with(a.rei, n.h/n.ah)
1300s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh))
1300s > 
1300s > a.rei$f<-with(a.rei, n.a/N)
1300s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1))
1300s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2)))
1300s > 
1300s > V
1300s [1] 70761.47
1300s > Vphase1
1300s [1] 44325.47
1300s > Vphase2
1300s [1] 26436
1300s > vcov(tot2)
1300s          [,1]
1300s [1,] 70761.47
1300s attr(,"phases")
1300s attr(,"phases")$phase1
1300s          [,1]
1300s [1,] 44325.47
1300s 
1300s attr(,"phases")$phase2
1300s       [,1]
1300s [1,] 26436
1300s 
1300s > 
1300s > ## comparing to regression
1300s > reg<-svyglm(y~I(y<4), design=des.rei2)
1300s > mn<-svymean(~y, subset(des.rei2,y>3))
1300s > all.equal(as.vector(coef(reg))[1],as.vector(coef(mn)))
1300s [1] TRUE
1300s > all.equal(as.vector(SE(reg))[1],as.vector(SE(mn)))
1300s [1] TRUE
1300s > vcov(mn)
1300s           [,1]
1300s [1,] 0.3292258
1300s attr(,"phases")
1300s attr(,"phases")$phase1
1300s           [,1]
1300s [1,] 0.1599264
1300s 
1300s attr(,"phases")$phase2
1300s           [,1]
1300s [1,] 0.1692994
1300s 
1300s > vcov(reg)
1300s              (Intercept) I(y < 4)TRUE
1300s (Intercept)    0.3292258   -0.3292258
1300s I(y < 4)TRUE  -0.3292258    0.5901907
1300s attr(,"phases")
1300s attr(,"phases")$phase1
1300s              (Intercept) I(y < 4)TRUE
1300s (Intercept)    0.1599264   -0.1599264
1300s I(y < 4)TRUE  -0.1599264    0.2588542
1300s 
1300s attr(,"phases")$phase2
1300s              (Intercept) I(y < 4)TRUE
1300s (Intercept)    0.1692994   -0.1692994
1300s I(y < 4)TRUE  -0.1692994    0.3313365
1300s 
1300s > 
1300s > 
1300s BEGIN TEST fpc.R
1300s 
1300s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1300s Copyright (C) 2023 The R Foundation for Statistical Computing
1300s Platform: x86_64-pc-linux-gnu (64-bit)
1300s 
1300s R is free software and comes with ABSOLUTELY NO WARRANTY.
1300s You are welcome to redistribute it under certain conditions.
1300s Type 'license()' or 'licence()' for distribution details.
1300s 
1300s R is a collaborative project with many contributors.
1300s Type 'contributors()' for more information and
1300s 'citation()' on how to cite R or R packages in publications.
1300s 
1300s Type 'demo()' for some demos, 'help()' for on-line help, or
1300s 'help.start()' for an HTML browser interface to help.
1300s Type 'q()' to quit R.
1300s 
1300s > library(survey)
1300s Loading required package: grid
1300s Loading required package: Matrix
1301s Loading required package: survival
1301s 
1301s Attaching package: 'survey'
1301s 
1301s The following object is masked from 'package:graphics':
1301s 
1301s     dotchart
1301s 
1301s > ## check many permutations of fpc specification
1301s > example(fpc)
1301s 
1301s fpc> data(fpc)
1301s 
1301s fpc> fpc
1301s   stratid psuid weight nh Nh   x
1301s 1       1     1      3  5 15 2.8
1301s 2       1     2      3  5 15 4.1
1301s 3       1     3      3  5 15 6.8
1301s 4       1     4      3  5 15 6.8
1301s 5       1     5      3  5 15 9.2
1301s 6       2     1      4  3 12 3.7
1301s 7       2     2      4  3 12 6.6
1301s 8       2     3      4  3 12 4.2
1301s 
1301s fpc> withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 
1301s fpc+    data=fpc, nest=TRUE)
1301s 
1301s fpc> withoutfpc
1301s Stratified Independent Sampling design (with replacement)
1301s withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 
1301s    data=fpc, nest=TRUE)
1301s 
1301s fpc> svymean(~x, withoutfpc)
1301s     mean     SE
1301s x 5.4481 0.7413
1301s 
1301s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid,
1301s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE)
1301s 
1301s fpc> withfpc
1301s Stratified Independent Sampling design
1301s withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid,
1301s fpc=~Nh, variables=~x, data=fpc, nest=TRUE)
1301s 
1301s fpc> svymean(~x, withfpc)
1301s     mean    SE
1301s x 5.4481 0.616
1301s 
1301s fpc> ## Other equivalent forms 
1301s fpc> withfpc<-svydesign(prob=~I(1/weight), ids=~psuid, strata=~stratid,
1301s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE)
1301s 
1301s fpc> svymean(~x, withfpc)
1301s     mean    SE
1301s x 5.4481 0.616
1301s 
1301s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid,
1301s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE)
1301s 
1301s fpc> svymean(~x, withfpc)
1301s     mean    SE
1301s x 5.4481 0.616
1301s 
1301s fpc> withfpc<-svydesign(weights=~weight, ids=~interaction(stratid,psuid),
1301s fpc+ strata=~stratid, fpc=~I(nh/Nh), variables=~x, data=fpc)
1301s 
1301s fpc> svymean(~x, withfpc)
1301s     mean    SE
1301s x 5.4481 0.616
1301s 
1301s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, fpc=~Nh,
1301s fpc+  variables=~x,data=fpc,nest=TRUE)
1301s 
1301s fpc> svymean(~x, withfpc)
1301s     mean    SE
1301s x 5.4481 0.616
1301s 
1301s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid,
1301s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE)
1301s 
1301s fpc> svymean(~x, withfpc)
1301s     mean    SE
1301s x 5.4481 0.616
1301s > 
1301s > 
1301s BEGIN TEST glm-scoping.R
1302s 
1302s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1302s Copyright (C) 2023 The R Foundation for Statistical Computing
1302s Platform: x86_64-pc-linux-gnu (64-bit)
1302s 
1302s R is free software and comes with ABSOLUTELY NO WARRANTY.
1302s You are welcome to redistribute it under certain conditions.
1302s Type 'license()' or 'licence()' for distribution details.
1302s 
1302s R is a collaborative project with many contributors.
1302s Type 'contributors()' for more information and
1302s 'citation()' on how to cite R or R packages in publications.
1302s 
1302s Type 'demo()' for some demos, 'help()' for on-line help, or
1302s 'help.start()' for an HTML browser interface to help.
1302s Type 'q()' to quit R.
1302s 
1302s > ## bug report from Thomas Leeper, fixed in version 3.32-3
1302s > 
1302s > library("survey")
1302s Loading required package: grid
1302s Loading required package: Matrix
1302s Loading required package: survival
1303s 
1303s Attaching package: 'survey'
1303s 
1303s The following object is masked from 'package:graphics':
1303s 
1303s     dotchart
1303s 
1303s > data(api)
1303s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
1303s > 
1303s > # pass `family` directly (WORKS!)
1303s > svyglm(api00~ell+meals+mobility, design=dstrat, family = gaussian())
1303s Stratified Independent Sampling design
1303s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
1303s     fpc = ~fpc)
1303s 
1303s Call:  svyglm(formula = api00 ~ ell + meals + mobility, design = dstrat, 
1303s     family = gaussian())
1303s 
1303s Coefficients:
1303s (Intercept)          ell        meals     mobility  
1303s    820.8873      -0.4806      -3.1415       0.2257  
1303s 
1303s Degrees of Freedom: 199 Total (i.e. Null);  194 Residual
1303s Null Deviance:	    3023000 
1303s Residual Deviance: 1029000 	AIC: 2308
1303s > 
1303s > # passing `family` via ... (WORKS!)
1303s > myfun1 <- function(formula, design, ...) {
1303s +     svyglm(formula, design = design, ...)
1303s + }
1303s > myfun1(api00~ell+meals+mobility, design=dstrat, family = gaussian())
1303s Stratified Independent Sampling design
1303s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
1303s     fpc = ~fpc)
1303s 
1303s Call:  svyglm(formula = formula, design = design, family = ..1)
1303s 
1303s Coefficients:
1303s (Intercept)          ell        meals     mobility  
1303s    820.8873      -0.4806      -3.1415       0.2257  
1303s 
1303s Degrees of Freedom: 199 Total (i.e. Null);  194 Residual
1303s Null Deviance:	    3023000 
1303s Residual Deviance: 1029000 	AIC: 2308
1303s > 
1303s > # passing `family` via default argument (DOES NOT WORK!)
1303s > myfun2 <- function(formula, design, family = gaussian()) {
1303s +     svyglm(formula, design = design, family = family)
1303s + }
1303s > myfun2(api00~ell+meals+mobility, design=dstrat, family = gaussian())
1303s Stratified Independent Sampling design
1303s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
1303s     fpc = ~fpc)
1303s 
1303s Call:  svyglm(formula = formula, design = design, family = family)
1303s 
1303s Coefficients:
1303s (Intercept)          ell        meals     mobility  
1303s    820.8873      -0.4806      -3.1415       0.2257  
1303s 
1303s Degrees of Freedom: 199 Total (i.e. Null);  194 Residual
1303s Null Deviance:	    3023000 
1303s Residual Deviance: 1029000 	AIC: 2308
1303s > 
1303s BEGIN TEST kalton.R
1303s 
1303s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1303s Copyright (C) 2023 The R Foundation for Statistical Computing
1303s Platform: x86_64-pc-linux-gnu (64-bit)
1303s 
1303s R is free software and comes with ABSOLUTELY NO WARRANTY.
1303s You are welcome to redistribute it under certain conditions.
1303s Type 'license()' or 'licence()' for distribution details.
1303s 
1303s R is a collaborative project with many contributors.
1303s Type 'contributors()' for more information and
1303s 'citation()' on how to cite R or R packages in publications.
1303s 
1303s Type 'demo()' for some demos, 'help()' for on-line help, or
1303s 'help.start()' for an HTML browser interface to help.
1303s Type 'q()' to quit R.
1303s 
1303s > library(survey)
1303s Loading required package: grid
1303s Loading required package: Matrix
1304s Loading required package: survival
1304s 
1304s Attaching package: 'survey'
1304s 
1304s > 
1304s > ab<-expand.grid(a=factor(1:4),b=factor(1:3))
1304s The following object is masked from 'package:graphics':
1304s 
1304s     dotchart
1304s 
1304s > 
1304s > kaltonsample<-ab[rep(1:12,c(20,50,100,30,40,140,50,100,40,310,50,70)),]
1304s > 
1304s > kaltonpop<-ab[rep(1:12,c(80,60,170,55,40,150,60,165,55,340,200,125)),]
1304s > 
1304s > jointpop<-colSums(model.matrix(~a*b,kaltonpop))
1304s > marginalpop<-colSums(model.matrix(~a+b,kaltonpop))
1304s > gregpop<-colSums(model.matrix(~as.numeric(a)+as.numeric(b),kaltonpop))
1304s > 
1304s > dkalton<-svydesign(id=~1,data=kaltonsample)
1304s > 
1304s > dps<-postStratify(dkalton,~a+b,xtabs(~a+b,kaltonpop))
1304s Warning message:
1304s In svydesign.default(id = ~1, data = kaltonsample) :
1304s   No weights or probabilities supplied, assuming equal probability
1304s > 
1304s > drake<-rake(dkalton, list(~a,~b),list(xtabs(~a,kaltonpop),xtabs(~b,kaltonpop)),control=list(epsilon=0.0001))
1304s > 
1304s > dcalps<-calibrate(dkalton, ~a*b, jointpop)
1304s > dcalrake<-calibrate(dkalton,~a+b, marginalpop, calfun="raking")
1304s > dlinear<-calibrate(dkalton, ~a+b, marginalpop)
1304s > 
1304s > dtrunclinear<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2))
1304s > 
1304s > dlogit<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2),calfun="logit")
1304s > 
1304s > dgreg<-calibrate(dkalton,~as.numeric(a)+as.numeric(b), gregpop)
1304s > 
1304s > 
1304s > #table A
1304s >  round(svytable(~a+b,dps)/xtabs(~a+b,kaltonsample),2)
1304s    b
1304s a      1    2    3
1304s   1 4.00 1.00 1.38
1304s   2 1.20 1.07 1.10
1304s   3 1.70 1.20 4.00
1304s   4 1.83 1.65 1.79
1304s >  round(svytable(~a+b,dcalps)/xtabs(~a+b,kaltonsample),2)
1304s    b
1304s a      1    2    3
1304s   1 4.00 1.00 1.37
1304s   2 1.20 1.07 1.10
1304s   3 1.70 1.20 4.00
1304s   4 1.83 1.65 1.79
1304s > 
1304s > #table B
1304s >  round(svytable(~a+b,drake)/xtabs(~a+b,kaltonsample),2)
1304s    b
1304s a      1    2    3
1304s   1 1.81 1.45 2.02
1304s   2 1.08 0.87 1.21
1304s   3 2.20 1.76 2.45
1304s   4 1.83 1.47 2.04
1304s >  round(svytable(~a+b,dcalrake)/xtabs(~a+b,kaltonsample),2)
1304s    b
1304s a      1    2    3
1304s   1 1.81 1.45 2.02
1304s   2 1.08 0.87 1.21
1304s   3 2.20 1.76 2.45
1304s   4 1.83 1.47 2.04
1304s > 
1304s > #table C
1304s > round(svytable(~a+b,dlinear)/xtabs(~a+b,kaltonsample),2)
1304s    b
1304s a      1    2    3
1304s   1 1.82 1.50 1.97
1304s   2 1.09 0.78 1.24
1304s   3 2.19 1.88 2.34
1304s   4 1.83 1.52 1.98
1304s > 
1304s > #table D
1304s > round(svytable(~a+b,dgreg)/xtabs(~a+b,kaltonsample),2)
1304s    b
1304s a      1    2    3
1304s   1 1.21 1.17 1.14
1304s   2 1.43 1.40 1.36
1304s   3 1.66 1.62 1.59
1304s   4 1.88 1.85 1.81
1304s > 
1304s > #table G
1304s > round(svytable(~a+b,dlogit)/xtabs(~a+b,kaltonsample),2)
1304s    b
1304s a      1    2    3
1304s   1 1.87 1.46 1.98
1304s   2 1.08 0.74 1.27
1304s   3 2.17 2.09 2.18
1304s   4 1.89 1.49 1.99
1304s > 
1304s > #table G
1304s > round(svytable(~a+b,dtrunclinear)/xtabs(~a+b,kaltonsample),2)
1304s    b
1304s a      1    2    3
1304s   1 1.81 1.48 1.99
1304s   2 1.08 0.75 1.26
1304s   3 2.20 2.00 2.20
1304s   4 1.83 1.50 2.00
1304s > 
1304s BEGIN TEST logranktest.R
1304s 
1304s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1304s Copyright (C) 2023 The R Foundation for Statistical Computing
1304s Platform: x86_64-pc-linux-gnu (64-bit)
1304s 
1304s R is free software and comes with ABSOLUTELY NO WARRANTY.
1304s You are welcome to redistribute it under certain conditions.
1304s Type 'license()' or 'licence()' for distribution details.
1304s 
1304s R is a collaborative project with many contributors.
1304s Type 'contributors()' for more information and
1304s 'citation()' on how to cite R or R packages in publications.
1304s 
1304s Type 'demo()' for some demos, 'help()' for on-line help, or
1304s 'help.start()' for an HTML browser interface to help.
1304s Type 'q()' to quit R.
