0s autopkgtest [20:20:24]: starting date and time: 2024-03-16 20:20:24+0000 0s autopkgtest [20:20:24]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [20:20:24]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yrhysdh3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade r-cran-survey --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-13.secgroup --name adt-noble-arm64-r-cran-survey-20240316-202024-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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/ 170s autopkgtest [20:23:14]: testbed dpkg architecture: arm64 170s autopkgtest [20:23:14]: testbed apt version: 2.7.12 170s autopkgtest [20:23:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 171s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 171s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 171s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3704 kB] 172s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 172s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 172s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 172s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 172s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 172s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 172s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4012 kB] 172s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 172s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 172s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 173s Fetched 9112 kB in 2s (5533 kB/s) 174s Reading package lists... 176s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s Calculating upgrade... 178s The following packages will be REMOVED: 178s libglib2.0-0 libssl3 178s The following NEW packages will be installed: 178s libglib2.0-0t64 libssl3t64 xdg-user-dirs 178s The following packages have been kept back: 178s curl 178s The following packages will be upgraded: 178s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 178s ubuntu-minimal ubuntu-standard 178s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 178s Need to get 4613 kB of archives. 178s After this operation, 211 kB of additional disk space will be used. 178s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 179s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 179s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 179s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 179s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 179s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 179s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 179s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 179s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 179s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 180s Fetched 4613 kB in 1s (5447 kB/s) 180s (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 ... 74758 files and directories currently installed.) 180s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 180s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 180s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 180s udisks2 depends on libglib2.0-0 (>= 2.77.0). 180s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 180s python3-gi depends on libglib2.0-0 (>= 2.77.0). 180s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 180s netplan.io depends on libglib2.0-0 (>= 2.70.0). 180s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 180s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 180s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 180s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 180s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 180s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 180s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 180s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 180s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 180s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 180s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 180s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 180s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 180s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 180s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 180s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 180s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 180s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 180s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 180s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 180s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 180s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 180s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 180s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 180s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 180s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 180s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 180s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 180s fwupd depends on libglib2.0-0 (>= 2.79.0). 180s bolt depends on libglib2.0-0 (>= 2.56.0). 180s 180s (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 ... 74758 files and directories currently installed.) 180s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 181s Selecting previously unselected package libglib2.0-0t64:arm64. 181s (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 ... 74733 files and directories currently installed.) 181s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 181s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 181s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 181s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 181s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 181s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 182s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 182s wget depends on libssl3 (>= 3.0.0). 182s u-boot-tools depends on libssl3 (>= 3.0.0). 182s tnftp depends on libssl3 (>= 3.0.0). 182s tcpdump depends on libssl3 (>= 3.0.0). 182s systemd-resolved depends on libssl3 (>= 3.0.0). 182s systemd depends on libssl3 (>= 3.0.0). 182s sudo depends on libssl3 (>= 3.0.0). 182s sbsigntool depends on libssl3 (>= 3.0.0). 182s rsync depends on libssl3 (>= 3.0.0). 182s python3-cryptography depends on libssl3 (>= 3.0.0). 182s openssh-server depends on libssl3 (>= 3.0.10). 182s openssh-client depends on libssl3 (>= 3.0.10). 182s mtd-utils depends on libssl3 (>= 3.0.0). 182s mokutil depends on libssl3 (>= 3.0.0). 182s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 182s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 182s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 182s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 182s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 182s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 182s libnvme1 depends on libssl3 (>= 3.0.0). 182s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 182s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 182s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 182s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 182s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 182s kmod depends on libssl3 (>= 3.0.0). 182s dhcpcd-base depends on libssl3 (>= 3.0.0). 182s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 182s 182s (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 ... 74758 files and directories currently installed.) 182s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 182s Selecting previously unselected package libssl3t64:arm64. 182s (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 ... 74747 files and directories currently installed.) 182s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 182s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 183s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 183s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 183s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 183s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 183s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 183s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 183s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 183s Unpacking ubuntu-minimal (1.536) over (1.535) ... 183s Selecting previously unselected package xdg-user-dirs. 183s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 183s Unpacking xdg-user-dirs (0.18-1) ... 183s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 183s Unpacking ubuntu-standard (1.536) over (1.535) ... 183s Setting up ubuntu-minimal (1.536) ... 183s Setting up xdg-user-dirs (0.18-1) ... 183s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 183s Setting up libtirpc-common (1.3.4+ds-1.1) ... 183s Setting up ubuntu-standard (1.536) ... 183s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 183s No schema files found: doing nothing. 183s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 183s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 183s Setting up openssl (3.0.13-0ubuntu1) ... 183s Setting up readline-common (8.2-3.1) ... 183s Processing triggers for man-db (2.12.0-3) ... 184s Processing triggers for install-info (7.1-3) ... 184s Processing triggers for libc-bin (2.39-0ubuntu2) ... 185s Reading package lists... 185s Building dependency tree... 185s Reading state information... 185s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 186s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 186s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 186s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 187s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 188s Reading package lists... 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 189s Calculating upgrade... 