1304s 
1304s > ## StackOverflow 63333282
1304s > 
1304s > library(survey)
1304s Loading required package: grid
1304s Loading required package: Matrix
1305s Loading required package: survival
1305s 
1305s Attaching package: 'survey'
1305s 
1305s The following object is masked from 'package:graphics':
1305s 
1305s     dotchart
1305s 
1305s > D = data.frame(unique_id = 1:135,
1305s +                
1305s +                weights = rep(1,135),
1305s +                
1305s +                event_time = c(0.53512437, 1.35655869, 2.00414189, 2.37276648, 3.20343526, 0.96618494, 2.57894309, 0.94575080, 1.25347833, 1.44416450, 5.04038200, 7.80587169 ,
1305s +                               
1305s +                               6.53631154, 6.31914568, 7.00146597, 9.67616088, 7.94212358, 9.70693890, 10.67575835, 10.06764688, 12.29175616, 13.60092871, 13.12508566, 14.66417522,
1305s +                               
1305s +                               15.35250691, 0.93368707, 0.19087611, 3.15533767, 4.40821633, 17.54334957, 17.95177642, 15.50903946, 16.48376185, 20.87956697, 21.24571398, 22.34297263,
1305s +                               
1305s +                               23.36042629, 21.01760215, 23.84785038, 26.06105822, 4.16866350, 1.96922485, 0.66199008, 6.76987830, 1.55617685, 0.19095871, 3.13291784, 5.43159409,
1305s +                               
1305s +                               9.55805671, 4.31437322, 0.78259860, 5.26415156, 3.45095686, 1.69128712, 8.41942426, 3.33748695, 6.08516173, 2.72897404, 0.22789783, 0.86348009,
1305s +                               
1305s +                               2.35707587, 2.97477615, 12.33273800, 0.58532123, 0.14586238, 10.67948547, 4.07655972, 3.94405136, 0.37226898, 1.42558725, 1.47680658, 4.22506540,
1305s +                               
1305s +                               1.56703478, 8.37484756, 12.54015087, 1.80994787, 3.66453633, 1.02834532, 1.99065652, 1.23577436, 16.21981618, 14.35039798, 4.15321606, 2.79740679,
1305s +                               
1305s +                               0.35538726, 7.46823358, 1.66329088, 7.46525382, 2.62734831, 3.19057957, 0.33317193, 0.09122886, 9.14616245, 2.48542578, 2.37569263, 5.48499630,
1305s +                               
1305s +                               2.22749399, 2.64816296, 0.97101545, 1.42468625, 1.27668904, 0.03692447, 1.98783210, 5.47692729, 3.88316178, 0.32921277, 1.77225345, 9.33268901,
1305s +                               
1305s +                               2.44517775, 1.49813702, 2.56059172, 3.43194832, 1.22955630, 3.56263947, 9.07060099, 3.58312362, 2.22755370, 4.24783776, 3.46364804, 1.61671354,
1305s +                               
1305s +                               11.10973565, 7.18764270, 1.80400046, 6.39833474, 6.72825192, 6.46063344, 5.76855531, 5.27157807, 4.66154734, 3.50019718, 2.27156678, 3.28531594,
1305s +                               
1305s +                               2.35699896, 2.94956000, 8.85381736),
1305s +                
1305s +                event_flag = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1,
1305s +                               
1305s +                               1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1,
1305s +                               
1305s +                               1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0),
1305s +                
1305s +                group = c(rep("group1", 40), rep("group2", 95)))
1305s > 
1305s > 
1305s > 
1305s > svykm_formula = as.formula("Surv(event_time, event_flag) ~ group")
1305s > 
1305s > svy_design = svydesign( ids = ~unique_id , weights = ~weights, data = D )
1305s > 
1305s > a<-svylogrank(formula = svykm_formula, design = svy_design)
1305s > 
1305s > ii<-with(D, order(event_time, event_flag))
1305s > 
1305s > svy_design2 = svydesign( ids = ~unique_id , weights = ~weights, data = D[ii,] )
1305s > 
1305s > b<-svylogrank(formula = svykm_formula, design = svy_design2)
1305s > d<-svylogrank(formula = svykm_formula, design = svy_design, method = "large")
1305s > 
1305s > f<- svylogrank(formula = svykm_formula, design = svy_design, method = "score")
1305s > 
1305s > 
1305s > stopifnot(all.equal(a[[2]],b[[2]]))
1305s > 
1305s > stopifnot(all.equal(a[[2]],d[[2]]))
1305s > 
1305s > stopifnot(all.equal(a[[2]],f[-1]))
1305s > 
1305s > 
1305s BEGIN TEST lonely.psu.R
1306s 
1306s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1306s Copyright (C) 2023 The R Foundation for Statistical Computing
1306s Platform: x86_64-pc-linux-gnu (64-bit)
1306s 
1306s R is free software and comes with ABSOLUTELY NO WARRANTY.
1306s You are welcome to redistribute it under certain conditions.
1306s Type 'license()' or 'licence()' for distribution details.
1306s 
1306s R is a collaborative project with many contributors.
1306s Type 'contributors()' for more information and
1306s 'citation()' on how to cite R or R packages in publications.
1306s 
1306s Type 'demo()' for some demos, 'help()' for on-line help, or
1306s 'help.start()' for an HTML browser interface to help.
1306s Type 'q()' to quit R.
1306s 
1306s > 
1306s > ## lonely PSUs by design
1306s > library(survey)
1306s Loading required package: grid
1306s Loading required package: Matrix
1306s Loading required package: survival
1307s 
1307s Attaching package: 'survey'
1307s 
1307s The following object is masked from 'package:graphics':
1307s 
1307s     dotchart
1307s 
1307s > data(api)
1307s > ## not certainty PSUs by fpc
1307s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1)
1307s > summary(ds)
1307s Stratified Independent Sampling design (with replacement)
1307s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1)
1307s Probabilities:
1307s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1307s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
1307s Stratum Sizes: 
1307s            61 135 178 197 255 406 413 437 448 510 568 637 716 778 815
1307s obs        13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
1307s design.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
1307s actual.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
1307s Data variables:
1307s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1307s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1307s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1307s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1307s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1307s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1307s [37] "api.stu"  "fpc"      "pw"      
1307s > 
1307s > options(survey.lonely.psu="fail")
1307s > try(svymean(~api00,ds))
1307s > try(svymean(~api00, as.svrepdesign(ds)))
1307s Error in onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1],  : 
1307s   Stratum (413) has only one PSU at stage 1
1307s > options(survey.lonely.psu="remove")
1307s > svymean(~api00,ds)
1307s Error in jknweights(design$strata[, 1], design$cluster[, 1], fpc = fpc,  : 
1307s   Stratum413has only one PSU
1307s         mean     SE
1307s api00 644.17 5.8058
1307s > svymean(~api00, as.svrepdesign(ds))
1307s         mean     SE
1307s api00 644.17 5.8058
1307s > options(survey.lonely.psu="certainty")
1307s > svymean(~api00,ds)
1307s         mean     SE
1307s api00 644.17 5.8058
1307s > svymean(~api00, as.svrepdesign(ds))
1307s         mean     SE
1307s api00 644.17 5.8058
1307s > options(survey.lonely.psu="adjust")
1307s > svymean(~api00,ds)
1307s         mean     SE
1307s api00 644.17 5.8281
1307s > svymean(~api00, as.svrepdesign(ds))
1307s         mean     SE
1307s api00 644.17 5.8267
1307s > options(survey.lonely.psu="average")
1307s > svymean(~api00,ds)
1307s         mean     SE
1307s api00 644.17 6.0096
1307s > svymean(~api00, as.svrepdesign(ds))
1307s         mean     SE
1307s api00 644.17 5.8217
1307s > 
1307s > ## fpc specified
1307s > fpc<-ifelse(apiclus1$dnum==413, 1,1000)
1307s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1,fpc=fpc)
1307s > summary(ds)
1307s Stratified Independent Sampling design
1307s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1, 
1307s     fpc = fpc)
1307s Probabilities:
1307s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1307s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
1307s Stratum Sizes: 
1307s            61 135 178 197 255 406 413 437 448 510 568 637 716 778 815
1307s obs        13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
1307s design.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
1307s actual.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
1307s Population stratum sizes (PSUs): 
1307s  135  178  197  255  406  413  437  448  510  568   61  637  716  778  815 
1307s 1000 1000 1000 1000 1000    1 1000 1000 1000 1000 1000 1000 1000 1000 1000 
1307s Data variables:
1307s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1307s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1307s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1307s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1307s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1307s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1307s [37] "api.stu"  "fpc"      "pw"      
1307s > 
1307s > options(survey.lonely.psu="fail")
1307s > try(svymean(~api00,ds))
1307s         mean     SE
1307s api00 644.17 5.7344
1307s > svymean(~api00, as.svrepdesign(ds))
1307s         mean     SE
1307s api00 644.17 5.7344
1307s > options(survey.lonely.psu="remove")
1307s > svymean(~api00,ds)
1307s         mean     SE
1307s api00 644.17 5.7344
1307s > svymean(~api00, as.svrepdesign(ds))
1307s         mean     SE
1307s api00 644.17 5.7344
1307s > options(survey.lonely.psu="certainty")
1307s > svymean(~api00,ds)
1307s         mean     SE
1307s api00 644.17 5.7344
1307s > svymean(~api00, as.svrepdesign(ds))
1307s         mean     SE
1307s api00 644.17 5.7344
1307s > options(survey.lonely.psu="adjust")
1307s > svymean(~api00,ds)
1307s         mean     SE
1307s api00 644.17 5.7344
1307s > svymean(~api00, as.svrepdesign(ds))
1307s         mean     SE
1307s api00 644.17 5.7344
1307s > options(survey.lonely.psu="average")
1307s > svymean(~api00,ds)
1307s         mean     SE
1307s api00 644.17 5.7344
1307s > svymean(~api00, as.svrepdesign(ds))
1307s         mean     SE
1307s api00 644.17 5.7501
1307s > 
1307s > rs<-as.svrepdesign(ds)
1307s > svytotal(~api00,rs)
1307s         total    SE
1307s api00 3989986 35616
1307s > SE(svytotal(~api00,subset(rs, dnum==413)))==0
1307s [1] TRUE
1307s > 
1307s > ## lonely PSUs after subsetting
1307s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413))
1307s > ds1<-ds[-31,]
1307s > summary(ds1)
1307s Stratified Independent Sampling design (with replacement)
1307s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 
1307s     dnum != 413))
1307s Probabilities:
1307s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1307s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
1307s Stratum Sizes: 
1307s            61 135 178 197 255 406 437 448 510 568 637 716 778 815
1307s obs        13  34   4  13  16   1   4  12  21   9  11  37   2   4
1307s design.PSU 13  34   4  13  16   2   4  12  21   9  11  37   2   4
1307s actual.PSU 13  34   4  13  16   1   4  12  21   9  11  37   2   4
1307s Data variables:
1307s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1307s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1307s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1307s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1307s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1307s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1307s [37] "api.stu"  "fpc"      "pw"      
1307s > 
1307s > options(survey.lonely.psu="fail")
1307s > svymean(~api00,ds1)
1307s         mean     SE
1307s api00 645.14 5.8909
1307s > options(survey.lonely.psu="remove")
1307s > svymean(~api00,ds1)
1307s         mean     SE
1307s api00 645.14 5.8909
1307s > options(survey.lonely.psu="certainty")
1307s > svymean(~api00,ds1)
1307s         mean     SE
1307s api00 645.14 5.8909
1307s > options(survey.lonely.psu="adjust")
1307s > svymean(~api00,ds1)
1307s         mean     SE
1307s api00 645.14 5.8909
1307s > options(survey.lonely.psu="average")
1307s > svymean(~api00,ds1)
1307s         mean     SE
1307s api00 645.14 5.8909
1307s > 
1307s > ## with adjustment
1307s > options(survey.adjust.domain.lonely=TRUE)
1307s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413))
1307s > ds1<-ds[-31,]
1307s > summary(ds1)
1307s Stratified Independent Sampling design (with replacement)
1307s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 
1307s     dnum != 413))
1307s Probabilities:
1307s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1307s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
1307s Stratum Sizes: 
1307s            61 135 178 197 255 406 437 448 510 568 637 716 778 815
1307s obs        13  34   4  13  16   1   4  12  21   9  11  37   2   4
1307s design.PSU 13  34   4  13  16   2   4  12  21   9  11  37   2   4
1307s actual.PSU 13  34   4  13  16   1   4  12  21   9  11  37   2   4
1307s Data variables:
1307s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
1307s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
1307s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
1307s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
1307s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
1307s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
1307s [37] "api.stu"  "fpc"      "pw"      
1307s > 
1307s > options(survey.lonely.psu="fail")
1307s > try(svymean(~api00,ds1))
1307s         mean     SE
1307s api00 645.14 5.8909
1307s > options(survey.lonely.psu="remove")
1307s > svymean(~api00,ds1)
1307s Warning message:
1307s In onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1],  :
1307s   Stratum (406) has only one PSU at stage 1
1307s Warning message:
1307s In onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1],  :
1307s   Stratum (406) has only one PSU at stage 1
1307s         mean     SE
1307s api00 645.14 5.8909
1307s > options(survey.lonely.psu="certainty")
1307s > svymean(~api00,ds1)
1307s Warning message:
1307s In onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1],  :
1307s   Stratum (406) has only one PSU at stage 1
1307s         mean     SE
1307s api00 645.14 5.8909
1307s > options(survey.lonely.psu="adjust")
1307s > svymean(~api00,ds1)
1307s         mean     SE
1307s api00 645.14 5.9119
1307s > options(survey.lonely.psu="average")
1307s > svymean(~api00,ds1)
1307s Warning message:
1307s In onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1],  :
1307s   Stratum (406) has only one PSU at stage 1
1307s Warning message:
1307s In onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1],  :
1307s   Stratum (406) has only one PSU at stage 1
1307s         mean     SE
1307s api00 645.14 6.0914
1307s > 
1307s BEGIN TEST mtcars-var.R
1307s 
1307s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1307s Copyright (C) 2023 The R Foundation for Statistical Computing
1307s Platform: x86_64-pc-linux-gnu (64-bit)
1307s 
1307s R is free software and comes with ABSOLUTELY NO WARRANTY.
1307s You are welcome to redistribute it under certain conditions.
1307s Type 'license()' or 'licence()' for distribution details.
1307s 
1307s R is a collaborative project with many contributors.
1307s Type 'contributors()' for more information and
1307s 'citation()' on how to cite R or R packages in publications.
1307s 
1307s Type 'demo()' for some demos, 'help()' for on-line help, or
1307s 'help.start()' for an HTML browser interface to help.
1307s Type 'q()' to quit R.
1307s 
1307s > library(survey)
1307s Loading required package: grid
1307s Loading required package: Matrix
1308s Loading required package: survival
1308s 
1308s Attaching package: 'survey'
1308s 
1308s The following object is masked from 'package:graphics':
1308s 
1308s     dotchart
1308s 
1308s > 
1308s > # don't throw an error on domains of size 1, just return NA
1308s > input <- mtcars
1308s > input$carb <- factor(input$carb)
1308s > design <- svydesign(ids = ~0, weights = NULL, data = input)
1308s > svyby(
1308s +   ~mpg,
1308s +   ~carb,
1308s +   design,
1308s +   svyvar
1308s + )
1308s   carb      mpg         se
1308s 1    1 36.01619 11.2823286
1308s 2    2 29.94444  9.0030898
1308s 3    3  1.11000  0.4604066
1308s 4    4 15.29656  4.3174617
1308s 6    6       NA         NA
1308s 8    8       NA         NA
1308s > 
1308s > 
1308s > ## same n with na.rm=TRUE as subset(, !is.na)
1308s > input$mpg[1]<-NA
1308s > design <- svydesign(ids = ~0, weights = NULL, data = input)
1308s > stopifnot(all.equal(svyvar(~mpg, design, na.rm=TRUE),
1308s +           svyvar(~mpg, subset(design, !is.na(mpg)))))
1308s > 
1308s BEGIN TEST multistage.R
1308s 
1308s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1308s Copyright (C) 2023 The R Foundation for Statistical Computing
1308s Platform: x86_64-pc-linux-gnu (64-bit)
1308s 
1308s R is free software and comes with ABSOLUTELY NO WARRANTY.