189s The following packages have been kept back: 189s curl 189s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 193s autopkgtest [20:23:37]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 193s autopkgtest [20:23:37]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-survey 195s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-survey 4.2-1-1 (dsc) [2212 B] 195s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-survey 4.2-1-1 (tar) [2153 kB] 195s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-survey 4.2-1-1 (diff) [4304 B] 196s gpgv: Signature made Wed Jun 28 12:15:39 2023 UTC 196s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 196s gpgv: issuer "tille@debian.org" 196s gpgv: Can't check signature: No public key 196s dpkg-source: warning: cannot verify inline signature for ./r-cran-survey_4.2-1-1.dsc: no acceptable signature found 196s autopkgtest [20:23:40]: testing package r-cran-survey version 4.2-1-1 196s autopkgtest [20:23:40]: build not needed 200s autopkgtest [20:23:44]: test run-unit-test: preparing testbed 201s Reading package lists... 201s Building dependency tree... 201s Reading state information... 202s Starting pkgProblemResolver with broken count: 0 202s Starting 2 pkgProblemResolver with broken count: 0 202s Done 202s The following additional packages will be installed: 202s curl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 202s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libcurl4t64 202s libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 202s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 202s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 202s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 202s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 202s libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 libthai-data 202s libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 202s libxft2 libxrender1 libxss1 libxt6t64 littler node-normalize.css r-base-core 202s r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 r-cran-blob 202s r-cran-boot r-cran-brio r-cran-broom r-cran-cachem r-cran-callr r-cran-car 202s r-cran-cardata r-cran-caret r-cran-cellranger r-cran-class r-cran-cli 202s r-cran-clipr r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer 202s r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi 202s r-cran-desc r-cran-diagram r-cran-diffobj r-cran-digest r-cran-dplyr 202s r-cran-e1071 r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver 202s r-cran-fastmap r-cran-forcats r-cran-foreach r-cran-foreign r-cran-formula 202s r-cran-fs r-cran-future r-cran-future.apply r-cran-generics r-cran-ggplot2 202s r-cran-globals r-cran-glue r-cran-gower r-cran-gtable r-cran-hardhat 202s r-cran-haven r-cran-highr r-cran-hms r-cran-ipred r-cran-isoband 202s r-cran-iterators r-cran-jsonlite r-cran-kernsmooth r-cran-knitr 202s r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv 202s r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate r-cran-magrittr 202s r-cran-maptools r-cran-mass r-cran-matrix r-cran-matrixmodels 202s r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-minqa r-cran-mitools 202s r-cran-modelmetrics r-cran-munsell r-cran-nlme r-cran-nloptr r-cran-nnet 202s r-cran-numderiv r-cran-openxlsx r-cran-parallelly r-cran-pbkrtest 202s r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten 202s r-cran-pkgload r-cran-plogr r-cran-plyr r-cran-praise r-cran-prettyunits 202s r-cran-proc r-cran-processx r-cran-prodlim r-cran-progress r-cran-progressr 202s r-cran-proxy r-cran-ps r-cran-purrr r-cran-quantreg r-cran-r.methodss3 202s r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp 202s r-cran-rcpparmadillo r-cran-rcppeigen r-cran-readr r-cran-readxl 202s r-cran-recipes r-cran-rematch r-cran-rematch2 r-cran-reshape2 r-cran-rio 202s r-cran-rlang r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-sandwich 202s r-cran-scales r-cran-shape r-cran-sp r-cran-sparsem r-cran-squarem 202s r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey r-cran-survival 202s r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect 202s r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs 202s r-cran-viridislite r-cran-vroom r-cran-waldo r-cran-withr r-cran-writexl 202s r-cran-xfun r-cran-yaml r-cran-zip r-cran-zoo unzip x11-common xdg-utils zip 202s Suggested packages: 202s fonts-mathjax-extras fonts-stix libjs-mathjax-doc tcl8.6 tk8.6 202s libjs-html5shiv elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 202s r-cran-roxygen2 r-cran-rmarkdown r-cran-ff r-cran-covr r-cran-bbmle 202s r-cran-cluster r-cran-cmprsk r-cran-coda r-cran-emmeans r-cran-epir 202s r-cran-gam r-cran-gee r-cran-geepack r-cran-glmnet r-cran-gmm r-cran-hmisc 202s r-cran-irlba r-cran-interp r-cran-ks r-cran-lavaan r-cran-leaps 202s r-cran-lsmeans r-cran-maps r-cran-mclust r-cran-metafor r-cran-modeldata 202s r-cran-multcomp r-cran-network r-cran-ordinal r-cran-plm r-cran-psych 202s r-cran-robust r-cran-robustbase r-cran-rsample r-cran-spdep 202s r-cran-spatialreg r-cran-spelling r-cran-systemfit r-cran-tseries 202s r-cran-bradleyterry2 r-cran-ellipse r-cran-mlbench r-cran-party r-cran-pls 202s r-cran-randomforest r-cran-rann r-cran-rstudioapi r-cran-slider 202s r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs 202s r-cran-png r-cran-jpeg r-cran-viridis r-cran-rmysql r-cran-tinytest 202s r-cran-markdown r-cran-th.data r-cran-magick r-cran-sf r-cran-getopt 202s r-cran-rgeos r-cran-spatstat.geom r-cran-raster r-cran-polyclip 202s r-cran-plotrix r-cran-spatstat.linnet r-cran-spatstat.utils r-cran-spatstat 202s r-cran-httr r-cran-rodbc r-cran-formattable r-cran-nanotime 202s r-cran-palmerpenguins r-cran-units r-cran-vdiffr r-cran-inline r-cran-hexbin 202s r-cran-bench r-cran-here r-cran-htmltools r-cran-runit 202s Recommended packages: 202s javascript-common r-recommended r-base-dev r-doc-html r-cran-dynlm 202s r-cran-effects r-cran-fgarch r-cran-forecast r-cran-plm r-cran-pscl 202s r-cran-rgl r-cran-rocr r-cran-scatterplot3d r-cran-strucchange 202s r-cran-systemfit r-cran-tseries r-cran-urca r-cran-covr r-cran-cliapp 202s r-cran-mockery r-cran-earth r-cran-mda r-cran-mlmetrics r-cran-fastica 202s r-cran-kernlab r-cran-themis r-cran-htmltools r-cran-htmlwidgets 202s r-cran-rmarkdown r-cran-rstudioapi r-cran-whoami r-cran-bench r-cran-decor 202s r-cran-lobstr r-cran-spelling r-cran-later r-cran-httpuv r-cran-webutils 202s r-cran-xts r-cran-nanotime r-cran-gh r-cran-dbplyr r-cran-rmysql 202s r-cran-rpostgresql r-cran-unitizer r-cran-rhpcblasctl r-cran-r.rsp 202s r-cran-markdown r-cran-hexbin r-cran-hmisc r-cran-mapproj r-cran-maps 202s r-cran-multcomp r-cran-profvis r-cran-ragg r-cran-sf r-cran-svglite 202s r-cran-vdiffr r-cran-xml2 r-cran-devtools r-cran-modeldata r-cran-roxygen2 202s r-cran-usethis r-cran-testit r-cran-mlbench r-cran-httr r-cran-bslib 202s r-cran-formatr r-cran-gridsvg r-cran-jpeg r-cran-magick r-cran-png 202s r-cran-reticulate r-cran-sass r-cran-tikzdevice r-cran-tinytex 202s r-cran-webshot node-highlight.js r-cran-ellipse r-cran-fields r-cran-geepack 202s r-bioc-graph r-cran-bookdown r-cran-igraph r-cran-lavasearch2 r-cran-mets 202s r-cran-optimx r-cran-polycor r-cran-lintr r-cran-tidyverse r-cran-base64enc 202s r-cran-r.devices r-cran-bitops r-cran-mathjaxr r-cran-mockr r-cran-remotes 202s r-cran-doparallel r-cran-itertools r-cran-logcondens r-cran-webfakes 202s r-cran-pbmcapply r-cran-furrr r-cran-shiny r-cran-commonmark r-cran-cba 202s r-cran-pingr r-cran-ddalpha r-cran-dials r-cran-rann r-cran-rcpproll 202s r-cran-rsample r-cran-rspectra r-cran-splines2 r-cran-dbitest r-cran-gert 202s r-cran-rvest r-cran-dichromat r-cran-gstat r-cran-deldir r-cran-terra 202s r-cran-raster r-cran-setrng r-cran-formattable r-cran-pkgdown r-cran-zeallot 202s r-cran-mime r-cran-renv r-cran-runit libfile-mimeinfo-perl libnet-dbus-perl 202s libx11-protocol-perl x11-utils x11-xserver-utils 202s The following packages will be REMOVED: 202s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 202s The following NEW packages will be installed: 202s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 202s fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax libblas3 202s libcairo2 libcurl4t64 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 202s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 202s libjpeg8 libjs-bootstrap libjs-highlight.js libjs-jquery 202s libjs-jquery-datatables libjs-mathjax liblapack3 liblerc4 libnlopt0 202s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 202s libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 libreadline8t64 202s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc3t64 202s libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 202s libxt6t64 littler node-normalize.css r-base-core r-cran-abind r-cran-aer 202s r-cran-backports r-cran-bit r-cran-bit64 r-cran-blob r-cran-boot r-cran-brio 202s r-cran-broom r-cran-cachem r-cran-callr r-cran-car r-cran-cardata 202s r-cran-caret r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr 202s r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer r-cran-cpp11 202s r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-desc 202s r-cran-diagram r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-e1071 202s r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap 202s r-cran-forcats r-cran-foreach r-cran-foreign r-cran-formula r-cran-fs 202s r-cran-future r-cran-future.apply r-cran-generics r-cran-ggplot2 202s r-cran-globals r-cran-glue r-cran-gower r-cran-gtable r-cran-hardhat 202s r-cran-haven r-cran-highr r-cran-hms r-cran-ipred r-cran-isoband 202s r-cran-iterators r-cran-jsonlite r-cran-kernsmooth r-cran-knitr 202s r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv 202s r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate r-cran-magrittr 202s r-cran-maptools r-cran-mass r-cran-matrix r-cran-matrixmodels 202s r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-minqa r-cran-mitools 202s r-cran-modelmetrics r-cran-munsell r-cran-nlme r-cran-nloptr r-cran-nnet 202s r-cran-numderiv r-cran-openxlsx r-cran-parallelly r-cran-pbkrtest 202s r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten 202s r-cran-pkgload r-cran-plogr r-cran-plyr r-cran-praise r-cran-prettyunits 202s r-cran-proc r-cran-processx r-cran-prodlim r-cran-progress r-cran-progressr 202s r-cran-proxy r-cran-ps r-cran-purrr r-cran-quantreg r-cran-r.methodss3 202s r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp 202s r-cran-rcpparmadillo r-cran-rcppeigen r-cran-readr r-cran-readxl 202s r-cran-recipes r-cran-rematch r-cran-rematch2 r-cran-reshape2 r-cran-rio 202s r-cran-rlang r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-sandwich 202s r-cran-scales r-cran-shape r-cran-sp r-cran-sparsem r-cran-squarem 202s r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey r-cran-survival 202s r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect 202s r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs 202s r-cran-viridislite r-cran-vroom r-cran-waldo r-cran-withr r-cran-writexl 202s r-cran-xfun r-cran-yaml r-cran-zip r-cran-zoo unzip x11-common xdg-utils zip 202s The following packages will be upgraded: 202s curl 203s 1 upgraded, 215 newly installed, 5 to remove and 0 not upgraded. 