1308s You are welcome to redistribute it under certain conditions.
1308s Type 'license()' or 'licence()' for distribution details.
1308s 
1308s R is a collaborative project with many contributors.
1308s Type 'contributors()' for more information and
1308s 'citation()' on how to cite R or R packages in publications.
1308s 
1308s Type 'demo()' for some demos, 'help()' for on-line help, or
1308s 'help.start()' for an HTML browser interface to help.
1308s Type 'q()' to quit R.
1308s 
1308s > ## 
1308s > ## Check that multistage samples still work
1308s > ##
1308s > library(survey)
1308s Loading required package: grid
1308s Loading required package: Matrix
1309s Loading required package: survival
1309s 
1309s Attaching package: 'survey'
1309s 
1309s The following object is masked from 'package:graphics':
1309s 
1309s     dotchart
1309s 
1309s > example(mu284)
1309s 
1309s mu284> data(mu284)
1309s 
1309s mu284> (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284))
1309s 2 - level Cluster Sampling design
1309s With (5, 15) clusters.
1309s (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284))
1309s 
1309s mu284> (ytotal<-svytotal(~y1, dmu284))
1309s    total     SE
1309s y1 15080 2274.3
1309s 
1309s mu284> vcov(ytotal)
1309s         y1
1309s y1 5172234
1309s > 
1309s > 
1309s BEGIN TEST na_action.R
1309s 
1309s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1309s Copyright (C) 2023 The R Foundation for Statistical Computing
1309s Platform: x86_64-pc-linux-gnu (64-bit)
1309s 
1309s R is free software and comes with ABSOLUTELY NO WARRANTY.
1309s You are welcome to redistribute it under certain conditions.
1309s Type 'license()' or 'licence()' for distribution details.
1309s 
1309s R is a collaborative project with many contributors.
1309s Type 'contributors()' for more information and
1309s 'citation()' on how to cite R or R packages in publications.
1309s 
1309s Type 'demo()' for some demos, 'help()' for on-line help, or
1309s 'help.start()' for an HTML browser interface to help.
1309s Type 'q()' to quit R.
1309s 
1310s Loading required package: grid
1310s > ## from Terry Therneau
1310s > library(survey)
1310s Loading required package: Matrix
1310s Loading required package: survival
1311s 
1311s Attaching package: 'survey'
1311s 
1311s > load("naa.rda")
1311s The following object is masked from 'package:graphics':
1311s 
1311s     dotchart
1311s 
1311s > 
1311s > fit1e <- svyglm( pseudo ~ age34 + ccr5 + factor(times),  design= adata.s,na.action=na.exclude)
1311s > fit1o <- svyglm( pseudo ~ age34 + ccr5 + factor(times),  design= adata.s)
1311s > all.equal(coef(fit1e),coef(fit1o))
1311s [1] TRUE
1311s > all.equal(vcov(fit1e),vcov(fit1o))
1311s [1] TRUE
1311s > 
1311s BEGIN TEST newquantile.R
1311s 
1311s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1311s Copyright (C) 2023 The R Foundation for Statistical Computing
1311s Platform: x86_64-pc-linux-gnu (64-bit)
1311s 
1311s R is free software and comes with ABSOLUTELY NO WARRANTY.
1311s You are welcome to redistribute it under certain conditions.
1311s Type 'license()' or 'licence()' for distribution details.
1311s 
1311s R is a collaborative project with many contributors.
1311s Type 'contributors()' for more information and
1311s 'citation()' on how to cite R or R packages in publications.
1311s 
1311s Type 'demo()' for some demos, 'help()' for on-line help, or
1311s 'help.start()' for an HTML browser interface to help.
1311s Type 'q()' to quit R.
1311s 
1311s > ## quantiles with equal weights
1311s > 
1311s > library(survey)
1311s Loading required package: grid
1311s Loading required package: Matrix
1312s Loading required package: survival
1312s 
1312s Attaching package: 'survey'
1312s 
1312s The following object is masked from 'package:graphics':
1312s 
1312s     dotchart
1312s 
1312s > data(api)
1312s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1312s > 
1312s > 
1312s > for(i in 1:9){
1312s +     print(i)
1312s +     all.equal(
1312s +         as.vector(coef(svyquantile(~ell, dclus1, c(0.2,0.5,0.9), qrule=paste0("hf",i)))),
1312s +         as.vector(quantile(apiclus1$ell,  c(0.2,0.5,0.9), type=i))
1312s +     )
1312s +     
1312s + }
1312s [1] 1
1312s [1] 2
1312s [1] 3
1312s [1] 4
1312s [1] 5
1312s [1] 6
1312s [1] 7
1312s [1] 8
1312s [1] 9
1312s > 
1312s BEGIN TEST nwts-cch.R
1312s 
1312s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1312s Copyright (C) 2023 The R Foundation for Statistical Computing
1312s Platform: x86_64-pc-linux-gnu (64-bit)
1312s 
1312s R is free software and comes with ABSOLUTELY NO WARRANTY.
1312s You are welcome to redistribute it under certain conditions.
1312s Type 'license()' or 'licence()' for distribution details.
1312s 
1312s R is a collaborative project with many contributors.
1312s Type 'contributors()' for more information and
1312s 'citation()' on how to cite R or R packages in publications.
1312s 
1312s Type 'demo()' for some demos, 'help()' for on-line help, or
1312s 'help.start()' for an HTML browser interface to help.
1312s Type 'q()' to quit R.
1312s 
1312s > library(survey)
1312s Loading required package: grid
1312s Loading required package: Matrix
1313s Loading required package: survival
1313s 
1313s Attaching package: 'survey'
1313s 
1313s > library(survival)
1313s > data(nwtco)
1313s The following object is masked from 'package:graphics':
1313s 
1313s     dotchart
1313s 
1313s > 
1313s > ntwco<-subset(nwtco, !is.na(edrel))
1313s > 
1313s > load("nwtco-subcohort.rda")
1313s > nwtco$subcohort<-subcohort
1313s > 
1313s > d_BorganII <- twophase(id=list(~seqno,~seqno),
1313s +                        strata=list(NULL,~interaction(instit,rel)),
1313s +                        data=nwtco, subset=~I(rel |subcohort))
1314s > 
1314s > ##Coefficient results same as Splus with code from
1314s > ## http://faculty.washington.edu/norm/software.html
1314s > ## SE slightly larger due to using sandwich variance.
1314s > 
1314s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganII)
1314s Call:
1314s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 
1314s     I(age/12), design = d_BorganII)
1314s 
1314s                    coef exp(coef) se(coef) robust se      z        p
1314s factor(stage)2  0.46286   1.58861  0.23762   0.18087  2.559  0.01049
1314s factor(stage)3  0.58309   1.79156  0.23965   0.17848  3.267  0.00109
1314s factor(stage)4  1.05967   2.88541  0.26182   0.20524  5.163 2.43e-07
1314s factor(histol)2 1.59744   4.94035  0.17688   0.13342 11.973  < 2e-16
1314s I(age/12)       0.02994   1.03039  0.02942   0.03337  0.897  0.36972
1314s 
1314s Likelihood ratio test=  on 5 df, p=
1314s n= 1062, number of events= 571 
1314s > 
1314s > ##
1314s > ## This gives higher standard errors. calibrate() does not recompute the
1314s > ## finite population correction if a calibration variable happens to predict
1314s > ## sampling perfectly. It probably should.
1314s > ##
1314s > d_BorganIIps<-calibrate(twophase(id=list(~seqno,~seqno),
1314s +                            strata=list(NULL,~rel),
1314s +                            data=nwtco, subset=~I(rel |subcohort)), 
1314s +                         phase=2, formula=~interaction(instit,rel),
1314s +                         epsilon=1e-10)
1314s > 
1314s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganIIps)
1314s Call:
1314s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 
1314s     I(age/12), design = d_BorganIIps)
1314s 
1314s                    coef exp(coef) se(coef) robust se      z        p
1314s factor(stage)2  0.46286   1.58861  0.23762   0.18076  2.561  0.01045
1314s factor(stage)3  0.58309   1.79156  0.23965   0.17838  3.269  0.00108
1314s factor(stage)4  1.05967   2.88541  0.26182   0.20513  5.166 2.39e-07
1314s factor(histol)2 1.59744   4.94035  0.17688   0.13044 12.246  < 2e-16
1314s I(age/12)       0.02994   1.03039  0.02942   0.03331  0.899  0.36876
1314s 
1314s Likelihood ratio test=  on 5 df, p=
1314s n= 1062, number of events= 571 
1314s > 
1314s BEGIN TEST nwts.R
1314s 
1314s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1314s Copyright (C) 2023 The R Foundation for Statistical Computing
1314s Platform: x86_64-pc-linux-gnu (64-bit)
1314s 
1314s R is free software and comes with ABSOLUTELY NO WARRANTY.
1314s You are welcome to redistribute it under certain conditions.
1314s Type 'license()' or 'licence()' for distribution details.
1314s 
1314s R is a collaborative project with many contributors.
1314s Type 'contributors()' for more information and
1314s 'citation()' on how to cite R or R packages in publications.
1314s 
1314s Type 'demo()' for some demos, 'help()' for on-line help, or
1314s 'help.start()' for an HTML browser interface to help.
1314s Type 'q()' to quit R.
1314s 
1314s > 
1314s > ## examples from Breslow & Chatterjee: Applied Statistics 1999 No. 4, p458
1314s > ## data from Norman Breslow's web page.
1314s > library(survey)
1314s Loading required package: grid
1314s Loading required package: Matrix
1315s Loading required package: survival
1315s 
1315s Attaching package: 'survey'
1315s 
1315s > load("nwts.rda")
1315s > nwtsnb<-nwts
1315s > nwtsnb$case<-nwts$case-nwtsb$case
1315s The following object is masked from 'package:graphics':
1315s 
1315s     dotchart
1315s 
1315s > nwtsnb$control<-nwts$control-nwtsb$control
1315s > 
1315s > a<-rbind(nwtsb,nwtsnb)
1315s > a$in.ccs<-rep(c(TRUE,FALSE),each=16)
1315s > 
1315s > b<-rbind(a,a)
1315s > b$rel<-rep(c(1,0),each=32)
1315s > b$n<-ifelse(b$rel,b$case,b$control)
1315s > 
1315s > index<-rep(1:64,b$n)
1315s > 
1315s > nwt.exp<-b[index,c(1:3,6,7)]
1315s > nwt.exp$id<-1:4088
1315s > 
1315s > dccs2<-twophase(id=list(~id,~id),subset=~in.ccs,
1315s +                 strata=list(NULL,~interaction(instit,rel)),data=nwt.exp)
1316s > 
1316s > dccs8<-twophase(id=list(~id,~id),subset=~in.ccs,
1316s +                 strata=list(NULL,~interaction(instit,stage,rel)),data=nwt.exp)
1316s > 
1316s > gccs8<-calibrate(dccs2,phase=2,formula=~interaction(instit,stage,rel))
1316s > 
1316s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs2))
1316s 
1316s Call:
1316s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs2, 
1316s     family = quasibinomial)
1316s 
1316s Survey design:
1316s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
1316s     subset = subset, data = data)
1316s 
1316s Coefficients:
1316s                                Estimate Std. Error t value Pr(>|t|)    
1316s (Intercept)                     -2.5701     0.1288 -19.955  < 2e-16 ***
1316s factor(stage)2                   0.5482     0.1979   2.769 0.005708 ** 
1316s factor(stage)3                   0.4791     0.2032   2.359 0.018515 *  
1316s factor(stage)4                   1.0037     0.2592   3.872 0.000114 ***
1316s factor(histol)2                  1.3505     0.3107   4.346 1.51e-05 ***
1316s factor(stage)2:factor(histol)2   0.1152     0.4410   0.261 0.793876    
1316s factor(stage)3:factor(histol)2   0.5066     0.4241   1.194 0.232548    
1316s factor(stage)4:factor(histol)2   0.9785     0.6214   1.575 0.115615    
1316s ---
1316s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1316s 
1316s (Dispersion parameter for quasibinomial family taken to be 1.000876)
1316s 
1316s Number of Fisher Scoring iterations: 4
1316s 
1316s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs8))
1316s 
1316s Call:
1316s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs8, 
1316s     family = quasibinomial)
1316s 
1316s Survey design:
1316s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
1316s     subset = subset, data = data)
1316s 
1316s Coefficients:
1316s                                Estimate Std. Error t value Pr(>|t|)    
1316s (Intercept)                    -2.71604    0.10827 -25.085  < 2e-16 ***
1316s factor(stage)2                  0.78141    0.14726   5.306 1.35e-07 ***
1316s factor(stage)3                  0.80093    0.15250   5.252 1.80e-07 ***
1316s factor(stage)4                  1.07293    0.17817   6.022 2.33e-09 ***
1316s factor(histol)2                 1.45836    0.31780   4.589 4.96e-06 ***
1316s factor(stage)2:factor(histol)2 -0.04743    0.43495  -0.109    0.913    
1316s factor(stage)3:factor(histol)2  0.28064    0.41298   0.680    0.497    
1316s factor(stage)4:factor(histol)2  0.90983    0.63774   1.427    0.154    
1316s ---
1316s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1316s 
1316s (Dispersion parameter for quasibinomial family taken to be 1.000876)
1316s 
1316s Number of Fisher Scoring iterations: 4
1316s 
1316s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=gccs8))
1316s 
1316s Call:
1316s svyglm(formula = rel ~ factor(stage) * factor(histol), design = gccs8, 
1316s     family = quasibinomial)
1316s 
1316s Survey design:
1316s calibrate(dccs2, phase = 2, formula = ~interaction(instit, stage, 
1316s     rel))
1316s 
1316s Coefficients:
1316s                                Estimate Std. Error t value Pr(>|t|)    
1316s (Intercept)                    -2.71604    0.10878 -24.968  < 2e-16 ***
1316s factor(stage)2                  0.78141    0.14729   5.305 1.35e-07 ***
1316s factor(stage)3                  0.80093    0.15212   5.265 1.68e-07 ***
1316s factor(stage)4                  1.07293    0.17905   5.993 2.77e-09 ***
1316s factor(histol)2                 1.45836    0.31757   4.592 4.88e-06 ***
1316s factor(stage)2:factor(histol)2 -0.04743    0.43432  -0.109    0.913    
1316s factor(stage)3:factor(histol)2  0.28064    0.41231   0.681    0.496    
1316s factor(stage)4:factor(histol)2  0.90983    0.63187   1.440    0.150    
1316s ---
1316s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1316s 
1316s (Dispersion parameter for quasibinomial family taken to be 1.000876)
1316s 
1316s Number of Fisher Scoring iterations: 4
1316s 
1316s > 
1316s > ## check subsets of calibrated designs.
1316s > summary(svyglm(rel~factor(stage),
1316s +                family=quasibinomial,design=subset(dccs8,histol==1)))
1316s 
1316s Call:
1316s svyglm(formula = rel ~ factor(stage), design = subset(dccs8, 
1316s     histol == 1), family = quasibinomial)
1316s 
1316s Survey design:
1316s subset(dccs8, histol == 1)
1316s 
1316s Coefficients:
1316s                Estimate Std. Error t value Pr(>|t|)    
1316s (Intercept)     -2.7160     0.1083 -25.085  < 2e-16 ***
1316s factor(stage)2   0.7814     0.1473   5.306 1.48e-07 ***
1316s factor(stage)3   0.8009     0.1525   5.252 1.97e-07 ***
1316s factor(stage)4   1.0729     0.1782   6.022 2.73e-09 ***
1316s ---
1316s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1316s 
1316s (Dispersion parameter for quasibinomial family taken to be 1.001333Warning messages:
1316s 1: )
1316s 
1316s Number of Fisher Scoring iterations: 4
1316s 
1316s In `[.twophase2`(x, r, ) : 1 strata have only one PSU in this subset.
1316s 2: In summary.glm(g) :
1316s   observations with zero weight not used for calculating dispersion
1316s 3: In summary.glm(glm.object) :
1316s   observations with zero weight not used for calculating dispersion
1316s 4: In `[.twophase2`(design, nas == 0, ) :
1316s   1 strata have only one PSU in this subset.
1316s 5: In `[.twophase2`(design, nas == 0, ) :
1316s   1 strata have only one PSU in this subset.
1316s > summary(svyglm(rel~factor(stage),
1316s +                family=quasibinomial,design=subset(gccs8,histol==1)))
1316s 
1316s Call:
1316s Warning messages:
1316s 1: In summary.glm(g) :
1316s   observations with zero weight not used for calculating dispersion
1316s 2: In summary.glm(glm.object) :
1316s   observations with zero weight not used for calculating dispersion
1316s svyglm(formula = rel ~ factor(stage), design = subset(gccs8, 
1316s     histol == 1), family = quasibinomial)
1316s 
1316s Survey design:
1316s subset(gccs8, histol == 1)
1316s 
1316s Coefficients:
1316s                Estimate Std. Error t value Pr(>|t|)    
1316s (Intercept)     -2.7160     0.1082 -25.105  < 2e-16 ***
1316s factor(stage)2   0.7814     0.1457   5.363 1.10e-07 ***
1316s factor(stage)3   0.8009     0.1504   5.324 1.34e-07 ***
1316s factor(stage)4   1.0729     0.1759   6.101 1.70e-09 ***
1316s ---
1316s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1316s 
1316s (Dispersion parameter for quasibinomial family taken to be 1.001333)
1316s 
1316s Number of Fisher Scoring iterations: 4
1316s 
1316s > 
1316s > 
1316s BEGIN TEST poisson.R
1316s 
1316s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1316s Copyright (C) 2023 The R Foundation for Statistical Computing
1316s Platform: x86_64-pc-linux-gnu (64-bit)
1316s 
1316s R is free software and comes with ABSOLUTELY NO WARRANTY.
1316s You are welcome to redistribute it under certain conditions.
1316s Type 'license()' or 'licence()' for distribution details.
1316s 
1316s R is a collaborative project with many contributors.
1316s Type 'contributors()' for more information and
1316s 'citation()' on how to cite R or R packages in publications.
1316s 
1316s Type 'demo()' for some demos, 'help()' for on-line help, or
1316s 'help.start()' for an HTML browser interface to help.
1316s Type 'q()' to quit R.
1316s 
1316s > ## check poisson sampling
1316s > library(survey)
1316s Loading required package: grid
1316s Loading required package: Matrix
1317s Loading required package: survival
1317s 
1317s Attaching package: 'survey'
1317s 
1317s The following object is masked from 'package:graphics':
1317s 
1317s     dotchart
1317s 
1317s > data(api)
1317s > set.seed(2021-7-15)
1317s > apipop$prob<-apipop$api00/1000
1317s > insample<-rbinom(nrow(apipop),1,apipop$prob)
1317s > apipois<-apipop[insample,]
1317s > des<-svydesign(id=~1, prob=~prob, pps=poisson_sampling(apipois$prob), data=apipois)
1317s > 
1317s > stopifnot(isTRUE(all.equal(
1317s +  as.vector(SE(svytotal(~api00,design=des))),
1317s +  as.vector(sqrt(sum( (apipois$api00*weights(des))^2*(1-apipois$prob))))
1317s +  )))
1317s >  
1317s > 
1317s BEGIN TEST pps.R
1318s 
1318s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1318s Copyright (C) 2023 The R Foundation for Statistical Computing
1318s Platform: x86_64-pc-linux-gnu (64-bit)
1318s 
1318s R is free software and comes with ABSOLUTELY NO WARRANTY.
1318s You are welcome to redistribute it under certain conditions.
1318s Type 'license()' or 'licence()' for distribution details.
1318s 
1318s R is a collaborative project with many contributors.
1318s Type 'contributors()' for more information and
1318s 'citation()' on how to cite R or R packages in publications.
1318s 
1318s Type 'demo()' for some demos, 'help()' for on-line help, or
1318s 'help.start()' for an HTML browser interface to help.
1318s Type 'q()' to quit R.
1318s 
1318s > library(survey)
1318s Loading required package: grid
1318s Loading required package: Matrix
1319s Loading required package: survival
1319s 
1319s Attaching package: 'survey'
1319s 
1319s The following object is masked from 'package:graphics':
1319s 
1319s     dotchart
1319s 
1319s > data(election)
1319s > 
1319s > dpps<- svydesign(id=~1, weights=~wt, fpc=~p, data=election_pps, pps="brewer")
1319s > dppswr <-svydesign(id=~1, weights=~wt, data=election_pps)
1319s > svytotal(~Bush+Kerry+Nader, dpps)
1319s          total      SE
1319s Bush  64518472 2447629
1319s Kerry 51202102 2450787
1319s Nader   478530  102420
1319s > svytotal(~Bush+Kerry+Nader, dppswr)
1319s          total      SE
1319s Bush  64518472 2671455
1319s Kerry 51202102 2679433
1319s Nader   478530  105303
1319s > 
1319s > ##subsets
1319s > svytotal(~Bush+Kerry+Nader, subset(dpps, Nader>0))
1319s          total      SE
1319s Bush  34944285 5399833
1319s Kerry 25581714 4028434
1319s Nader   478530  102420
1319s > 
1319s > ##multistage: should agree with STRS analysis
1319s > data(api)
1319s > dclus2<-svydesign(id = ~dnum + snum, fpc = ~fpc1 + fpc2, data = apiclus2)
1319s > dclus2pps<-svydesign(id = ~dnum + snum, fpc = ~I(40/fpc1) + I(pmin(1,5/fpc2)), data = apiclus2)
1319s > 
1319s > all.equal(svytotal(~sch.wide,dclus2), svytotal(~sch.wide,dclus2pps))
1319s [1] TRUE
1319s > all.equal(svymean(~sch.wide,dclus2), svymean(~sch.wide,dclus2pps))
1319s [1] TRUE
1319s > all.equal(svytotal(~enroll,dclus2), svytotal(~enroll,dclus2pps))
1319s [1] TRUE
1319s > 
1319s > ## the new without-replacement methods
1319s > data(election)
1319s > dpps_br<- svydesign(id=~1,  fpc=~p, data=election_pps, pps="brewer")
1319s > dpps_ov<- svydesign(id=~1,  fpc=~p, data=election_pps, pps="overton")
1319s > dpps_hr<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40))
1319s > dpps_hr1<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR())
1319s > dpps_ht<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=ppsmat(election_jointprob))
1319s > ## Yates-Grundy type
1319s > dpps_yg<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=ppsmat(election_jointprob),variance="YG")
1319s > dpps_hryg<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40),variance="YG")
1319s > 
1319s > ## The with-replacement approximation
1319s > svytotal(~Bush+Kerry+Nader, dpps_ht)
1319s          total      SE
1319s Bush  64518472 2604404
1319s Kerry 51202102 2523712
1319s Nader   478530  102326
1319s > svytotal(~Bush+Kerry+Nader, dpps_yg)
1319s          total      SE
1319s Bush  64518472 2406526
1319s Kerry 51202102 2408091
1319s Nader   478530  101664
1319s > svytotal(~Bush+Kerry+Nader, dpps_hr)
1319s          total      SE
1319s Bush  64518472 2624662
1319s Kerry 51202102 2525222
1319s Nader   478530  102793
1319s > svytotal(~Bush+Kerry+Nader, dpps_hryg)
1319s          total      SE
1319s Bush  64518472 2436738
1319s Kerry 51202102 2439845
1319s Nader   478530  102016
1319s > svytotal(~Bush+Kerry+Nader, dpps_hr1)
1319s          total      SE
1319s Bush  64518472 2472753
1319s Kerry 51202102 2426842
1319s Nader   478530  102595
1319s > svytotal(~Bush+Kerry+Nader, dpps_br)
1319s          total      SE
1319s Bush  64518472 2447629
1319s Kerry 51202102 2450787
1319s Nader   478530  102420
1319s > svytotal(~Bush+Kerry+Nader, dpps_ov)
1319s          total      SE
1319s Bush  64518472 2939608
1319s Kerry 51202102 1964632
1319s Nader   478530  104373
1319s > 
1319s > ## subsets
1319s > svytotal(~Bush+Kerry+Nader, subset(dpps_ht, Nader>0))
1319s          total      SE
1319s Bush  34944285 5406348
1319s Kerry 25581714 4047741
1319s Nader   478530  102326
1319s > svytotal(~Bush+Kerry+Nader, subset(dpps_hryg, Nader>0))
1319s          total      SE
1319s Bush  34944285 5377659
1319s Kerry 25581714 4010908
1319s Nader   478530  102016
1319s > 
1319s > ## counts
1319s > svyby(~Bush+Kerry+Nader,~I(Nader>0), unwtd.count,design=dpps_ht)
1319s       I(Nader > 0) counts se
1319s FALSE        FALSE     19  0
1319s TRUE          TRUE     21  0
1319s > 
1319s BEGIN TEST quantile.R
1319s 
1319s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1319s Copyright (C) 2023 The R Foundation for Statistical Computing
1319s Platform: x86_64-pc-linux-gnu (64-bit)
1319s 
1319s R is free software and comes with ABSOLUTELY NO WARRANTY.
1319s You are welcome to redistribute it under certain conditions.
1319s Type 'license()' or 'licence()' for distribution details.
1319s 
1319s R is a collaborative project with many contributors.
1319s Type 'contributors()' for more information and
1319s 'citation()' on how to cite R or R packages in publications.
1319s 
1319s Type 'demo()' for some demos, 'help()' for on-line help, or
1319s 'help.start()' for an HTML browser interface to help.
1319s Type 'q()' to quit R.
1319s 
1319s > library(survey)
1319s Loading required package: grid
1319s Loading required package: Matrix
1320s Loading required package: survival
1320s 
1320s Attaching package: 'survey'
1320s 
1320s The following object is masked from 'package:graphics':
1320s 
1320s     dotchart
1320s 
1320s > set.seed(42)
1320s > 
1320s > df<-data.frame(x=exp(rnorm(1000)))
1320s > df$y<-round(df$x,1)
1320s > ddf<-svydesign(id=~1,data=df)
1320s Warning message:
1320s In svydesign.default(id = ~1, data = df) :
1320s   No weights or probabilities supplied, assuming equal probability
1320s > rdf<-as.svrepdesign(ddf)
1321s > 
1321s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
1321s       0.01        0.1        0.5        0.9       0.99 
1321s 0.01543792 0.01264453 0.03386225 0.16131948 2.10605799 
1321s > 
1321s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
1321s                x
1321s q0.01 0.01554946
1321s q0.1  0.01425828
1321s q0.5  0.03428012
1321s q0.9  0.16457488
1321s q0.99 1.88672412
1321s > 
1321s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
1321s       0.01        0.1        0.5        0.9       0.99 
1321s 0.01545209 0.01265608 0.03388011 0.16145776 2.10061576 
1321s > 
1321s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
1321s                x
1321s q0.01 0.01556240
1321s q0.1  0.01420086
1321s q0.5  0.03430175
1321s q0.9  0.16461019
1321s q0.99 1.88818131
1321s > 
1321s > 
1321s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald")
1321s $quantiles
1321s         0.01       0.1       0.5  0.9 0.99
1321s y 0.02352941 0.2230769 0.9340909 3.55  9.4
1321s 
1321s $CIs
1321s , , y
1321s 
1321s              0.01       0.1       0.5      0.9      0.99
1321s (lower 0.01594200 0.2020115 0.8578143 3.207543  7.568142
1321s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632
1321s 
1321s 
1321s > 
1321s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)
1321s Statistic:
1321s         y
1321s q0.01 0.1
1321s q0.1  0.3
1321s q0.5  1.0
1321s q0.9  3.6
1321s q0.99 9.4
1321s SE:
1321s                y
1321s q0.01 0.02547977
1321s q0.1  0.02547977
1321s q0.5  0.02547977
1321s q0.9  0.15287859
1321s q0.99 1.88302540
1321s > 
1321s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf)
1321s $quantiles
1321s         0.01       0.1       0.5  0.9 0.99
1321s y 0.02352941 0.2230769 0.9340909 3.55  9.4
1321s 
1321s $CIs
1321s , , y
1321s 
1321s              0.01       0.1       0.5      0.9      0.99
1321s (lower 0.01594200 0.2020115 0.8578143 3.207543  7.568142
1321s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632
1321s 
1321s 
1321s > 
1321s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf)
1321s Statistic:
1321s         y
1321s q0.01 0.1
1321s q0.1  0.3
1321s q0.5  1.0
1321s q0.9  3.6
1321s q0.99 9.4
1321s SE:
1321s                y
1321s q0.01 0.02551067
1321s q0.1  0.02551067
1321s q0.5  0.02551067
1321s q0.9  0.15306404
1321s q0.99 1.88450896
1321s > 
1321s > 
1321s > 
1321s > df<-data.frame(x=exp(rnorm(20)))
1321s > df$y<-round(df$x,1)
1321s > ddf<-svydesign(id=~1,data=df)
1321s Warning message:
1321s In svydesign.default(id = ~1, data = df) :
1321s   No weights or probabilities supplied, assuming equal probability
1321s > rdf<-as.svrepdesign(ddf)
1321s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
1321s       0.01        0.1        0.5        0.9       0.99 
1321s 0.03576771 0.07329496 0.30149917 2.03440784 1.88468597 
1321s > 
1321s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
1321s                x
1321s q0.01 0.00000000
1321s q0.1  0.04598541
1321s q0.5  0.25943731
1321s q0.9  2.12343073
1321s q0.99 1.91998924
1321s > 
1321s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
1321s       0.01        0.1        0.5        0.9       0.99 
1321s 0.03637398 0.07470310 0.29938115 2.16381289 2.00708994 
1321s > 
1321s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
1321s                x
1321s q0.01 0.00000000
1321s q0.1  0.04732818
1321s q0.5  0.24957966
1321s q0.9  2.25211815
1321s q0.99 2.04043154
1321s > 
1321s > 
1321s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald")
1321s $quantiles
1321s   0.01  0.1  0.5 0.9 0.99
1321s y  0.1 0.15 0.75 2.4 8.68
1321s 
1321s $CIs
1321s , , y
1321s 
1321s            0.01       0.1       0.5      0.9       0.99
1321s (lower 0.100000 0.1000000 0.3674054 1.352279  0.5674674
1321s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000
1321s 
1321s 
1321s > 
1321s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)
1321s Statistic:
1321s          y
1321s q0.01 0.10
1321s q0.1  0.20
1321s q0.5  0.80
1321s q0.9  2.40
1321s q0.99 8.68
1321s SE:
1321s                y
1321s q0.01 0.00000000
1321s q0.1  0.02611112
1321s q0.5  0.26542051
1321s q0.9  2.10908603
1321s q0.99 1.91777710
1321s > 
1321s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf)
1321s $quantiles
1321s   0.01  0.1  0.5 0.9 0.99
1321s y  0.1 0.15 0.75 2.4 8.68
1321s 
1321s $CIs
1321s , , y
1321s 
1321s            0.01       0.1       0.5      0.9       0.99
1321s (lower 0.100000 0.1000000 0.3674054 1.352279  0.5674674
1321s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000
1321s 
1321s 
1321s > 
1321s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf)
1321s Statistic:
1321s          y
1321s q0.01 0.10
1321s q0.1  0.20
1321s q0.5  0.80
1321s q0.9  2.40
1321s q0.99 8.68
1321s SE:
1321s                y
1321s q0.01 0.00000000
1321s q0.1  0.02551067
1321s q0.5  0.25244616
1321s q0.9  2.23558589
1321s q0.99 2.03881114
1321s > 
1321s BEGIN TEST quantiles-chile.R
1321s 
1321s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1321s Copyright (C) 2023 The R Foundation for Statistical Computing
1321s Platform: x86_64-pc-linux-gnu (64-bit)
1321s 
1321s R is free software and comes with ABSOLUTELY NO WARRANTY.