203s Need to get 161 MB/161 MB of archives. 203s After this operation, 326 MB of additional disk space will be used. 203s Get:1 /tmp/autopkgtest.8gUBgk/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B] 203s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 203s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 203s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 203s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 203s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 203s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 203s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 204s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 204s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 204s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 204s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 204s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 204s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 205s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 205s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 205s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 205s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 205s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 205s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 205s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 205s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 205s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 205s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 205s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 205s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 205s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 205s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 205s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 205s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 205s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 205s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 205s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 205s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 205s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 205s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 206s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 206s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 206s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 206s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 206s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 206s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 206s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 206s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 206s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 206s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 206s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 206s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 206s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 206s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 206s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 206s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 206s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 206s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 206s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 206s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 206s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 207s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 207s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 207s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 207s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-abind all 1.4-5-2 [63.6 kB] 207s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cardata all 3.0.5-1 [1819 kB] 207s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 207s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 207s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 207s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 208s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 208s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nnet arm64 7.3-19-2 [111 kB] 208s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-boot all 1.3-30-1 [619 kB] 208s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 208s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 208s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-minqa arm64 1.2.6-1 [107 kB] 208s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 libnlopt0 arm64 2.7.1-5build2 [174 kB] 208s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-brio arm64 1.1.4-1 [37.7 kB] 208s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ps arm64 1.7.6-1 [313 kB] 208s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB] 208s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-processx arm64 3.8.3-1 [345 kB] 208s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-callr all 3.7.3-2 [425 kB] 208s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 208s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-desc all 1.4.3-1 [359 kB] 208s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-digest arm64 0.6.34-1 [182 kB] 208s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-evaluate all 0.23-1 [90.2 kB] 208s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jsonlite arm64 1.8.8+dfsg-1 [441 kB] 208s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 208s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 208s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 208s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 208s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-crayon all 1.5.2-1 [164 kB] 208s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fs arm64 1.6.3+dfsg-1 [227 kB] 208s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgbuild all 1.4.3-1 [209 kB] 208s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rprojroot all 2.0.4-1 [124 kB] 208s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB] 208s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgload all 1.3.4-1 [207 kB] 208s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-praise all 1.0.0-4build1 [20.3 kB] 208s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-diffobj arm64 0.3.5-1 [1116 kB] 208s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 208s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 208s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 208s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 208s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 208s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB] 208s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB] 208s Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-waldo all 0.5.2-1build1 [120 kB] 209s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-testthat arm64 3.2.1-1 [1678 kB] 209s Get:105 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nloptr arm64 2.0.3-1 [375 kB] 209s Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppeigen arm64 0.3.3.9.4-1 [1180 kB] 209s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 209s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lme4 arm64 1.1-35.1-4 [4116 kB] 209s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-backports arm64 1.4.1-1 [101 kB] 209s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 209s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyselect arm64 1.2.0+dfsg-1 [218 kB] 209s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dplyr arm64 1.1.4-1 [1513 kB] 209s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB] 209s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-purrr arm64 1.0.2-1 [501 kB] 209s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringi arm64 1.8.3-1 [869 kB] 209s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 209s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB] 209s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 209s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-broom all 1.0.5+dfsg-1 [1729 kB] 209s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] 209s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xfun arm64 0.41+dfsg-1 [415 kB] 209s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-highr all 0.10+dfsg-1 [38.3 kB] 209s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-yaml arm64 2.3.8-1 [107 kB] 209s Get:124 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 209s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-knitr all 1.45+dfsg-1 [917 kB] 210s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pbkrtest all 0.5.2-2 [182 kB] 210s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sparsem arm64 1.81-1 [902 kB] 210s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrixmodels all 0.5-3-1 [361 kB] 210s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 210s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrixstats arm64 1.2.0-1 [475 kB] 210s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpparmadillo arm64 0.12.8.0.0-1 [859 kB] 210s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 210s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 210s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-farver arm64 2.1.1-1 [1336 kB] 210s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 210s Get:136 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB] 210s Get:137 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB] 210s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 210s Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 210s Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 210s Get:141 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 210s Get:142 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-class arm64 7.3-22-2 [88.2 kB] 210s Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-proxy arm64 0.4-27-1 [181 kB] 210s Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-e1071 arm64 1.7-14-1 [556 kB] 210s Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-codetools all 0.2-19-1 [90.5 kB] 210s Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-iterators all 1.0.14-1 [336 kB] 210s Get:147 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreach all 1.5.2-1 [124 kB] 210s Get:148 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-data.table arm64 1.14.10+dfsg-1 [1844 kB] 210s Get:149 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-modelmetrics arm64 1.2.2.2-1build1 [121 kB] 210s Get:150 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-plyr arm64 1.8.9-1 [831 kB] 210s Get:151 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-proc arm64 1.18.5-1 [963 kB] 210s Get:152 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tzdb arm64 0.4.0-2 [512 kB] 210s Get:153 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-clock arm64 0.7.0-1.1 [1736 kB] 210s Get:154 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gower arm64 1.0.1-1 [206 kB] 210s Get:155 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-hardhat all 1.3.1+dfsg-1 [554 kB] 210s Get:156 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rpart arm64 4.1.23-1 [660 kB] 210s Get:157 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-shape all 1.4.6-1 [770 kB] 210s Get:158 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-diagram all 1.6.5-2 [656 kB] 210s Get:159 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-kernsmooth arm64 2.23-22-1 [91.1 kB] 210s Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-globals all 0.16.2-1 [117 kB] 210s Get:161 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-listenv all 0.9.1+dfsg-1 [112 kB] 210s Get:162 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-parallelly arm64 1.37.1-1 [364 kB] 210s Get:163 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-future all 1.33.1+dfsg-1 [634 kB] 210s Get:164 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-future.apply all 1.11.1+dfsg-1 [171 kB] 211s Get:165 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-progressr all 0.14.0-1 [338 kB] 211s Get:166 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-squarem all 2021.1-1 [179 kB] 211s Get:167 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lava all 1.7.3+dfsg-1 [2166 kB] 211s Get:168 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-prodlim arm64 2023.08.28-1 [407 kB] 211s Get:169 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ipred arm64 0.9-14-1 [383 kB] 211s Get:170 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-timechange arm64 0.3.0-1 [172 kB] 211s Get:171 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lubridate arm64 1.9.3+dfsg-1 [1010 kB] 211s Get:172 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-timedate arm64 4032.109-1 [1229 kB] 211s Get:173 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-recipes all 1.0.9+dfsg-1 [1964 kB] 211s Get:174 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-reshape2 arm64 1.4.4-2build1 [110 kB] 211s Get:175 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-caret arm64 6.0-94+dfsg-1 [3434 kB] 211s Get:176 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-conquer arm64 1.3.3-1 [440 kB] 211s Get:177 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-quantreg arm64 5.97-1 [1527 kB] 211s Get:178 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sp arm64 1:2.1-2+dfsg-1 [1448 kB] 211s Get:179 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreign arm64 0.8.86-1 [240 kB] 211s Get:180 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-maptools arm64 1:1.1-8+dfsg-1 [1365 kB] 211s Get:181 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-forcats all 1.0.0-1 [369 kB] 211s Get:182 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-hms all 1.1.3-1 [96.5 kB] 211s Get:183 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-clipr all 0.8.0-1 [53.5 kB] 211s Get:184 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-bit arm64 4.0.5-1 [1057 kB] 211s Get:185 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-bit64 arm64 4.0.5-1 [467 kB] 211s Get:186 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-prettyunits all 1.2.0-1 [162 kB] 211s Get:187 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-progress all 1.2.3-1 [91.9 kB] 211s Get:188 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vroom arm64 1.6.5-1 [832 kB] 211s Get:189 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-readr arm64 2.1.5-1 [756 kB] 211s Get:190 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-haven arm64 2.5.4-1 [338 kB] 211s Get:191 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-curl arm64 5.2.0+dfsg-1 [189 kB] 211s Get:192 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rematch all 2.0.0-1 [18.3 kB] 211s Get:193 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cellranger all 1.1.0-3 [102 kB] 211s Get:194 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-readxl arm64 1.4.3-1 [726 kB] 211s Get:195 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-writexl arm64 1.5.0-1 [157 kB] 211s Get:196 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 211s Get:197 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r.oo all 1.26.0-1 [955 kB] 211s Get:198 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r.utils all 2.12.3-1 [1386 kB] 211s Get:199 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-zip arm64 2.3.1-1 [125 kB] 211s Get:200 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-openxlsx arm64 4.2.5.2-1 [1925 kB] 211s Get:201 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rio all 1.0.1-1 [529 kB] 211s Get:202 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-car all 3.1-2-2 [1692 kB] 212s Get:203 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-zoo arm64 1.8-12-2 [984 kB] 212s Get:204 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lmtest arm64 0.9.40-1 [396 kB] 212s Get:205 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sandwich all 3.1-0-1 [1484 kB] 212s Get:206 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-formula all 1.2-5-1 [158 kB] 212s Get:207 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-aer all 1.2-12-1 [2582 kB] 212s Get:208 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-blob all 1.2.4-1 [49.8 kB] 212s Get:209 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fastmap arm64 1.1.1-1 [69.6 kB] 212s Get:210 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cachem arm64 1.0.8-1 [72.3 kB] 212s Get:211 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dbi all 1.2.2-1 [823 kB] 212s Get:212 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB] 212s Get:213 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mitools all 2.4-2build1 [265 kB] 212s Get:214 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-plogr all 0.2.0-3build1 [15.1 kB] 212s Get:215 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rsqlite arm64 2.3.4-1 [1371 kB] 212s Get:216 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survey all 4.2-1-1 [3189 kB] 214s Preconfiguring packages ... 214s Fetched 161 MB in 10s (16.1 MB/s) 214s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 214s wget depends on libpsl5 (>= 0.16.0). 214s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 214s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 214s 214s (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 ... 74774 files and directories currently installed.) 214s Removing libpsl5:arm64 (0.21.2-1build1) ... 215s Selecting previously unselected package libpsl5t64:arm64. 215s (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 ... 74769 files and directories currently installed.) 215s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 215s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 215s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 215s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 215s (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 ... 74775 files and directories currently installed.) 215s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 215s Selecting previously unselected package libcurl4t64:arm64. 215s (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 ... 74770 files and directories currently installed.) 215s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 215s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 215s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 215s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 215s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 215s 215s (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 ... 74776 files and directories currently installed.) 215s Removing libpng16-16:arm64 (1.6.43-1) ... 215s Selecting previously unselected package libpng16-16t64:arm64. 215s (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 ... 