1321s You are welcome to redistribute it under certain conditions.
1321s Type 'license()' or 'licence()' for distribution details.
1321s 
1321s R is a collaborative project with many contributors.
1321s Type 'contributors()' for more information and
1321s 'citation()' on how to cite R or R packages in publications.
1321s 
1321s Type 'demo()' for some demos, 'help()' for on-line help, or
1321s 'help.start()' for an HTML browser interface to help.
1321s Type 'q()' to quit R.
1321s 
1321s > library(survey)
1321s Loading required package: grid
1321s Loading required package: Matrix
1322s Loading required package: survival
1322s 
1322s Attaching package: 'survey'
1322s 
1322s The following object is masked from 'package:graphics':
1322s 
1322s     dotchart
1322s 
1322s > datos <- readRDS("datos_ejemplo.rds")
1322s > 
1322s > design <- svydesign(id = ~id_directorio, strata = ~estrato, weights = ~f_pers, check.strata = TRUE, data = datos)
1322s > set.seed(234262762)
1322s > repdesign <- as.svrepdesign(design, type = "subbootstrap", replicates=20)
1322s > options(survey.lonely.psu="remove")
1322s > 
1322s > values<-datos$ing_t_p[datos$CL_GRUPO_OCU_08=="ISCO08_6"]
1322s > 
1322s > suppressWarnings({
1322s + f0<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math"))
1322s + f0.5<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school"))
1322s + })
1322s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5)))
1322s [1] TRUE
1322s > 
1322s > suppressWarnings({
1322s + f0<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math"))
1322s + f0.5<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school"))
1322s + })
1322s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5)))
1322s [1] TRUE
1322s > 
1322s BEGIN TEST rakecheck.R
1322s 
1322s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1322s Copyright (C) 2023 The R Foundation for Statistical Computing
1322s Platform: x86_64-pc-linux-gnu (64-bit)
1322s 
1322s R is free software and comes with ABSOLUTELY NO WARRANTY.
1322s You are welcome to redistribute it under certain conditions.
1322s Type 'license()' or 'licence()' for distribution details.
1322s 
1322s R is a collaborative project with many contributors.
1322s Type 'contributors()' for more information and
1322s 'citation()' on how to cite R or R packages in publications.
1322s 
1322s Type 'demo()' for some demos, 'help()' for on-line help, or
1322s 'help.start()' for an HTML browser interface to help.
1322s Type 'q()' to quit R.
1322s 
1323s > library(survey)
1323s Loading required package: grid
1323s Loading required package: Matrix
1323s Loading required package: survival
1324s 
1324s Attaching package: 'survey'
1324s 
1324s The following object is masked from 'package:graphics':
1324s 
1324s     dotchart
1324s 
1324s > 
1324s > data(api)
1324s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1324s > rclus1 <- as.svrepdesign(dclus1)
1324s > 
1324s > ## population marginal totals for each stratum
1324s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018))
1324s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122))
1324s > 
1324s > rclus1r <- rake(rclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
1324s > 
1324s > svymean(~api00, rclus1r)
1324s         mean     SE
1324s api00 641.23 26.873
1324s > svytotal(~enroll, rclus1r)
1324s          total     SE
1324s enroll 3647300 463511
1324s > 
1324s > ff<-~stype+sch.wide
1324s > poptotals<-colSums(model.matrix(ff,model.frame(ff,apipop)))
1324s > rclus1g<-calibrate(rclus1, ~stype+sch.wide, poptotals,calfun="raking")
1324s > 
1324s > svymean(~api00,rclus1g)
1324s         mean     SE
1324s api00 641.23 26.874
1324s > svytotal(~enroll,rclus1g)
1324s          total     SE
1324s enroll 3647280 463582
1324s > 
1324s > summary(weights(rclus1g)/weights(rclus1r))
1324s        V1           V2          V3          V4           V5          V6   
1324s  Min.   :1    Min.   :1   Min.   :1   Min.   :1    Min.   :1   Min.   :1  
1324s  1st Qu.:1    1st Qu.:1   1st Qu.:1   1st Qu.:1    1st Qu.:1   1st Qu.:1  
1324s  Median :1    Median :1   Median :1   Median :1    Median :1   Median :1  
1324s  Mean   :1    Mean   :1   Mean   :1   Mean   :1    Mean   :1   Mean   :1  
1324s  3rd Qu.:1    3rd Qu.:1   3rd Qu.:1   3rd Qu.:1    3rd Qu.:1   3rd Qu.:1  
1324s  Max.   :1    Max.   :1   Max.   :1   Max.   :1    Max.   :1   Max.   :1  
1324s  NA's   :11   NA's   :4   NA's   :2   NA's   :13   NA's   :2   NA's   :4  
1324s        V7          V8           V9         V10          V11    
1324s  Min.   :1   Min.   :1    Min.   :1   Min.   :1    Min.   :1   
1324s  1st Qu.:1   1st Qu.:1    1st Qu.:1   1st Qu.:1    1st Qu.:1   
1324s  Median :1   Median :1    Median :1   Median :1    Median :1   
1324s  Mean   :1   Mean   :1    Mean   :1   Mean   :1    Mean   :1   
1324s  3rd Qu.:1   3rd Qu.:1    3rd Qu.:1   3rd Qu.:1    3rd Qu.:1   
1324s  Max.   :1   Max.   :1    Max.   :1   Max.   :1    Max.   :1   
1324s  NA's   :4   NA's   :16   NA's   :9   NA's   :34   NA's   :21  
1324s       V12              V13          V14         V15    
1324s  Min.   :0.9997   Min.   :1    Min.   :1   Min.   :1   
1324s  1st Qu.:1.0001   1st Qu.:1    1st Qu.:1   1st Qu.:1   
1324s  Median :1.0001   Median :1    Median :1   Median :1   
1324s  Mean   :1.0000   Mean   :1    Mean   :1   Mean   :1   
1324s  3rd Qu.:1.0001   3rd Qu.:1    3rd Qu.:1   3rd Qu.:1   
1324s  Max.   :1.0002   Max.   :1    Max.   :1   Max.   :1   
1324s  NA's   :37       NA's   :13   NA's   :1   NA's   :12  
1324s > 
1324s > 
1324s > ## Do it for a design without replicate weights
1324s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
1324s > 
1324s > svymean(~api00, dclus1r)
1324s         mean     SE
1324s api00 641.23 23.704
1324s > svytotal(~enroll, dclus1r)
1324s          total     SE
1324s enroll 3647300 400603
1324s > 
1324s > dclus1g<-calibrate(dclus1, ~stype+sch.wide, poptotals,calfun="raking")
1324s > 
1324s > svymean(~api00,dclus1g)
1324s         mean     SE
1324s api00 641.23 23.704
1324s > svytotal(~enroll,dclus1g)
1324s          total     SE
1324s enroll 3647280 400603
1324s > 
1324s > summary(weights(dclus1g)/weights(dclus1r))
1324s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1324s       1       1       1       1       1       1 
1324s > 
1324s > 
1324s > 
1324s > ## Example of raking with partial joint distributions
1324s > pop.table <- xtabs(~stype+sch.wide,apipop)
1324s > pop.imp<-data.frame(comp.imp=c("No","Yes"),Freq=c(1712,4482))
1324s > dclus1r2<-rake(dclus1, list(~stype+sch.wide, ~comp.imp),
1324s +                list(pop.table, pop.imp))
1324s > svymean(~api00, dclus1r2)
1324s         mean     SE
1324s api00 642.62 22.732
1324s > 
1324s > ff1 <-~stype*sch.wide+comp.imp
1324s > 
1324s > poptotals1<-colSums(model.matrix(ff1,model.frame(ff1,apipop)))
1324s > dclus1g2<-calibrate(dclus1, ~stype*sch.wide+comp.imp, poptotals1, calfun="raking")
1324s > 
1324s > svymean(~api00, dclus1g2)
1324s         mean     SE
1324s api00 642.61 22.731
1324s > 
1324s > summary(weights(dclus1r2)/weights(dclus1g2))
1324s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1324s   0.999   1.000   1.000   1.000   1.000   1.002 
1324s > 
1324s BEGIN TEST raowuboot.R
1324s 
1324s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1324s Copyright (C) 2023 The R Foundation for Statistical Computing
1324s Platform: x86_64-pc-linux-gnu (64-bit)
1324s 
1324s R is free software and comes with ABSOLUTELY NO WARRANTY.
1324s You are welcome to redistribute it under certain conditions.
1324s Type 'license()' or 'licence()' for distribution details.
1324s 
1324s R is a collaborative project with many contributors.
1324s Type 'contributors()' for more information and
1324s 'citation()' on how to cite R or R packages in publications.
1324s 
1324s Type 'demo()' for some demos, 'help()' for on-line help, or
1324s 'help.start()' for an HTML browser interface to help.
1324s Type 'q()' to quit R.
1324s 
1324s > ## regression test for bug reported by Richard Valliant
1324s > library(survey)
1324s Loading required package: grid
1324s Loading required package: Matrix
1325s Loading required package: survival
1325s 
1325s Attaching package: 'survey'
1325s 
1325s The following object is masked from 'package:graphics':
1325s 
1325s     dotchart
1325s 
1325s > s<-subbootweights(c(1,1),1:2, 50)
1325s > stopifnot(all(s$repweights$weights %in% c(0,2)))
1325s > 
1325s BEGIN TEST regTermTest-missing.R
1325s 
1325s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1325s Copyright (C) 2023 The R Foundation for Statistical Computing
1325s Platform: x86_64-pc-linux-gnu (64-bit)
1325s 
1325s R is free software and comes with ABSOLUTELY NO WARRANTY.
1325s You are welcome to redistribute it under certain conditions.
1325s Type 'license()' or 'licence()' for distribution details.
1325s 
1325s R is a collaborative project with many contributors.
1325s Type 'contributors()' for more information and
1325s 'citation()' on how to cite R or R packages in publications.
1325s 
1325s Type 'demo()' for some demos, 'help()' for on-line help, or
1325s 'help.start()' for an HTML browser interface to help.
1325s Type 'q()' to quit R.
1325s 
1325s > library(survey)
1325s Loading required package: grid
1325s Loading required package: Matrix
1326s Loading required package: survival
1326s 
1326s Attaching package: 'survey'
1326s 
1326s The following object is masked from 'package:graphics':
1326s 
1326s     dotchart
1326s 
1326s > data(nhanes)
1326s > design <- svydesign(id=~SDMVPSU, strata=~SDMVSTRA, weights=~WTMEC2YR, nest=TRUE,data=nhanes)
1326s > 
1326s > a<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR,  design = subset(design,!is.na(HI_CHOL)), family=quasibinomial)
1326s > b<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR,  design =design , family=quasibinomial)
1326s > 
1326s > ta<-regTermTest(a, ~HI_CHOL)
1326s > tb<-regTermTest(b, ~HI_CHOL)
1326s > 
1326s > stopifnot(isTRUE(all.equal(ta$chisq, tb$chisq)))
1326s > stopifnot(isTRUE(all.equal(ta$lambda, tb$lambda)))
1326s > 
1326s BEGIN TEST regpredict.R
1326s 
1326s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1326s Copyright (C) 2023 The R Foundation for Statistical Computing
1326s Platform: x86_64-pc-linux-gnu (64-bit)
1326s 
1326s R is free software and comes with ABSOLUTELY NO WARRANTY.
1326s You are welcome to redistribute it under certain conditions.
1326s Type 'license()' or 'licence()' for distribution details.
1326s 
1326s R is a collaborative project with many contributors.
1326s Type 'contributors()' for more information and
1326s 'citation()' on how to cite R or R packages in publications.
1326s 
1326s Type 'demo()' for some demos, 'help()' for on-line help, or
1326s 'help.start()' for an HTML browser interface to help.
1326s Type 'q()' to quit R.
1326s 
1327s > library(survey)
1327s Loading required package: grid
1327s Loading required package: Matrix
1327s Loading required package: survival
1328s 
1328s Attaching package: 'survey'
1328s 
1328s > data(api)
1328s The following object is masked from 'package:graphics':
1328s 
1328s     dotchart
1328s 
1328s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
1328s > 
1328s > 
1328s > ## regression estimator of total, three ways
1328s > pop<-data.frame(enroll=sum(apipop$enroll, na.rm=TRUE))
1328s > npop <- sum(!is.na(apipop$enroll))
1328s > 
1328s > api.reg <- svyglm(api.stu~enroll, design=dstrat)
1328s > a <- predict(api.reg, newdata=pop, total=npop)
1328s > b <- svytotal(~api.stu, calibrate(dstrat, ~enroll, pop=c(npop, pop$enroll)))
1328s > 
1328s > all.equal(as.vector(coef(a)),as.vector(coef(b)))
1328s [1] TRUE
1328s > all.equal(as.vector(SE(a)), as.vector(SE(b)))
1328s [1] TRUE
1328s > if(!is.null(getOption("DEBUG"))){ ## uses 6194x6194 matrix
1328s +     d <- predict(api.reg, newdata=na.omit(apipop[,"enroll",drop=FALSE]))
1328s +     all.equal(as.vector(coef(a)), as.vector(sum(coef(d))))
1328s +     all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d)))))
1328s + }
1328s > 
1328s > ## classical ratio estimator, four ways.
1328s > api.reg2 <- svyglm(api.stu~enroll-1, design=dstrat,
1328s +                    family=quasi(link="identity", var="mu"))
1328s > 
1328s > a <- predict(api.reg2, newdata=pop, total=npop)
1328s > b <- svytotal(~api.stu,
1328s +               calibrate(dstrat, ~enroll-1, pop= pop$enroll, variance=2))
1328s > e <- predict(svyratio(~api.stu, ~enroll, dstrat),total=pop$enroll)
1328s > 
1328s > all.equal(as.vector(coef(a)),as.vector(coef(b)))
1328s [1] TRUE
1328s > all.equal(as.vector(SE(a)), as.vector(SE(b)))
1328s [1] TRUE
1328s > all.equal(as.vector(coef(a)),as.vector(e$total))
1328s [1] TRUE
1328s > all.equal(as.vector(SE(a)), as.vector(e$se))
1328s [1] TRUE
1328s > if(!is.null(getOption("DEBUG"))){## uses 6194x6194 matrix
1328s +     d <- predict(api.reg2, newdata=na.omit(apipop[,"enroll",drop=FALSE]))
1328s +     all.equal(as.vector(coef(a)), as.vector(sum(coef(d))))
1328s +     all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d)))))
1328s + }
1328s > 
1328s BEGIN TEST rss_scores.R
1328s 
1328s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1328s Copyright (C) 2023 The R Foundation for Statistical Computing
1328s Platform: x86_64-pc-linux-gnu (64-bit)
1328s 
1328s R is free software and comes with ABSOLUTELY NO WARRANTY.
1328s You are welcome to redistribute it under certain conditions.
1328s Type 'license()' or 'licence()' for distribution details.
1328s 
1328s R is a collaborative project with many contributors.
1328s Type 'contributors()' for more information and
1328s 'citation()' on how to cite R or R packages in publications.