74766 files and directories currently installed.) 215s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 215s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 215s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 215s parted depends on libreadline8 (>= 6.0). 215s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 215s gpgsm depends on libreadline8 (>= 6.0). 215s gpgconf depends on libreadline8 (>= 6.0). 215s gpg depends on libreadline8 (>= 6.0). 215s gawk depends on libreadline8 (>= 6.0). 215s fdisk depends on libreadline8 (>= 6.0). 215s 215s (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 ... 74777 files and directories currently installed.) 215s Removing libreadline8:arm64 (8.2-3) ... 215s Selecting previously unselected package libreadline8t64:arm64. 215s (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 ... 74765 files and directories currently installed.) 215s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 215s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 215s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 215s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 215s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 215s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 215s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 215s lsof depends on libtirpc3 (>= 1.0.2). 215s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 215s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 215s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 215s iproute2 depends on libtirpc3 (>= 1.0.2). 215s 215s (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 ... 74785 files and directories currently installed.) 215s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 215s Selecting previously unselected package libtirpc3t64:arm64. 215s (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 ... 74779 files and directories currently installed.) 215s Preparing to unpack .../000-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 215s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 215s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 215s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 215s Selecting previously unselected package fonts-dejavu-mono. 215s Preparing to unpack .../001-fonts-dejavu-mono_2.37-8_all.deb ... 215s Unpacking fonts-dejavu-mono (2.37-8) ... 215s Selecting previously unselected package fonts-dejavu-core. 215s Preparing to unpack .../002-fonts-dejavu-core_2.37-8_all.deb ... 215s Unpacking fonts-dejavu-core (2.37-8) ... 215s Selecting previously unselected package fontconfig-config. 216s Preparing to unpack .../003-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 216s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 216s Selecting previously unselected package libfontconfig1:arm64. 216s Preparing to unpack .../004-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 216s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 216s Selecting previously unselected package fontconfig. 216s Preparing to unpack .../005-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 216s Unpacking fontconfig (2.15.0-1ubuntu1) ... 216s Selecting previously unselected package fonts-glyphicons-halflings. 216s Preparing to unpack .../006-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 216s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 216s Selecting previously unselected package fonts-mathjax. 216s Preparing to unpack .../007-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 216s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 216s Selecting previously unselected package libblas3:arm64. 216s Preparing to unpack .../008-libblas3_3.12.0-3_arm64.deb ... 216s Unpacking libblas3:arm64 (3.12.0-3) ... 216s Selecting previously unselected package libpixman-1-0:arm64. 216s Preparing to unpack .../009-libpixman-1-0_0.42.2-1_arm64.deb ... 216s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 216s Selecting previously unselected package libxcb-render0:arm64. 216s Preparing to unpack .../010-libxcb-render0_1.15-1_arm64.deb ... 216s Unpacking libxcb-render0:arm64 (1.15-1) ... 216s Selecting previously unselected package libxcb-shm0:arm64. 216s Preparing to unpack .../011-libxcb-shm0_1.15-1_arm64.deb ... 216s Unpacking libxcb-shm0:arm64 (1.15-1) ... 216s Selecting previously unselected package libxrender1:arm64. 216s Preparing to unpack .../012-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 216s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 216s Selecting previously unselected package libcairo2:arm64. 216s Preparing to unpack .../013-libcairo2_1.18.0-1_arm64.deb ... 216s Unpacking libcairo2:arm64 (1.18.0-1) ... 216s Selecting previously unselected package libdatrie1:arm64. 216s Preparing to unpack .../014-libdatrie1_0.2.13-3_arm64.deb ... 216s Unpacking libdatrie1:arm64 (0.2.13-3) ... 216s Selecting previously unselected package libdeflate0:arm64. 216s Preparing to unpack .../015-libdeflate0_1.19-1_arm64.deb ... 216s Unpacking libdeflate0:arm64 (1.19-1) ... 216s Selecting previously unselected package libgfortran5:arm64. 216s Preparing to unpack .../016-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 216s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 216s Selecting previously unselected package libgomp1:arm64. 216s Preparing to unpack .../017-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 216s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 216s Selecting previously unselected package libgraphite2-3:arm64. 216s Preparing to unpack .../018-libgraphite2-3_1.3.14-2_arm64.deb ... 216s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 216s Selecting previously unselected package libharfbuzz0b:arm64. 216s Preparing to unpack .../019-libharfbuzz0b_8.3.0-2_arm64.deb ... 216s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 216s Selecting previously unselected package x11-common. 216s Preparing to unpack .../020-x11-common_1%3a7.7+23ubuntu2_all.deb ... 216s Unpacking x11-common (1:7.7+23ubuntu2) ... 216s Selecting previously unselected package libice6:arm64. 216s Preparing to unpack .../021-libice6_2%3a1.0.10-1build2_arm64.deb ... 216s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 216s Selecting previously unselected package libjpeg-turbo8:arm64. 217s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 217s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 217s Selecting previously unselected package libjpeg8:arm64. 217s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_arm64.deb ... 217s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 217s Selecting previously unselected package libjs-bootstrap. 217s Preparing to unpack .../024-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 217s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 217s Selecting previously unselected package libjs-highlight.js. 217s Preparing to unpack .../025-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 217s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 217s Selecting previously unselected package libjs-jquery. 217s Preparing to unpack .../026-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 217s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 217s Selecting previously unselected package libjs-jquery-datatables. 217s Preparing to unpack .../027-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 217s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 217s Selecting previously unselected package liblapack3:arm64. 217s Preparing to unpack .../028-liblapack3_3.12.0-3_arm64.deb ... 217s Unpacking liblapack3:arm64 (3.12.0-3) ... 217s Selecting previously unselected package liblerc4:arm64. 217s Preparing to unpack .../029-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 217s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 217s Selecting previously unselected package libthai-data. 217s Preparing to unpack .../030-libthai-data_0.1.29-2_all.deb ... 217s Unpacking libthai-data (0.1.29-2) ... 217s Selecting previously unselected package libthai0:arm64. 217s Preparing to unpack .../031-libthai0_0.1.29-2_arm64.deb ... 217s Unpacking libthai0:arm64 (0.1.29-2) ... 217s Selecting previously unselected package libpango-1.0-0:arm64. 217s Preparing to unpack .../032-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 217s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 217s Selecting previously unselected package libpangoft2-1.0-0:arm64. 217s Preparing to unpack .../033-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 217s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 217s Selecting previously unselected package libpangocairo-1.0-0:arm64. 217s Preparing to unpack .../034-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 217s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 217s Selecting previously unselected package libpaper1:arm64. 217s Preparing to unpack .../035-libpaper1_1.1.29_arm64.deb ... 217s Unpacking libpaper1:arm64 (1.1.29) ... 217s Selecting previously unselected package libpaper-utils. 217s Preparing to unpack .../036-libpaper-utils_1.1.29_arm64.deb ... 217s Unpacking libpaper-utils (1.1.29) ... 217s Selecting previously unselected package libsharpyuv0:arm64. 217s Preparing to unpack .../037-libsharpyuv0_1.3.2-0.4_arm64.deb ... 217s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 217s Selecting previously unselected package libsm6:arm64. 217s Preparing to unpack .../038-libsm6_2%3a1.2.3-1build2_arm64.deb ... 217s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 217s Selecting previously unselected package libtcl8.6:arm64. 217s Preparing to unpack .../039-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 217s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 217s Selecting previously unselected package libjbig0:arm64. 217s Preparing to unpack .../040-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 217s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 217s Selecting previously unselected package libwebp7:arm64. 