1328s 
1328s Type 'demo()' for some demos, 'help()' for on-line help, or
1328s 'help.start()' for an HTML browser interface to help.
1328s Type 'q()' to quit R.
1328s 
1328s > ## Example from Rao, Scott, and Skinner 1998 Statistica Sinica
1328s > library(survey)
1328s Loading required package: grid
1328s Loading required package: Matrix
1329s Loading required package: survival
1329s 
1329s Attaching package: 'survey'
1329s 
1329s > data(myco)
1329s The following object is masked from 'package:graphics':
1329s 
1329s     dotchart
1329s 
1329s > dmyco<-svydesign(id=~1, strata=~interaction(Age,leprosy),weights=~wt,data=myco)
1329s > m_full<-svyglm(leprosy~I((Age+7.5)^-2)+Scar, family=quasibinomial, design=dmyco)
1329s > m_null<-svyglm(leprosy~I((Age+7.5)^-2), family=quasibinomial, design=dmyco)
1329s > 
1329s > stopifnot(isTRUE(all.equal(coef(m_null), c(`(Intercept)`=-4.6, `I((Age + 7.5)^-2)`=-427),tol=1e-2)))
1329s > 
1329s > s<-svyscoretest(m_full, ~Scar)
1329s > stopifnot(abs(s[1]-10.73)<0.05)
1329s > 
1329s > t<-svyscoretest(m_full,~Scar,method="individual")
1329s > stopifnot(abs(coef(t)- -32.61)<0.1)
1329s > stopifnot(abs(vcov(t)-99.1)<0.1)
1329s >  
1329s > 
1329s BEGIN TEST scoping.R
1329s 
1329s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1329s Copyright (C) 2023 The R Foundation for Statistical Computing
1329s Platform: x86_64-pc-linux-gnu (64-bit)
1329s 
1329s R is free software and comes with ABSOLUTELY NO WARRANTY.
1329s You are welcome to redistribute it under certain conditions.
1329s Type 'license()' or 'licence()' for distribution details.
1329s 
1329s R is a collaborative project with many contributors.
1329s Type 'contributors()' for more information and
1329s 'citation()' on how to cite R or R packages in publications.
1329s 
1329s Type 'demo()' for some demos, 'help()' for on-line help, or
1329s 'help.start()' for an HTML browser interface to help.
1329s Type 'q()' to quit R.
1329s 
1329s > 
1329s > ## regression test for testing regression
1329s > 
1329s > library(survey)
1329s Loading required package: grid
1329s Loading required package: Matrix
1330s Loading required package: survival
1330s 
1330s Attaching package: 'survey'
1330s 
1330s The following object is masked from 'package:graphics':
1330s 
1330s     dotchart
1330s 
1330s > data(api)
1330s > 
1330s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
1330s > 
1330s > 
1330s > f<-function(){
1330s +   form<-acs.46~stype
1330s +   svyglm(formula=form, design = dstrat)  
1330s + }
1330s > 
1330s > g<-function(form){
1330s +   svyglm(formula=form, design = dstrat)  
1330s + }
1330s > f()
1330s Stratified Independent Sampling design
1330s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
1330s     fpc = ~fpc)
1330s 
1330s Call:  svyglm(formula = form, design = dstrat)
1330s 
1330s Coefficients:
1330s (Intercept)       stypeH       stypeM  
1330s     28.7449       0.7551       0.4022  
1330s 
1330s Degrees of Freedom: 133 Total (i.e. Null);  129 Residual
1330s   (66 observations deleted due to missingness)
1330s Null Deviance:	    1838 
1330s Residual Deviance: 1835 	AIC: 719.8
1330s > g(acs.46~stype)
1330s Stratified Independent Sampling design
1330s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
1330s     fpc = ~fpc)
1330s 
1330s Call:  svyglm(formula = form, design = dstrat)
1330s 
1330s Coefficients:
1330s (Intercept)       stypeH       stypeM  
1330s     28.7449       0.7551       0.4022  
1330s 
1330s Degrees of Freedom: 133 Total (i.e. Null);  129 Residual
1330s   (66 observations deleted due to missingness)
1330s Null Deviance:	    1838 
1330s Residual Deviance: 1835 	AIC: 719.8
1330s > 
1330s > f<-function(){
1330s +   form<-Surv(acs.46)~stype
1330s +   svycoxph(formula=form, design = dstrat)  
1330s + }
1330s > 
1330s > g<-function(form){
1330s +   svycoxph(formula=form, design = dstrat)  
1330s + }
1330s > 
1330s > f()
1330s Call:
1330s svycoxph(formula = form, design = dstrat)
1330s 
1330s           coef exp(coef) se(coef) robust se      z     p
1330s stypeH -0.6766    0.5083   1.0208    0.6652 -1.017 0.309
1330s stypeM -0.2509    0.7781   0.2308    0.2089 -1.201 0.230
1330s 
1330s Likelihood ratio test=  on 2 df, p=
1330s n= 134, number of events= 134 
1330s    (66 observations deleted due to missingness)
1330s > g(Surv(acs.46)~stype)
1330s Call:
1330s svycoxph(formula = form, design = dstrat)
1330s 
1330s           coef exp(coef) se(coef) robust se      z     p
1330s stypeH -0.6766    0.5083   1.0208    0.6652 -1.017 0.309
1330s stypeM -0.2509    0.7781   0.2308    0.2089 -1.201 0.230
1330s 
1330s Likelihood ratio test=  on 2 df, p=
1330s n= 134, number of events= 134 
1330s    (66 observations deleted due to missingness)
1330s > 
1330s > ## check coxph for a single predictor
1330s > svycoxph(Surv(acs.46)~api00,design=dstrat)
1330s Call:
1330s svycoxph(formula = Surv(acs.46) ~ api00, design = dstrat)
1330s 
1330s            coef exp(coef)  se(coef) robust se     z     p
1330s api00 6.060e-06 1.000e+00 6.244e-04 7.492e-04 0.008 0.994
1330s 
1330s Likelihood ratio test=  on 1 df, p=
1330s n= 134, number of events= 134 
1330s    (66 observations deleted due to missingness)
1330s > 
1330s BEGIN TEST survcurve.R
1330s 
1330s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1330s Copyright (C) 2023 The R Foundation for Statistical Computing
1330s Platform: x86_64-pc-linux-gnu (64-bit)
1330s 
1330s R is free software and comes with ABSOLUTELY NO WARRANTY.
1330s You are welcome to redistribute it under certain conditions.
1330s Type 'license()' or 'licence()' for distribution details.
1330s 
1330s R is a collaborative project with many contributors.
1330s Type 'contributors()' for more information and
1330s 'citation()' on how to cite R or R packages in publications.
1330s 
1330s Type 'demo()' for some demos, 'help()' for on-line help, or
1330s 'help.start()' for an HTML browser interface to help.
1330s Type 'q()' to quit R.
1330s 
1330s > library(survey)
1330s Loading required package: grid
1330s Loading required package: Matrix
1331s Loading required package: survival
1331s 
1331s Attaching package: 'survey'
1331s 
1331s > library(survival)
1331s The following object is masked from 'package:graphics':
1331s 
1331s     dotchart
1331s 
1331s > 
1331s > pbc2<-rbind(pbc,pbc)
1331s > pbc2$id<-rep(1:418,2)
1331s > 
1331s > dpbc1<-svydesign(id=~1, data=pbc)
1331s Warning message:
1331s In svydesign.default(id = ~1, data = pbc) :
1331s   No weights or probabilities supplied, assuming equal probability
1331s > dpbc2<-svydesign(id=~id, data=pbc2)
1332s > 
1332s > s1<-svykm(Surv(time,status>0)~1, subset(dpbc1, bili>6), se=TRUE)
1332s Warning message:
1332s In svydesign.default(id = ~id, data = pbc2) :
1332s   No weights or probabilities supplied, assuming equal probability
1332s > s2<-svykm(Surv(time,status>0)~1, subset(dpbc2, bili>6), se=TRUE)
1332s > 
1332s > (c1<-confint(s1,(1:5)*365))
1332s          0.025     0.975
1332s 365  0.6446215 0.8594153
1332s 730  0.5410938 0.7766848
1332s 1095 0.2683127 0.5103356
1332s 1460 0.1444731 0.3722001
1332s 1825 0.1009672 0.3204713
1332s > (c2<-confint(s2,(1:5)*365))
1332s          0.025     0.975
1332s 365  0.6446215 0.8594153
1332s 730  0.5410938 0.7766848
1332s 1095 0.2683127 0.5103356
1332s 1460 0.1444731 0.3722001
1332s 1825 0.1009672 0.3204713
1332s > all.equal(c1, c2)
1332s [1] TRUE
1332s > 
1332s > m1<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc1)
1332s > m2<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc2)
1332s > 
1332s > d<-data.frame(bili=c(5,10))
1332s > p1<-predict(m1, se=TRUE, newdata=d,type="curve")
1332s > p2<-predict(m2, se=TRUE, newdata=d,type="curve")
1333s > 
1333s > (pc1<-confint(p1[[1]],(1:5)*365))
1333s          0.025     0.975
1333s 365  0.8410027 0.9266263
1333s 730  0.7371114 0.8548312
1333s 1095 0.5517779 0.7018583
1333s 1460 0.4335073 0.5992819
1333s 1825 0.3260899 0.5046241
1333s > (pc2<-confint(p2[[1]],(1:5)*365))
1333s          0.025     0.975
1333s 365  0.8409490 0.9267054
1333s 730  0.7370152 0.8549432
1333s 1095 0.5515848 0.7019513
1333s 1460 0.4332252 0.5992968
1333s 1825 0.3257172 0.5045795
1333s > all.equal(pc1, pc2)
1333s [1] "Mean relative difference: 0.0002070722"
1333s > 
1333s > (q1<-quantile(p1[[2]]))
1333s 0.75  0.5 0.25 
1333s  489  930 1492 
1333s > (q2<-quantile(p2[[2]]))
1333s 0.75  0.5 0.25 
1333s  489  930 1492 
1333s > all.equal(q1,q2)
1333s [1] TRUE
1333s > 
1333s BEGIN TEST svyby-strings.R
1334s 
1334s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1334s Copyright (C) 2023 The R Foundation for Statistical Computing
1334s Platform: x86_64-pc-linux-gnu (64-bit)
1334s 
1334s R is free software and comes with ABSOLUTELY NO WARRANTY.
1334s You are welcome to redistribute it under certain conditions.
1334s Type 'license()' or 'licence()' for distribution details.
1334s 
1334s R is a collaborative project with many contributors.
1334s Type 'contributors()' for more information and
1334s 'citation()' on how to cite R or R packages in publications.
1334s 
1334s Type 'demo()' for some demos, 'help()' for on-line help, or
1334s 'help.start()' for an HTML browser interface to help.
1334s Type 'q()' to quit R.
1334s 
1334s > 
1334s > ## check that stringsAsFactors fixes the string levels problem
1334s > data(api, package = "survey")
1334s > des <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc)
1335s > est0 <-
1335s +   survey::svyby(design=des, formula=~cname, by=~both, FUN=survey::svymean, keep.var=TRUE, stringsAsFactors=TRUE) 
1335s > 
1335s > stopifnot(isTRUE(all(dim(est0)==c(2,23))))
1335s > 
1335s BEGIN TEST svyby_bug.R
1335s 
1335s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1335s Copyright (C) 2023 The R Foundation for Statistical Computing
1335s Platform: x86_64-pc-linux-gnu (64-bit)
1335s 
1335s R is free software and comes with ABSOLUTELY NO WARRANTY.
1335s You are welcome to redistribute it under certain conditions.
1335s Type 'license()' or 'licence()' for distribution details.
1335s 
1335s R is a collaborative project with many contributors.
1335s Type 'contributors()' for more information and
1335s 'citation()' on how to cite R or R packages in publications.
1335s 
1335s Type 'demo()' for some demos, 'help()' for on-line help, or
1335s 'help.start()' for an HTML browser interface to help.
1335s Type 'q()' to quit R.
1335s 
1335s > library(survey)
1335s Loading required package: grid
1335s Loading required package: Matrix
1336s Loading required package: survival
1336s 
1336s Attaching package: 'survey'
1336s 
1336s The following object is masked from 'package:graphics':
1336s 
1336s     dotchart
1336s 
1336s > options(warn=2)
1336s > 
1336s > ## Caused warnings and unhelpful results in 4.1_1 (Guilherme Jacob)
1336s > data(api)
1336s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1336s > svyby(~api99, ~stype, dclus1, svymean )
1336s   stype    api99       se
1336s E     E 607.7917 22.81660
1336s H     H 595.7143 41.76400
1336s M     M 608.6000 32.56064
1336s > 
1336s > set.seed(123)
1336s > apiclus1$api99[ sample.int( nrow(apiclus1) , 5 ) ] <- NA
1336s > dclus1.na <-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1336s > 
1336s > # subsetting w/ na.rm = FALSE...
1336s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = FALSE )
1336s       mean  SE
1336s api99   NA NaN
1336s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = FALSE )
1336s         mean     SE
1336s api99 595.71 41.764
1336s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = FALSE )
1336s       mean  SE
1336s api99   NA NaN
1336s > 
1336s > # ... looks like this:
1336s > svyby(~api99, ~stype, dclus1.na , svymean )
1336s   stype    api99     se
1336s E     E       NA    NaN
1336s H     H 595.7143 41.764
1336s M     M       NA    NaN
1336s > 
1336s > # subsetting w/ na.rm = TRUE...
1336s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = TRUE )
1336s         mean     SE
1336s api99 606.53 22.901
1336s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = TRUE )
1336s         mean     SE
1336s api99 595.71 41.764
1336s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = TRUE )
1336s         mean     SE
1336s api99 613.39 33.224
1336s > 
1336s > # ... looks like this
1336s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE )
1336s   stype    api99       se
1336s E     E 606.5319 22.90084
1336s H     H 595.7143 41.76400
1336s M     M 613.3913 33.22358
1336s > 
1336s > # Without missing values, this works:
1336s > svyby(~api99, ~stype, dclus1 , svymean , na.rm = TRUE , covmat = TRUE )
1336s   stype    api99       se
1336s E     E 607.7917 22.81660
1336s H     H 595.7143 41.76400
1336s M     M 608.6000 32.56064
1336s > 
1336s > # ... but this breaks!
1336s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE , covmat = TRUE )
1336s   stype    api99       se
1336s E     E 606.5319 22.90084
1336s H     H 595.7143 41.76400
1336s M     M 613.3913 33.22358
1336s > 
1336s > # ... and i don't think this is the expected behavior
1336s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , covmat = TRUE )
1336s   stype    api99     se
1336s E     E       NA    NaN
1336s H     H 595.7143 41.764
1336s M     M       NA    NaN
1336s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , na.rm = TRUE , covmat = TRUE )
1336s   stype    api99       se
1336s E     E 606.5319 22.90084
1336s H     H 595.7143 41.76400
1336s M     M 613.3913 33.22358
1336s > 
1336s > 
1336s > ## <TL> Now some more as tests
1336s > svyby(~api99, ~stype, dclus1.na , svytotal , na.rm = TRUE , covmat = TRUE )
1336s   stype     api99       se
1336s E     E 2894629.0 792809.8
1336s H     H  282283.9 101492.9
1336s M     M  477513.4 107555.5
1336s > svyby(~api99, ~stype, dclus1.na , svyratio , na.rm = TRUE , denominator=~api00, covmat = TRUE )
1336s   stype api99/api00 se.api99/api00
1336s E     E   0.9367750    0.006365702
1336s H     H   0.9630485    0.010520785
1336s M     M   0.9682246    0.009390982
1336s > 
1336s > ff<-function(f,d,...,na.rm=TRUE) svyglm(f,d,...)
1336s > svyby(api99~1, ~stype, dclus1.na , ff , na.rm = TRUE , covmat = TRUE )
1336s   stype (Intercept) se.(Intercept)
1336s E     E    606.5319       22.90084
1336s H     H    595.7143       41.76400
1336s M     M    613.3913       33.22358
1336s > 
1336s BEGIN TEST svyby_se.R
1336s 
1336s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1336s Copyright (C) 2023 The R Foundation for Statistical Computing
1336s Platform: x86_64-pc-linux-gnu (64-bit)
1336s 
1336s R is free software and comes with ABSOLUTELY NO WARRANTY.
1336s You are welcome to redistribute it under certain conditions.
1336s Type 'license()' or 'licence()' for distribution details.
1336s 
1336s R is a collaborative project with many contributors.
1336s Type 'contributors()' for more information and
1336s 'citation()' on how to cite R or R packages in publications.
1336s 
1336s Type 'demo()' for some demos, 'help()' for on-line help, or
1336s 'help.start()' for an HTML browser interface to help.
1336s Type 'q()' to quit R.
1336s 
1336s > library(survey)
1336s Loading required package: grid
1336s Loading required package: Matrix
1337s Loading required package: survival
1338s 
1338s Attaching package: 'survey'
1338s 
1338s The following object is masked from 'package:graphics':
1338s 
1338s     dotchart
1338s 
1338s > data(api)
1338s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
1338s > 
1338s > a<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("ci","se"))
1338s > b<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("se","ci"))
1338s > 
1338s > 
1338s > stopifnot(all.equal(SE(a),SE(b)))
1338s > 
1338s BEGIN TEST svycontrast.R
1338s 
1338s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1338s Copyright (C) 2023 The R Foundation for Statistical Computing
1338s Platform: x86_64-pc-linux-gnu (64-bit)
1338s 
1338s R is free software and comes with ABSOLUTELY NO WARRANTY.
1338s You are welcome to redistribute it under certain conditions.
1338s Type 'license()' or 'licence()' for distribution details.
1338s 
1338s R is a collaborative project with many contributors.
1338s Type 'contributors()' for more information and
1338s 'citation()' on how to cite R or R packages in publications.
1338s 
1338s Type 'demo()' for some demos, 'help()' for on-line help, or
1338s 'help.start()' for an HTML browser interface to help.
1338s Type 'q()' to quit R.
1338s 
1338s > library(survey)
1338s Loading required package: grid
1338s Loading required package: Matrix
1339s Loading required package: survival
1339s 
1339s Attaching package: 'survey'
1339s 
1339s The following object is masked from 'package:graphics':
1339s 
1339s     dotchart
1339s 
1339s > data(api)
1339s > dclus2<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
1339s > rclus2<-as.svrepdesign(dclus2)
1339s > model<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2)
1339s > svycontrast(model, c(ell=1,meals=0))
1339s          contrast     SE
1339s contrast  -2.0592 1.6177
1339s > a<-svycontrast(model, c(0,1,0,0))
1339s > 
1339s > model2<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2,return.replicates=TRUE)
1339s > svycontrast(model2, c(ell=1,meals=0))
1339s          contrast     SE
1339s contrast  -2.0592 1.6177
1339s > a2<-svycontrast(model2, c(0,1,0,0))
1339s > stopifnot(!is.null(a2$replicates))
1339s > 
1339s BEGIN TEST svyivreg-var.R
1339s 
1339s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1339s Copyright (C) 2023 The R Foundation for Statistical Computing
1339s Platform: x86_64-pc-linux-gnu (64-bit)
1339s 
1339s R is free software and comes with ABSOLUTELY NO WARRANTY.
1339s You are welcome to redistribute it under certain conditions.
1339s Type 'license()' or 'licence()' for distribution details.
1339s 
1339s R is a collaborative project with many contributors.
1339s Type 'contributors()' for more information and
1339s 'citation()' on how to cite R or R packages in publications.
1339s 
1339s Type 'demo()' for some demos, 'help()' for on-line help, or
1339s 'help.start()' for an HTML browser interface to help.
1339s Type 'q()' to quit R.
1339s 
1339s > 
1339s > library(survey)
1339s Loading required package: grid
1339s Loading required package: Matrix
1340s Loading required package: survival
1340s 
1340s Attaching package: 'survey'
1340s 
1340s The following object is masked from 'package:graphics':
1340s 
1340s     dotchart
1340s 
1340s > data(api)
1340s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
1340s > a<-summary(svyglm(api00~ell+meals+mobility, design=dstrat))
1340s > b<- summary(svyivreg(api00~ell+meals+mobility, design=dstrat))
1340s > stopifnot(isTRUE(all.equal(a$cov.scaled, b$vcov)))
1340s > 
1340s BEGIN TEST svyivreg.R
1340s 
1340s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1340s Copyright (C) 2023 The R Foundation for Statistical Computing
1340s Platform: x86_64-pc-linux-gnu (64-bit)
1340s 
1340s R is free software and comes with ABSOLUTELY NO WARRANTY.
1340s You are welcome to redistribute it under certain conditions.
1340s Type 'license()' or 'licence()' for distribution details.
1340s 
1340s R is a collaborative project with many contributors.
1340s Type 'contributors()' for more information and
1340s 'citation()' on how to cite R or R packages in publications.
1340s 
1340s Type 'demo()' for some demos, 'help()' for on-line help, or
1340s 'help.start()' for an HTML browser interface to help.
1340s Type 'q()' to quit R.
1340s 
1340s > library(survey)
1340s Loading required package: grid
1340s Loading required package: Matrix
1341s Loading required package: survival
1341s 
1341s Attaching package: 'survey'
1341s 
1341s The following object is masked from 'package:graphics':
1341s 
1341s     dotchart
1341s 
1341s > library(AER)
1341s Loading required package: car
1341s Loading required package: carData
1341s Loading required package: lmtest
1341s Loading required package: zoo
1341s 
1341s Attaching package: 'zoo'
1341s 
1341s The following objects are masked from 'package:base':
1341s 
1341s     as.Date, as.Date.numeric
1341s 
1341s Loading required package: sandwich
1342s > 
1342s > load("cigsw.rda")
1342s > 
1342s > des<-svydesign(id=~1, weights=~wt, data=cigsw)
1342s > m<-svyivreg(log(packs) ~ log(rprice) + log(rincome) | log(rincome) + tdiff + I(tax/cpi), design=des)
1342s > 
1342s > all.equal(as.vector(coef(m)), c(10.42009 , -1.588135, 0.6140887),tolerance=1e-6)
1342s [1] TRUE
1342s > all.equal(as.vector(SE(m)), c( 1.047699, .3394232,  .3614382 ),tolerance=1e-6)
1342s [1] TRUE
1342s > 
1342s BEGIN TEST svyolr-rake-subset.R
1342s 
1342s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1342s Copyright (C) 2023 The R Foundation for Statistical Computing
1342s Platform: x86_64-pc-linux-gnu (64-bit)
1342s 
1342s R is free software and comes with ABSOLUTELY NO WARRANTY.
1342s You are welcome to redistribute it under certain conditions.
1342s Type 'license()' or 'licence()' for distribution details.
1342s 
1342s R is a collaborative project with many contributors.
1342s Type 'contributors()' for more information and
1342s 'citation()' on how to cite R or R packages in publications.
1342s 
1342s Type 'demo()' for some demos, 'help()' for on-line help, or
1342s 'help.start()' for an HTML browser interface to help.
1342s Type 'q()' to quit R.
1342s 
1342s > library(survey)
1342s Loading required package: grid
1342s Loading required package: Matrix
1343s Loading required package: survival
1343s 
1343s Attaching package: 'survey'
1343s 
1343s The following object is masked from 'package:graphics':
1343s 
1343s     dotchart
1343s 
1343s > data(api)
1343s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1343s > 
1343s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100)))
1343s > 
1343s > ## population marginal totals for each stratum
1343s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018))
1343s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122))
1343s > 
1343s > 
1343s > ## rake with the population totals
1343s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
1343s > 
1343s > # works
1343s > m <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1)
1343s > 
1343s > # fails in 4.1 (should work because svyolr's default na.action is na.omit)
1343s > m2 <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1r)
1343s > 
1343s > # fails in 4.1 (should work because NA values are subsetted out)
1343s > m3 <- svyolr(mealcat~avg.ed+mobility+stype, design=subset( dclus1r , !is.na( avg.ed ) ) )
1343s > 
1343s BEGIN TEST svyolr.R
1343s 
1343s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1343s Copyright (C) 2023 The R Foundation for Statistical Computing
1343s Platform: x86_64-pc-linux-gnu (64-bit)
1343s 
1343s R is free software and comes with ABSOLUTELY NO WARRANTY.
1343s You are welcome to redistribute it under certain conditions.
1343s Type 'license()' or 'licence()' for distribution details.
1343s 
1343s R is a collaborative project with many contributors.
1343s Type 'contributors()' for more information and
1343s 'citation()' on how to cite R or R packages in publications.
1343s 
1343s Type 'demo()' for some demos, 'help()' for on-line help, or
1343s 'help.start()' for an HTML browser interface to help.
1343s Type 'q()' to quit R.
1343s 
1343s > library(survey)
1343s Loading required package: grid
1343s Loading required package: Matrix
1344s Loading required package: survival
1344s 
1344s Attaching package: 'survey'
1344s 
1344s The following object is masked from 'package:graphics':
1344s 
1344s     dotchart
1344s 
1344s > 
1344s > ################################################################################
1344s > # Example from svyolr: runs OK
1344s > data(api)
1344s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
1344s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100)))
1344s > 
1344s > m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1)
1344s > m
1344s Call:
1344s svyolr(mealcat ~ avg.ed + mobility + stype, design = dclus1)
1344s 
1344s Coefficients:
1344s     avg.ed   mobility     stypeH     stypeM 
1344s -2.6999217  0.0325042 -1.7574715 -0.6191463 
1344s 
1344s Intercepts:
1344s   (0,25]|(25,50]  (25,50]|(50,75] (50,75]|(75,100] 
1344s        -8.857919        -6.586464        -4.924938 
1344s > 
1344s > ## Use regTermTest for testing multiple parameters
1344s > test<-regTermTest(m, ~avg.ed+stype, method="LRT")
1344s > ################################################################################
1344s > 
1344s > ################################################################################
1344s > # If we wrap everything into a function: error b/c it looks for design variable
1344s > # dclus1 in .GlobalEnv
1344s > 
1344s > foo <- function(x){
1344s +   dclus1<-svydesign(id=~dnum, weights=~pw, data=x, fpc=~fpc)
1344s +   dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100)))
1344s + 
1344s +   m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1)
1344s +   ## Use regTermTest for testing multiple parameters
1344s +   regTermTest(m, ~avg.ed+stype, method="LRT")
1344s + }
1344s > 
1344s > # OK
1344s > foo(apiclus1)
1344s Working (Rao-Scott+F) LRT for avg.ed stype
1344s  in svyolr(formula = mealcat ~ avg.ed + mobility + stype, design = dclus1)
1344s Working 2logLR =  0.6580304 p= 0.73257 
1344s (scale factors:  2.7 0.22 0.11 );  denominator df= 10
1344s > 
1344s > # Clean-up everything but apiclus1 and foo
1344s > rm(list = setdiff(ls(),c('apiclus1','foo','test')))
1344s > 
1344s > # Error
1344s > test2<-foo(apiclus1)
1344s > ################################################################################
1344s > all.equal(test,test2)
1344s [1] TRUE
1344s > 
1344s > 
1344s BEGIN TEST toy_example_for_postStratify.R
1344s 
1344s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1344s Copyright (C) 2023 The R Foundation for Statistical Computing
1344s Platform: x86_64-pc-linux-gnu (64-bit)
1344s 
1344s R is free software and comes with ABSOLUTELY NO WARRANTY.
1344s You are welcome to redistribute it under certain conditions.
1344s Type 'license()' or 'licence()' for distribution details.
1344s 
1344s R is a collaborative project with many contributors.
1344s Type 'contributors()' for more information and
1344s 'citation()' on how to cite R or R packages in publications.
1344s 
1344s Type 'demo()' for some demos, 'help()' for on-line help, or
1344s 'help.start()' for an HTML browser interface to help.
1344s Type 'q()' to quit R.
1344s 
1345s > library(survey)
1345s Loading required package: grid
1345s Loading required package: Matrix
1345s Loading required package: survival
1346s 
1346s Attaching package: 'survey'
1346s 
1346s > 
1346s > # Dummy data for testing nonresponse adjustments
1346s > toy <- data.frame(id = 1:10,
1346s +                   dummy = 1,
1346s + The following object is masked from 'package:graphics':
1346s 
1346s     dotchart
1346s 
1346s                   class = c(rep("A", 5), rep("B", 5)),
1346s +                   responded = c(rep(TRUE, 8), FALSE, FALSE),
1346s +                   weight = rep(100, 10))
1346s > 
1346s > # With jackknife replicate weights
1346s > toy_repweights <- matrix(rep(1000/9, 100), nrow = 10)
1346s > diag(toy_repweights) <- rep(0, 10)
1346s > 
1346s > # Scramble up which person is in which jackknife group
1346s > toy_repweights <- toy_repweights[sample(1:10, size = 10), ]
1346s > 
1346s > toy_design <- svrepdesign(variables = toy[, 1:4],
1346s +                           weights = toy$weight,
1346s +                           repweights = toy_repweights,
1346s +                           type = "JK1",
1346s +                           scale = 0.9)
1346s > 
1346s > # Get the sum of the weights for the full sample
1346s > poptotals <- as.data.frame(svyby(formula = ~dummy,
1346s +                                  by = ~class,
1346s +                                  design = toy_design,
1346s +                                  FUN = survey::svytotal))
1346s > 
1346s > poptotals$Freq <- poptotals$dummy
1346s > poptotals$dummy <- NULL
1346s > poptotals$se <- NULL
1346s > 
1346s > # Adjust the weights of the responding sample to match to the full sample
1346s > adjusted <-  postStratify(design = subset(toy_design, responded),
1346s +                           strata = ~class,
1346s +                           population = poptotals)
1346s > 
1346s > # This works for the weights...
1346s > svyby(formula = ~dummy,
1346s +       by = ~class,
1346s +       design = adjusted,
1346s +       FUN = survey::svytotal)
1346s   class dummy se
1346s A     A   500  0
1346s B     B   500  0
1346s > 
1346s > # ...and some, but not all, the replicate weights
1346s > stopifnot(all.equal(colSums(toy_design$repweights), colSums(adjusted$repweights)))
1346s > 
1346s > 
1346s > 
1346s BEGIN TEST twophase.R
1346s 
1346s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1346s Copyright (C) 2023 The R Foundation for Statistical Computing
1346s Platform: x86_64-pc-linux-gnu (64-bit)
1346s 
1346s R is free software and comes with ABSOLUTELY NO WARRANTY.
1346s You are welcome to redistribute it under certain conditions.
1346s Type 'license()' or 'licence()' for distribution details.
1346s 
1346s R is a collaborative project with many contributors.
1346s Type 'contributors()' for more information and
1346s 'citation()' on how to cite R or R packages in publications.
1346s 
1346s Type 'demo()' for some demos, 'help()' for on-line help, or
1346s 'help.start()' for an HTML browser interface to help.
1346s Type 'q()' to quit R.
1346s 
1346s > library(survey)
1346s Loading required package: grid
1346s Loading required package: Matrix
1347s Loading required package: survival
1347s 
1347s Attaching package: 'survey'
1347s 
1347s The following object is masked from 'package:graphics':
1347s 
1347s     dotchart
1347s 
1347s > 
1347s > ## two-phase simple random sampling.