217s Preparing to unpack .../041-libwebp7_1.3.2-0.4_arm64.deb ... 217s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 217s Selecting previously unselected package libtiff6:arm64. 217s Preparing to unpack .../042-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 217s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 217s Selecting previously unselected package libxft2:arm64. 217s Preparing to unpack .../043-libxft2_2.3.6-1_arm64.deb ... 217s Unpacking libxft2:arm64 (2.3.6-1) ... 217s Selecting previously unselected package libxss1:arm64. 217s Preparing to unpack .../044-libxss1_1%3a1.2.3-1build2_arm64.deb ... 217s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 217s Selecting previously unselected package libtk8.6:arm64. 217s Preparing to unpack .../045-libtk8.6_8.6.13-2_arm64.deb ... 217s Unpacking libtk8.6:arm64 (8.6.13-2) ... 217s Selecting previously unselected package libxt6t64:arm64. 218s Preparing to unpack .../046-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 218s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 218s Selecting previously unselected package zip. 218s Preparing to unpack .../047-zip_3.0-13_arm64.deb ... 218s Unpacking zip (3.0-13) ... 218s Selecting previously unselected package unzip. 218s Preparing to unpack .../048-unzip_6.0-28ubuntu3_arm64.deb ... 218s Unpacking unzip (6.0-28ubuntu3) ... 218s Selecting previously unselected package xdg-utils. 218s Preparing to unpack .../049-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 218s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 218s Selecting previously unselected package r-base-core. 218s Preparing to unpack .../050-r-base-core_4.3.3-2build1_arm64.deb ... 218s Unpacking r-base-core (4.3.3-2build1) ... 218s Selecting previously unselected package r-cran-littler. 218s Preparing to unpack .../051-r-cran-littler_0.3.19-1_arm64.deb ... 218s Unpacking r-cran-littler (0.3.19-1) ... 218s Selecting previously unselected package littler. 218s Preparing to unpack .../052-littler_0.3.19-1_all.deb ... 218s Unpacking littler (0.3.19-1) ... 218s Selecting previously unselected package node-normalize.css. 218s Preparing to unpack .../053-node-normalize.css_8.0.1-5_all.deb ... 218s Unpacking node-normalize.css (8.0.1-5) ... 219s Selecting previously unselected package r-cran-abind. 219s Preparing to unpack .../054-r-cran-abind_1.4-5-2_all.deb ... 219s Unpacking r-cran-abind (1.4-5-2) ... 219s Selecting previously unselected package r-cran-cardata. 219s Preparing to unpack .../055-r-cran-cardata_3.0.5-1_all.deb ... 219s Unpacking r-cran-cardata (3.0.5-1) ... 219s Selecting previously unselected package r-cran-mass. 219s Preparing to unpack .../056-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 219s Unpacking r-cran-mass (7.3-60.0.1-1) ... 219s Selecting previously unselected package r-cran-lattice. 219s Preparing to unpack .../057-r-cran-lattice_0.22-5-1_arm64.deb ... 219s Unpacking r-cran-lattice (0.22-5-1) ... 219s Selecting previously unselected package r-cran-nlme. 219s Preparing to unpack .../058-r-cran-nlme_3.1.164-1_arm64.deb ... 219s Unpacking r-cran-nlme (3.1.164-1) ... 219s Selecting previously unselected package r-cran-matrix. 219s Preparing to unpack .../059-r-cran-matrix_1.6-5-1_arm64.deb ... 219s Unpacking r-cran-matrix (1.6-5-1) ... 219s Selecting previously unselected package r-cran-mgcv. 219s Preparing to unpack .../060-r-cran-mgcv_1.9-1-1_arm64.deb ... 219s Unpacking r-cran-mgcv (1.9-1-1) ... 219s Selecting previously unselected package r-cran-nnet. 219s Preparing to unpack .../061-r-cran-nnet_7.3-19-2_arm64.deb ... 219s Unpacking r-cran-nnet (7.3-19-2) ... 219s Selecting previously unselected package r-cran-boot. 219s Preparing to unpack .../062-r-cran-boot_1.3-30-1_all.deb ... 219s Unpacking r-cran-boot (1.3-30-1) ... 219s Selecting previously unselected package r-cran-pkgkitten. 219s Preparing to unpack .../063-r-cran-pkgkitten_0.2.3-1_all.deb ... 219s Unpacking r-cran-pkgkitten (0.2.3-1) ... 219s Selecting previously unselected package r-cran-rcpp. 219s Preparing to unpack .../064-r-cran-rcpp_1.0.12-1_arm64.deb ... 219s Unpacking r-cran-rcpp (1.0.12-1) ... 220s Selecting previously unselected package r-cran-minqa. 220s Preparing to unpack .../065-r-cran-minqa_1.2.6-1_arm64.deb ... 220s Unpacking r-cran-minqa (1.2.6-1) ... 220s Selecting previously unselected package libnlopt0:arm64. 220s Preparing to unpack .../066-libnlopt0_2.7.1-5build2_arm64.deb ... 220s Unpacking libnlopt0:arm64 (2.7.1-5build2) ... 220s Selecting previously unselected package r-cran-brio. 220s Preparing to unpack .../067-r-cran-brio_1.1.4-1_arm64.deb ... 220s Unpacking r-cran-brio (1.1.4-1) ... 220s Selecting previously unselected package r-cran-ps. 220s Preparing to unpack .../068-r-cran-ps_1.7.6-1_arm64.deb ... 220s Unpacking r-cran-ps (1.7.6-1) ... 220s Selecting previously unselected package r-cran-r6. 220s Preparing to unpack .../069-r-cran-r6_2.5.1-1_all.deb ... 220s Unpacking r-cran-r6 (2.5.1-1) ... 220s Selecting previously unselected package r-cran-processx. 220s Preparing to unpack .../070-r-cran-processx_3.8.3-1_arm64.deb ... 220s Unpacking r-cran-processx (3.8.3-1) ... 220s Selecting previously unselected package r-cran-callr. 220s Preparing to unpack .../071-r-cran-callr_3.7.3-2_all.deb ... 220s Unpacking r-cran-callr (3.7.3-2) ... 220s Selecting previously unselected package r-cran-cli. 220s Preparing to unpack .../072-r-cran-cli_3.6.2-1_arm64.deb ... 220s Unpacking r-cran-cli (3.6.2-1) ... 220s Selecting previously unselected package r-cran-desc. 221s Preparing to unpack .../073-r-cran-desc_1.4.3-1_all.deb ... 221s Unpacking r-cran-desc (1.4.3-1) ... 221s Selecting previously unselected package r-cran-digest. 221s Preparing to unpack .../074-r-cran-digest_0.6.34-1_arm64.deb ... 221s Unpacking r-cran-digest (0.6.34-1) ... 221s Selecting previously unselected package r-cran-evaluate. 221s Preparing to unpack .../075-r-cran-evaluate_0.23-1_all.deb ... 221s Unpacking r-cran-evaluate (0.23-1) ... 221s Selecting previously unselected package r-cran-jsonlite. 221s Preparing to unpack .../076-r-cran-jsonlite_1.8.8+dfsg-1_arm64.deb ... 221s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 221s Selecting previously unselected package r-cran-glue. 221s Preparing to unpack .../077-r-cran-glue_1.7.0-1_arm64.deb ... 221s Unpacking r-cran-glue (1.7.0-1) ... 221s Selecting previously unselected package r-cran-rlang. 221s Preparing to unpack .../078-r-cran-rlang_1.1.3-1_arm64.deb ... 221s Unpacking r-cran-rlang (1.1.3-1) ... 221s Selecting previously unselected package r-cran-lifecycle. 221s Preparing to unpack .../079-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 221s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 221s Selecting previously unselected package r-cran-magrittr. 221s Preparing to unpack .../080-r-cran-magrittr_2.0.3-1_arm64.deb ... 221s Unpacking r-cran-magrittr (2.0.3-1) ... 221s Selecting previously unselected package r-cran-crayon. 221s Preparing to unpack .../081-r-cran-crayon_1.5.2-1_all.deb ... 221s Unpacking r-cran-crayon (1.5.2-1) ... 221s Selecting previously unselected package r-cran-fs. 221s Preparing to unpack .../082-r-cran-fs_1.6.3+dfsg-1_arm64.deb ... 221s Unpacking r-cran-fs (1.6.3+dfsg-1) ... 221s Selecting previously unselected package r-cran-pkgbuild. 221s Preparing to unpack .../083-r-cran-pkgbuild_1.4.3-1_all.deb ... 221s Unpacking r-cran-pkgbuild (1.4.3-1) ... 221s Selecting previously unselected package r-cran-rprojroot. 221s Preparing to unpack .../084-r-cran-rprojroot_2.0.4-1_all.deb ... 221s Unpacking r-cran-rprojroot (2.0.4-1) ... 221s Selecting previously unselected package r-cran-withr. 221s Preparing to unpack .../085-r-cran-withr_2.5.0-1_all.deb ... 221s Unpacking r-cran-withr (2.5.0-1) ... 221s Selecting previously unselected package r-cran-pkgload. 221s Preparing to unpack .../086-r-cran-pkgload_1.3.4-1_all.deb ... 221s Unpacking r-cran-pkgload (1.3.4-1) ... 221s Selecting previously unselected package r-cran-praise. 221s Preparing to unpack .../087-r-cran-praise_1.0.0-4build1_all.deb ... 221s Unpacking r-cran-praise (1.0.0-4build1) ... 221s Selecting previously unselected package r-cran-diffobj. 221s Preparing to unpack .../088-r-cran-diffobj_0.3.5-1_arm64.deb ... 221s Unpacking r-cran-diffobj (0.3.5-1) ... 221s Selecting previously unselected package r-cran-fansi. 221s Preparing to unpack .../089-r-cran-fansi_1.0.5-1_arm64.deb ... 221s Unpacking r-cran-fansi (1.0.5-1) ... 221s Selecting previously unselected package r-cran-utf8. 221s Preparing to unpack .../090-r-cran-utf8_1.2.4-1_arm64.deb ... 221s Unpacking r-cran-utf8 (1.2.4-1) ... 221s Selecting previously unselected package r-cran-vctrs. 221s Preparing to unpack .../091-r-cran-vctrs_0.6.5-1_arm64.deb ... 221s Unpacking r-cran-vctrs (0.6.5-1) ... 221s Selecting previously unselected package r-cran-pillar. 221s Preparing to unpack .../092-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 221s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 221s Selecting previously unselected package r-cran-pkgconfig. 222s Preparing to unpack .../093-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 222s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 222s Selecting previously unselected package r-cran-tibble. 222s Preparing to unpack .../094-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ... 222s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 222s Selecting previously unselected package r-cran-rematch2. 222s Preparing to unpack .../095-r-cran-rematch2_2.1.2-2build1_all.deb ... 222s Unpacking r-cran-rematch2 (2.1.2-2build1) ... 222s Selecting previously unselected package r-cran-waldo. 222s Preparing to unpack .../096-r-cran-waldo_0.5.2-1build1_all.deb ... 222s Unpacking r-cran-waldo (0.5.2-1build1) ... 222s Selecting previously unselected package r-cran-testthat. 222s Preparing to unpack .../097-r-cran-testthat_3.2.1-1_arm64.deb ... 222s Unpacking r-cran-testthat (3.2.1-1) ... 222s Selecting previously unselected package r-cran-nloptr. 222s Preparing to unpack .../098-r-cran-nloptr_2.0.3-1_arm64.deb ... 222s Unpacking r-cran-nloptr (2.0.3-1) ... 222s Selecting previously unselected package r-cran-rcppeigen. 222s Preparing to unpack .../099-r-cran-rcppeigen_0.3.3.9.4-1_arm64.deb ... 222s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 222s Selecting previously unselected package r-cran-statmod. 222s Preparing to unpack .../100-r-cran-statmod_1.5.0-1_arm64.deb ... 222s Unpacking r-cran-statmod (1.5.0-1) ... 222s Selecting previously unselected package r-cran-lme4. 222s Preparing to unpack .../101-r-cran-lme4_1.1-35.1-4_arm64.deb ... 222s Unpacking r-cran-lme4 (1.1-35.1-4) ... 222s Selecting previously unselected package r-cran-backports. 222s Preparing to unpack .../102-r-cran-backports_1.4.1-1_arm64.deb ... 222s Unpacking r-cran-backports (1.4.1-1) ... 222s Selecting previously unselected package r-cran-generics. 222s Preparing to unpack .../103-r-cran-generics_0.1.3-1_all.deb ... 222s Unpacking r-cran-generics (0.1.3-1) ... 222s Selecting previously unselected package r-cran-tidyselect. 222s Preparing to unpack .../104-r-cran-tidyselect_1.2.0+dfsg-1_arm64.deb ... 222s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 222s Selecting previously unselected package r-cran-dplyr. 222s Preparing to unpack .../105-r-cran-dplyr_1.1.4-1_arm64.deb ... 222s Unpacking r-cran-dplyr (1.1.4-1) ... 222s Selecting previously unselected package r-cran-ellipsis. 223s Preparing to unpack .../106-r-cran-ellipsis_0.3.2-2_arm64.deb ... 223s Unpacking r-cran-ellipsis (0.3.2-2) ... 223s Selecting previously unselected package r-cran-purrr. 223s Preparing to unpack .../107-r-cran-purrr_1.0.2-1_arm64.deb ... 223s Unpacking r-cran-purrr (1.0.2-1) ... 223s Selecting previously unselected package r-cran-stringi. 223s Preparing to unpack .../108-r-cran-stringi_1.8.3-1_arm64.deb ... 223s Unpacking r-cran-stringi (1.8.3-1) ... 223s Selecting previously unselected package r-cran-stringr. 223s Preparing to unpack .../109-r-cran-stringr_1.5.1-1_all.deb ... 223s Unpacking r-cran-stringr (1.5.1-1) ... 223s Selecting previously unselected package r-cran-cpp11. 223s Preparing to unpack .../110-r-cran-cpp11_0.4.7-1_all.deb ... 223s Unpacking r-cran-cpp11 (0.4.7-1) ... 223s Selecting previously unselected package r-cran-tidyr. 223s Preparing to unpack .../111-r-cran-tidyr_1.3.1-1_arm64.deb ... 223s Unpacking r-cran-tidyr (1.3.1-1) ... 223s Selecting previously unselected package r-cran-broom. 223s Preparing to unpack .../112-r-cran-broom_1.0.5+dfsg-1_all.deb ... 223s Unpacking r-cran-broom (1.0.5+dfsg-1) ... 223s Selecting previously unselected package r-cran-numderiv. 223s Preparing to unpack .../113-r-cran-numderiv_2016.8-1.1-3_all.deb ... 223s Unpacking r-cran-numderiv (2016.8-1.1-3) ... 223s Selecting previously unselected package r-cran-xfun. 223s Preparing to unpack .../114-r-cran-xfun_0.41+dfsg-1_arm64.deb ... 223s Unpacking r-cran-xfun (0.41+dfsg-1) ... 223s Selecting previously unselected package r-cran-highr. 223s Preparing to unpack .../115-r-cran-highr_0.10+dfsg-1_all.deb ... 223s Unpacking r-cran-highr (0.10+dfsg-1) ... 223s Selecting previously unselected package r-cran-yaml. 223s Preparing to unpack .../116-r-cran-yaml_2.3.8-1_arm64.deb ... 223s Unpacking r-cran-yaml (2.3.8-1) ... 223s Selecting previously unselected package libjs-mathjax. 223s Preparing to unpack .../117-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 223s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 224s Selecting previously unselected package r-cran-knitr. 224s Preparing to unpack .../118-r-cran-knitr_1.45+dfsg-1_all.deb ... 224s Unpacking r-cran-knitr (1.45+dfsg-1) ... 224s Selecting previously unselected package r-cran-pbkrtest. 224s Preparing to unpack .../119-r-cran-pbkrtest_0.5.2-2_all.deb ... 224s Unpacking r-cran-pbkrtest (0.5.2-2) ... 224s Selecting previously unselected package r-cran-sparsem. 224s Preparing to unpack .../120-r-cran-sparsem_1.81-1_arm64.deb ... 224s Unpacking r-cran-sparsem (1.81-1) ... 224s Selecting previously unselected package r-cran-matrixmodels. 224s Preparing to unpack .../121-r-cran-matrixmodels_0.5-3-1_all.deb ... 224s Unpacking r-cran-matrixmodels (0.5-3-1) ... 224s Selecting previously unselected package r-cran-survival. 224s Preparing to unpack .../122-r-cran-survival_3.5-8-1_arm64.deb ... 224s Unpacking r-cran-survival (3.5-8-1) ... 224s Selecting previously unselected package r-cran-matrixstats. 225s Preparing to unpack .../123-r-cran-matrixstats_1.2.0-1_arm64.deb ... 225s Unpacking r-cran-matrixstats (1.2.0-1) ... 225s Selecting previously unselected package r-cran-rcpparmadillo. 225s Preparing to unpack .../124-r-cran-rcpparmadillo_0.12.8.0.0-1_arm64.deb ... 225s Unpacking r-cran-rcpparmadillo (0.12.8.0.0-1) ... 225s Selecting previously unselected package r-cran-gtable. 225s Preparing to unpack .../125-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 225s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 225s Selecting previously unselected package r-cran-isoband. 225s Preparing to unpack .../126-r-cran-isoband_0.2.7-1_arm64.deb ... 225s Unpacking r-cran-isoband (0.2.7-1) ... 225s Selecting previously unselected package r-cran-farver. 225s Preparing to unpack .../127-r-cran-farver_2.1.1-1_arm64.deb ... 225s Unpacking r-cran-farver (2.1.1-1) ... 225s Selecting previously unselected package r-cran-labeling. 225s Preparing to unpack .../128-r-cran-labeling_0.4.3-1_all.deb ... 225s Unpacking r-cran-labeling (0.4.3-1) ... 225s Selecting previously unselected package r-cran-colorspace. 225s Preparing to unpack .../129-r-cran-colorspace_2.1-0+dfsg-1_arm64.deb ... 225s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 225s Selecting previously unselected package r-cran-munsell. 225s Preparing to unpack .../130-r-cran-munsell_0.5.0-2build1_all.deb ... 225s Unpacking r-cran-munsell (0.5.0-2build1) ... 225s Selecting previously unselected package r-cran-rcolorbrewer. 225s Preparing to unpack .../131-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 225s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 225s Selecting previously unselected package r-cran-viridislite. 225s Preparing to unpack .../132-r-cran-viridislite_0.4.2-2_all.deb ... 225s Unpacking r-cran-viridislite (0.4.2-2) ... 225s Selecting previously unselected package r-cran-scales. 225s Preparing to unpack .../133-r-cran-scales_1.3.0-1_all.deb ... 225s Unpacking r-cran-scales (1.3.0-1) ... 225s Selecting previously unselected package r-cran-ggplot2. 225s Preparing to unpack .../134-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 225s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 225s Selecting previously unselected package r-cran-class. 225s Preparing to unpack .../135-r-cran-class_7.3-22-2_arm64.deb ... 225s Unpacking r-cran-class (7.3-22-2) ... 225s Selecting previously unselected package r-cran-proxy. 225s Preparing to unpack .../136-r-cran-proxy_0.4-27-1_arm64.deb ... 225s Unpacking r-cran-proxy (0.4-27-1) ... 226s Selecting previously unselected package r-cran-e1071. 226s Preparing to unpack .../137-r-cran-e1071_1.7-14-1_arm64.deb ... 226s Unpacking r-cran-e1071 (1.7-14-1) ... 226s Selecting previously unselected package r-cran-codetools. 226s Preparing to unpack .../138-r-cran-codetools_0.2-19-1_all.deb ... 226s Unpacking r-cran-codetools (0.2-19-1) ... 226s Selecting previously unselected package r-cran-iterators. 226s Preparing to unpack .../139-r-cran-iterators_1.0.14-1_all.deb ... 226s Unpacking r-cran-iterators (1.0.14-1) ... 226s Selecting previously unselected package r-cran-foreach. 226s Preparing to unpack .../140-r-cran-foreach_1.5.2-1_all.deb ... 226s Unpacking r-cran-foreach (1.5.2-1) ... 226s Selecting previously unselected package r-cran-data.table. 226s Preparing to unpack .../141-r-cran-data.table_1.14.10+dfsg-1_arm64.deb ... 226s Unpacking r-cran-data.table (1.14.10+dfsg-1) ... 226s Selecting previously unselected package r-cran-modelmetrics. 226s Preparing to unpack .../142-r-cran-modelmetrics_1.2.2.2-1build1_arm64.deb ... 226s Unpacking r-cran-modelmetrics (1.2.2.2-1build1) ... 226s Selecting previously unselected package r-cran-plyr. 226s Preparing to unpack .../143-r-cran-plyr_1.8.9-1_arm64.deb ... 226s Unpacking r-cran-plyr (1.8.9-1) ... 226s Selecting previously unselected package r-cran-proc. 226s Preparing to unpack .../144-r-cran-proc_1.18.5-1_arm64.deb ... 226s Unpacking r-cran-proc (1.18.5-1) ... 226s Selecting previously unselected package r-cran-tzdb. 226s Preparing to unpack .../145-r-cran-tzdb_0.4.0-2_arm64.deb ... 226s Unpacking r-cran-tzdb (0.4.0-2) ... 226s Selecting previously unselected package r-cran-clock. 226s Preparing to unpack .../146-r-cran-clock_0.7.0-1.1_arm64.deb ... 226s Unpacking r-cran-clock (0.7.0-1.1) ... 226s Selecting previously unselected package r-cran-gower. 226s Preparing to unpack .../147-r-cran-gower_1.0.1-1_arm64.deb ... 226s Unpacking r-cran-gower (1.0.1-1) ... 226s Selecting previously unselected package r-cran-hardhat. 226s Preparing to unpack .../148-r-cran-hardhat_1.3.1+dfsg-1_all.deb ... 226s Unpacking r-cran-hardhat (1.3.1+dfsg-1) ... 226s Selecting previously unselected package r-cran-rpart. 226s Preparing to unpack .../149-r-cran-rpart_4.1.23-1_arm64.deb ... 226s Unpacking r-cran-rpart (4.1.23-1) ... 226s Selecting previously unselected package r-cran-shape. 227s Preparing to unpack .../150-r-cran-shape_1.4.6-1_all.deb ... 227s Unpacking r-cran-shape (1.4.6-1) ... 227s Selecting previously unselected package r-cran-diagram. 227s Preparing to unpack .../151-r-cran-diagram_1.6.5-2_all.deb ... 227s Unpacking r-cran-diagram (1.6.5-2) ... 227s Selecting previously unselected package r-cran-kernsmooth. 