1347s > data(pbc, package="survival")
1347s > pbc$id<-1:nrow(pbc)
1347s > pbc$randomized<-with(pbc, !is.na(trt) & trt>-9)
1347s > (d2pbc<-twophase(id=list(~id,~id), data=pbc, subset=~I(!randomized)))
1347s Two-phase sparse-matrix design:
1347s  twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
1347s     subset = subset, data = data)
1347s Phase 1:
1347s Independent Sampling design (with replacement)
1347s svydesign(ids = ~id)
1347s Phase 2:
1347s Independent Sampling design
1347s svydesign(ids = ~id, fpc = `*phase1*`)
1347s > m<-svymean(~bili, d2pbc)
1347s > all.equal(as.vector(coef(m)),with(pbc, mean(bili[!randomized])))
1347s [1] TRUE
1347s > all.equal(as.vector(SE(m)),
1347s +           with(pbc, sd(bili[!randomized])/sqrt(sum(!randomized))),
1347s +           tolerance=0.002)
1347s [1] TRUE
1347s > 
1347s > ## two-stage sampling as two-phase
1347s > data(mu284)
1347s > ii<-with(mu284, c(1:15, rep(1:5,n2[1:5]-3)))
1347s > mu284.1<-mu284[ii,]
1347s > mu284.1$id<-1:nrow(mu284.1)
1347s > mu284.1$sub<-rep(c(TRUE,FALSE),c(15,34-15))
1347s > dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)
1347s > ## first phase cluster sample, second phase stratified within cluster
1347s > (d2mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1),
1347s +                    fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="approx"))
1347s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 
1347s     NULL), data = mu284.1, subset = ~sub, method = "approx")
1347s Phase 1:
1347s 1 - level Cluster Sampling design
1347s With (5) clusters.
1347s svydesign(ids = ~id1, fpc = ~n1)
1347s Phase 2:
1347s Stratified Independent Sampling design
1347s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`)
1347s > (d22mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1),
1347s +                    fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="full"))
1347s Two-phase sparse-matrix design:
1347s  twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
1347s     subset = subset, data = data)
1347s Phase 1:
1347s 1 - level Cluster Sampling design
1347s With (5) clusters.
1347s svydesign(ids = ~id1, fpc = ~n1)
1347s Phase 2:
1347s Stratified Independent Sampling design
1347s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`)
1347s > summary(d2mu284)
1347s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 
1347s     NULL), data = mu284.1, subset = ~sub, method = "approx")
1347s Phase 1:
1347s 1 - level Cluster Sampling design
1347s With (5) clusters.
1347s svydesign(ids = ~id1, fpc = ~n1)
1347s Probabilities:
1347s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1347s     0.1     0.1     0.1     0.1     0.1     0.1 
1347s Population size (PSUs): 50 
1347s Phase 2:
1347s Stratified Independent Sampling design
1347s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`)
1347s Probabilities:
1347s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
1347s  0.3333  0.3750  0.4286  0.4674  0.6000  0.6000 
1347s Stratum Sizes: 
1347s            19 31 45 47 50
1347s obs         3  3  3  3  3
1347s design.PSU  3  3  3  3  3
1347s actual.PSU  3  3  3  3  3
1347s Population stratum sizes (PSUs): 
1347s 19 31 45 47 50 
1347s  5  7  8  5  9 
1347s Data variables:
1347s [1] "id1" "n1"  "id2" "y1"  "n2"  "id"  "sub"
1347s > t1<-svytotal(~y1, dmu284)
1347s > t2<-svytotal(~y1, d2mu284)
1347s > t22<-svytotal(~y1,d22mu284)
1347s > m1<-svymean(~y1, dmu284)
1347s > m2<-svymean(~y1, d2mu284)
1347s > m22<-svymean(~y1, d22mu284)
1347s > all.equal(coef(t1),coef(t2))
1347s [1] TRUE
1347s > all.equal(coef(t1),coef(t22))
1347s [1] TRUE
1347s > all.equal(coef(m1),coef(m2))
1347s [1] TRUE
1347s > all.equal(coef(m1),coef(m22))
1347s [1] TRUE
1347s > all.equal(as.vector(SE(m1)),as.vector(SE(m2)))
1347s [1] TRUE
1347s > all.equal(as.vector(SE(m1)),as.vector(SE(m22)))
1347s [1] TRUE
1347s > all.equal(as.vector(SE(t1)),as.vector(SE(t2)))
1347s [1] TRUE
1347s > all.equal(as.vector(SE(t1)),as.vector(SE(t22)))
1347s [1] TRUE
1347s > 
1347s > ## case-cohort design
1347s > ##this example requires R 2.3.1 or later for cch and data.
1347s > library("survival")
1347s > data(nwtco, package="survival")
1347s > ## unstratified, equivalent to Lin & Ying (1993)
1347s > print(dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel),
1347s +                  subset=~I(in.subcohort | rel), data=nwtco))
1348s Two-phase sparse-matrix design:
1348s  twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
1348s     subset = subset, data = data)
1348s Phase 1:
1348s Independent Sampling design (with replacement)
1348s svydesign(ids = ~seqno)
1348s Phase 2:
1348s Stratified Independent Sampling design
1348s svydesign(ids = ~seqno, strata = ~rel, fpc = `*phase1*`)
1348s > cch1<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12),
1348s +                design=dcchs)
1348s > dcchs2<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel),
1348s +                  subset=~I(in.subcohort | rel), data=nwtco,method="approx")
1348s > cch1.2<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12),
1348s +                design=dcchs)
1348s > all.equal(coef(cch1),coef(cch1.2))
1348s [1] TRUE
1348s > all.equal(SE(cch1),SE(cch1.2))
1348s [1] TRUE
1348s > ## Using survival::cch 
1348s > subcoh <- nwtco$in.subcohort
1348s > selccoh <- with(nwtco, rel==1|subcoh==1)
1348s > ccoh.data <- nwtco[selccoh,]
1348s > ccoh.data$subcohort <- subcoh[selccoh]
1348s > cch2<-cch(Surv(edrel, rel) ~ factor(stage) + factor(histol) + I(age/12),
1348s +           data =ccoh.data, subcoh = ~subcohort, id=~seqno,
1348s +           cohort.size=4028, method="LinYing", robust=TRUE)
1348s > 
1348s > print(all.equal(as.vector(coef(cch1)),as.vector(coef(cch2))))
1348s [1] TRUE
1348s > ## cch has smaller variances by a factor of 1.0005 because
1348s > ## there is a (n/(n-1)) in the survey phase1 varianace
1348s > print(all.equal(as.vector(SE(cch1)), as.vector(SE(cch2)),tolerance=0.0006))
1348s [1] TRUE
1348s > 
1348s > 
1348s > ## bug report from Takahiro Tsuchiya for version 3.4
1348s > ## We used to not match Sarndal exactly, because our old phase-one
1348s > ## estimator had a small bias for finite populations
1348s > rei<-read.table(tmp<-textConnection(
1348s + "  id   N n.a h n.ah n.h   sub  y
1348s + 1   1 300  20 1   12   5  TRUE  1
1348s + 2   2 300  20 1   12   5  TRUE  2
1348s + 3   3 300  20 1   12   5  TRUE  3
1348s + 4   4 300  20 1   12   5  TRUE  4
1348s + 5   5 300  20 1   12   5  TRUE  5
1348s + 6   6 300  20 1   12   5 FALSE NA
1348s + 7   7 300  20 1   12   5 FALSE NA
1348s + 8   8 300  20 1   12   5 FALSE NA
1348s + 9   9 300  20 1   12   5 FALSE NA
1348s + 10 10 300  20 1   12   5 FALSE NA
1348s + 11 11 300  20 1   12   5 FALSE NA
1348s + 12 12 300  20 1   12   5 FALSE NA
1348s + 13 13 300  20 2    8   3  TRUE  6
1348s + 14 14 300  20 2    8   3  TRUE  7
1348s + 15 15 300  20 2    8   3  TRUE  8
1348s + 16 16 300  20 2    8   3 FALSE NA
1348s + 17 17 300  20 2    8   3 FALSE NA
1348s + 18 18 300  20 2    8   3 FALSE NA
1348s + 19 19 300  20 2    8   3 FALSE NA
1348s + 20 20 300  20 2    8   3 FALSE NA
1348s + "), header=TRUE)
1348s > close(tmp)
1348s > 
1348s > des.rei <- twophase(id=list(~id,~id), strata=list(NULL,~h),
1348s +                     fpc=list(~N,NULL), subset=~sub, data=rei, method="approx")
1348s > tot<- svytotal(~y, des.rei)
1348s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h),
1348s +                     fpc=list(~N,NULL), subset=~sub, data=rei)
1348s > tot2<- svytotal(~y, des.rei2)
1348s > 
1348s > ## based on Sarndal et al (9.4.14)
1348s > rei$w.ah <- rei$n.ah / rei$n.a
1348s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE)
1348s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE)
1348s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y)
1348s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h))
1348s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1)))
1348s > 
1348s > a.rei$f.h<-with(a.rei, n.h/n.ah)
1348s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh))
1348s > 
1348s > a.rei$f<-with(a.rei, n.a/N)
1348s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1))
1348s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2)))
1348s > 
1348s > V
1348s [1] 36522.63
1348s > Vphase1
1348s [1] 24072.63
1348s > Vphase2
1348s [1] 12450
1348s > vcov(tot)
1348s          y
1348s y 35911.05
1348s attr(,"phases")
1348s attr(,"phases")$phase1
1348s          [,1]
1348s [1,] 23461.05
1348s 
1348s attr(,"phases")$phase2
1348s       y
1348s y 12450
1348s 
1348s > vcov(tot2)
1348s          [,1]
1348s [1,] 36522.63
1348s attr(,"phases")
1348s attr(,"phases")$phase1
1348s          [,1]
1348s [1,] 24072.63
1348s 
1348s attr(,"phases")$phase2
1348s       [,1]
1348s [1,] 12450
1348s 
1348s > ## phase 2 identical
1348s > all.equal(Vphase2,drop(attr(vcov(tot),"phases")$phase2))
1348s [1] TRUE
1348s > all.equal(Vphase2,drop(attr(vcov(tot2),"phases")$phase2))
1348s [1] TRUE
1348s > ## phase 1 differs by 2.6% for old twophase estimator
1348s > Vphase1/attr(vcov(tot),"phases")$phase1
1348s          [,1]
1348s [1,] 1.026068
1348s > all.equal(Vphase1,as.vector(attr(vcov(tot2),"phases")$phase1))
1348s [1] TRUE
1348s > 
1348s > 
1348s autopkgtest [01:26:44]: test run-unit-test: -----------------------]
1348s autopkgtest [01:26:44]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
1348s run-unit-test        PASS
1348s autopkgtest [01:26:44]: test pkg-r-autopkgtest: preparing testbed
1350s Note, using file '/tmp/autopkgtest.fzci4f/3-autopkgtest-satdep.dsc' to get the build dependencies
1350s Reading package lists...
1350s Building dependency tree...
1350s Reading state information...
1350s Starting pkgProblemResolver with broken count: 0
1350s Starting 2 pkgProblemResolver with broken count: 0
1351s Done
1351s The following NEW packages will be installed:
1351s   dctrl-tools gfortran gfortran-13 gfortran-13-x86-64-linux-gnu
1351s   gfortran-x86-64-linux-gnu icu-devtools libblas-dev libbz2-dev
1351s   libgfortran-13-dev libicu-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev
1351s   liblapack-dev liblzma-dev libncurses-dev libpcre2-16-0 libpcre2-32-0
1351s   libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev
1351s   pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-hexbin
1351s   zlib1g-dev
1351s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
1351s Need to get 35.2 MB of archives.
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1351s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 dctrl-tools amd64 2.24-3build2 [66.9 kB]
1351s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran-13-dev amd64 13.2.0-17ubuntu2 [942 kB]
1351s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.6 MB]
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1351s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1024 B]
1351s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran amd64 4:13.2.0-7ubuntu1 [1176 B]
1351s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 icu-devtools amd64 74.2-1ubuntu1 [212 kB]
1351s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libblas-dev amd64 3.12.0-3 [170 kB]
1351s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5ubuntu1 [33.6 kB]
1351s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libicu-dev amd64 74.2-1ubuntu1 [11.9 MB]
1351s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu1 [294 kB]
1351s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B]
1351s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B]
1351s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack-dev amd64 3.12.0-3 [5196 kB]
1351s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses-dev amd64 6.4+20240113-1ubuntu1 [384 kB]
1351s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-16-0 amd64 10.42-4ubuntu1 [211 kB]
1351s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-32-0 amd64 10.42-4ubuntu1 [198 kB]
1351s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-posix3 amd64 10.42-4ubuntu1 [6808 B]
1351s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-dev amd64 10.42-4ubuntu1 [743 kB]
1351s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB]
1351s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3ubuntu1 [896 kB]
1351s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libpng-dev amd64 1.6.43-1 [264 kB]
1351s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline-dev amd64 8.2-3 [167 kB]
1351s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB]
1351s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB]
1351s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 pkg-config amd64 1.8.1-2 [7170 B]
1351s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma-dev amd64 5.4.5-0.3 [205 kB]
1351s Get:28 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-dev all 4.3.2-1build1 [4336 B]
1351s Get:29 http://ftpmaster.internal/ubuntu noble/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
1351s Get:30 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-hexbin amd64 1.28.3-1 [1576 kB]
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1353s Setting up liblapack-dev:amd64 (3.12.0-3) ...
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1353s Setting up pkg-config:amd64 (1.8.1-2) ...
1353s Setting up gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
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1353s Setting up r-base-dev (4.3.2-1build1) ...
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1353s Processing triggers for libc-bin (2.39-0ubuntu6) ...
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1358s Building dependency tree...
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1358s Done
1359s The following NEW packages will be installed:
1359s   autopkgtest-satdep
1359s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
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1359s After this operation, 0 B of additional disk space will be used.
1359s Get:1 /tmp/autopkgtest.fzci4f/4-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B]
1359s Selecting previously unselected package autopkgtest-satdep.
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1360s Removing autopkgtest-satdep (0) ...
1361s autopkgtest [01:26:57]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
1361s autopkgtest [01:26:57]: test pkg-r-autopkgtest: [-----------------------
1361s Test: Try to load the R library survey
1361s 
1361s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1361s Copyright (C) 2023 The R Foundation for Statistical Computing
1361s Platform: x86_64-pc-linux-gnu (64-bit)
1361s 
1361s R is free software and comes with ABSOLUTELY NO WARRANTY.
1361s You are welcome to redistribute it under certain conditions.
1361s Type 'license()' or 'licence()' for distribution details.
1361s 
1361s R is a collaborative project with many contributors.
1361s Type 'contributors()' for more information and
1361s 'citation()' on how to cite R or R packages in publications.
1361s 
1361s Type 'demo()' for some demos, 'help()' for on-line help, or
1361s 'help.start()' for an HTML browser interface to help.
1361s Type 'q()' to quit R.
1361s 
1361s > library('survey')
1361s Loading required package: grid
1361s Loading required package: Matrix
1362s Loading required package: survival
1362s 
1362s Attaching package: ‘survey’
1362s 
1362s > 
1362s > 
1362s The following object is masked from ‘package:graphics’:
1362s 
1362s     dotchart
1362s 
1362s Other tests are currently unsupported!
1362s They will be progressively added.
1362s autopkgtest [01:26:58]: test pkg-r-autopkgtest: -----------------------]
1362s autopkgtest [01:26:58]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
1362s pkg-r-autopkgtest    PASS
1363s autopkgtest [01:26:59]: @@@@@@@@@@@@@@@@@@@@ summary
1363s run-unit-test        PASS
1363s pkg-r-autopkgtest    PASS
1373s Creating nova instance adt-noble-i386-r-cran-survey-20240324-010416-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240323.img (UUID 5df8a563-0957-4fdd-8453-862df650aaf8)...