227s Preparing to unpack .../152-r-cran-kernsmooth_2.23-22-1_arm64.deb ... 227s Unpacking r-cran-kernsmooth (2.23-22-1) ... 227s Selecting previously unselected package r-cran-globals. 227s Preparing to unpack .../153-r-cran-globals_0.16.2-1_all.deb ... 227s Unpacking r-cran-globals (0.16.2-1) ... 227s Selecting previously unselected package r-cran-listenv. 227s Preparing to unpack .../154-r-cran-listenv_0.9.1+dfsg-1_all.deb ... 227s Unpacking r-cran-listenv (0.9.1+dfsg-1) ... 227s Selecting previously unselected package r-cran-parallelly. 227s Preparing to unpack .../155-r-cran-parallelly_1.37.1-1_arm64.deb ... 227s Unpacking r-cran-parallelly (1.37.1-1) ... 227s Selecting previously unselected package r-cran-future. 227s Preparing to unpack .../156-r-cran-future_1.33.1+dfsg-1_all.deb ... 227s Unpacking r-cran-future (1.33.1+dfsg-1) ... 227s Selecting previously unselected package r-cran-future.apply. 227s Preparing to unpack .../157-r-cran-future.apply_1.11.1+dfsg-1_all.deb ... 227s Unpacking r-cran-future.apply (1.11.1+dfsg-1) ... 227s Selecting previously unselected package r-cran-progressr. 227s Preparing to unpack .../158-r-cran-progressr_0.14.0-1_all.deb ... 227s Unpacking r-cran-progressr (0.14.0-1) ... 227s Selecting previously unselected package r-cran-squarem. 227s Preparing to unpack .../159-r-cran-squarem_2021.1-1_all.deb ... 227s Unpacking r-cran-squarem (2021.1-1) ... 227s Selecting previously unselected package r-cran-lava. 227s Preparing to unpack .../160-r-cran-lava_1.7.3+dfsg-1_all.deb ... 227s Unpacking r-cran-lava (1.7.3+dfsg-1) ... 227s Selecting previously unselected package r-cran-prodlim. 227s Preparing to unpack .../161-r-cran-prodlim_2023.08.28-1_arm64.deb ... 227s Unpacking r-cran-prodlim (2023.08.28-1) ... 227s Selecting previously unselected package r-cran-ipred. 227s Preparing to unpack .../162-r-cran-ipred_0.9-14-1_arm64.deb ... 227s Unpacking r-cran-ipred (0.9-14-1) ... 227s Selecting previously unselected package r-cran-timechange. 227s Preparing to unpack .../163-r-cran-timechange_0.3.0-1_arm64.deb ... 227s Unpacking r-cran-timechange (0.3.0-1) ... 227s Selecting previously unselected package r-cran-lubridate. 227s Preparing to unpack .../164-r-cran-lubridate_1.9.3+dfsg-1_arm64.deb ... 227s Unpacking r-cran-lubridate (1.9.3+dfsg-1) ... 227s Selecting previously unselected package r-cran-timedate. 227s Preparing to unpack .../165-r-cran-timedate_4032.109-1_arm64.deb ... 227s Unpacking r-cran-timedate (4032.109-1) ... 227s Selecting previously unselected package r-cran-recipes. 227s Preparing to unpack .../166-r-cran-recipes_1.0.9+dfsg-1_all.deb ... 227s Unpacking r-cran-recipes (1.0.9+dfsg-1) ... 227s Selecting previously unselected package r-cran-reshape2. 227s Preparing to unpack .../167-r-cran-reshape2_1.4.4-2build1_arm64.deb ... 227s Unpacking r-cran-reshape2 (1.4.4-2build1) ... 227s Selecting previously unselected package r-cran-caret. 228s Preparing to unpack .../168-r-cran-caret_6.0-94+dfsg-1_arm64.deb ... 228s Unpacking r-cran-caret (6.0-94+dfsg-1) ... 228s Selecting previously unselected package r-cran-conquer. 228s Preparing to unpack .../169-r-cran-conquer_1.3.3-1_arm64.deb ... 228s Unpacking r-cran-conquer (1.3.3-1) ... 228s Selecting previously unselected package r-cran-quantreg. 228s Preparing to unpack .../170-r-cran-quantreg_5.97-1_arm64.deb ... 228s Unpacking r-cran-quantreg (5.97-1) ... 228s Selecting previously unselected package r-cran-sp. 228s Preparing to unpack .../171-r-cran-sp_1%3a2.1-2+dfsg-1_arm64.deb ... 228s Unpacking r-cran-sp (1:2.1-2+dfsg-1) ... 228s Selecting previously unselected package r-cran-foreign. 228s Preparing to unpack .../172-r-cran-foreign_0.8.86-1_arm64.deb ... 228s Unpacking r-cran-foreign (0.8.86-1) ... 228s Selecting previously unselected package r-cran-maptools. 228s Preparing to unpack .../173-r-cran-maptools_1%3a1.1-8+dfsg-1_arm64.deb ... 228s Unpacking r-cran-maptools (1:1.1-8+dfsg-1) ... 228s Selecting previously unselected package r-cran-forcats. 228s Preparing to unpack .../174-r-cran-forcats_1.0.0-1_all.deb ... 228s Unpacking r-cran-forcats (1.0.0-1) ... 229s Selecting previously unselected package r-cran-hms. 229s Preparing to unpack .../175-r-cran-hms_1.1.3-1_all.deb ... 229s Unpacking r-cran-hms (1.1.3-1) ... 229s Selecting previously unselected package r-cran-clipr. 229s Preparing to unpack .../176-r-cran-clipr_0.8.0-1_all.deb ... 229s Unpacking r-cran-clipr (0.8.0-1) ... 229s Selecting previously unselected package r-cran-bit. 229s Preparing to unpack .../177-r-cran-bit_4.0.5-1_arm64.deb ... 229s Unpacking r-cran-bit (4.0.5-1) ... 229s Selecting previously unselected package r-cran-bit64. 229s Preparing to unpack .../178-r-cran-bit64_4.0.5-1_arm64.deb ... 229s Unpacking r-cran-bit64 (4.0.5-1) ... 229s Selecting previously unselected package r-cran-prettyunits. 229s Preparing to unpack .../179-r-cran-prettyunits_1.2.0-1_all.deb ... 229s Unpacking r-cran-prettyunits (1.2.0-1) ... 230s Selecting previously unselected package r-cran-progress. 230s Preparing to unpack .../180-r-cran-progress_1.2.3-1_all.deb ... 230s Unpacking r-cran-progress (1.2.3-1) ... 230s Selecting previously unselected package r-cran-vroom. 230s Preparing to unpack .../181-r-cran-vroom_1.6.5-1_arm64.deb ... 230s Unpacking r-cran-vroom (1.6.5-1) ... 230s Selecting previously unselected package r-cran-readr. 230s Preparing to unpack .../182-r-cran-readr_2.1.5-1_arm64.deb ... 230s Unpacking r-cran-readr (2.1.5-1) ... 230s Selecting previously unselected package r-cran-haven. 230s Preparing to unpack .../183-r-cran-haven_2.5.4-1_arm64.deb ... 230s Unpacking r-cran-haven (2.5.4-1) ... 230s Selecting previously unselected package r-cran-curl. 230s Preparing to unpack .../184-r-cran-curl_5.2.0+dfsg-1_arm64.deb ... 230s Unpacking r-cran-curl (5.2.0+dfsg-1) ... 230s Selecting previously unselected package r-cran-rematch. 231s Preparing to unpack .../185-r-cran-rematch_2.0.0-1_all.deb ... 231s Unpacking r-cran-rematch (2.0.0-1) ... 231s Selecting previously unselected package r-cran-cellranger. 231s Preparing to unpack .../186-r-cran-cellranger_1.1.0-3_all.deb ... 231s Unpacking r-cran-cellranger (1.1.0-3) ... 231s Selecting previously unselected package r-cran-readxl. 231s Preparing to unpack .../187-r-cran-readxl_1.4.3-1_arm64.deb ... 231s Unpacking r-cran-readxl (1.4.3-1) ... 231s Selecting previously unselected package r-cran-writexl. 231s Preparing to unpack .../188-r-cran-writexl_1.5.0-1_arm64.deb ... 231s Unpacking r-cran-writexl (1.5.0-1) ... 231s Selecting previously unselected package r-cran-r.methodss3. 231s Preparing to unpack .../189-r-cran-r.methodss3_1.8.2-1_all.deb ... 231s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 231s Selecting previously unselected package r-cran-r.oo. 231s Preparing to unpack .../190-r-cran-r.oo_1.26.0-1_all.deb ... 231s Unpacking r-cran-r.oo (1.26.0-1) ... 231s Selecting previously unselected package r-cran-r.utils. 231s Preparing to unpack .../191-r-cran-r.utils_2.12.3-1_all.deb ... 231s Unpacking r-cran-r.utils (2.12.3-1) ... 231s Selecting previously unselected package r-cran-zip. 231s Preparing to unpack .../192-r-cran-zip_2.3.1-1_arm64.deb ... 231s Unpacking r-cran-zip (2.3.1-1) ... 231s Selecting previously unselected package r-cran-openxlsx. 231s Preparing to unpack .../193-r-cran-openxlsx_4.2.5.2-1_arm64.deb ... 231s Unpacking r-cran-openxlsx (4.2.5.2-1) ... 231s Selecting previously unselected package r-cran-rio. 231s Preparing to unpack .../194-r-cran-rio_1.0.1-1_all.deb ... 231s Unpacking r-cran-rio (1.0.1-1) ... 231s Selecting previously unselected package r-cran-car. 231s Preparing to unpack .../195-r-cran-car_3.1-2-2_all.deb ... 231s Unpacking r-cran-car (3.1-2-2) ... 231s Selecting previously unselected package r-cran-zoo. 231s Preparing to unpack .../196-r-cran-zoo_1.8-12-2_arm64.deb ... 231s Unpacking r-cran-zoo (1.8-12-2) ... 231s Selecting previously unselected package r-cran-lmtest. 231s Preparing to unpack .../197-r-cran-lmtest_0.9.40-1_arm64.deb ... 231s Unpacking r-cran-lmtest (0.9.40-1) ... 231s Selecting previously unselected package r-cran-sandwich. 231s Preparing to unpack .../198-r-cran-sandwich_3.1-0-1_all.deb ... 231s Unpacking r-cran-sandwich (3.1-0-1) ... 231s Selecting previously unselected package r-cran-formula. 231s Preparing to unpack .../199-r-cran-formula_1.2-5-1_all.deb ... 231s Unpacking r-cran-formula (1.2-5-1) ... 231s Selecting previously unselected package r-cran-aer. 231s Preparing to unpack .../200-r-cran-aer_1.2-12-1_all.deb ... 231s Unpacking r-cran-aer (1.2-12-1) ... 232s Selecting previously unselected package r-cran-blob. 232s Preparing to unpack .../201-r-cran-blob_1.2.4-1_all.deb ... 232s Unpacking r-cran-blob 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Platform: aarch64-unknown-linux-gnu (64-bit) 250s 250s R is free software and comes with ABSOLUTELY NO WARRANTY. 250s You are welcome to redistribute it under certain conditions. 250s Type 'license()' or 'licence()' for distribution details. 250s 250s R is a collaborative project with many contributors. 250s Type 'contributors()' for more information and 250s 'citation()' on how to cite R or R packages in publications. 250s 250s Type 'demo()' for some demos, 'help()' for on-line help, or 250s 'help.start()' for an HTML browser interface to help. 250s Type 'q()' to quit R. 250s 250s > ## simulated data with three-stage sample at phase 1, SRS at phase 2 250s > ## motivated by dietary biomarker substudy in HCHS 250s > 250s > library(survey) 250s Loading required package: grid 251s Loading required package: Matrix 251s Loading required package: survival 252s 252s Attaching package: 'survey' 252s 252s The following object is masked from 'package:graphics': 252s 252s dotchart 252s 252s > 252s > load("simdata1.RData") 252s > 252s > twophase.full = twophase(id=list(~block+house+ind,~1), 252s + strata=list(~strat,NULL), 252s + probs=list(~P.block+P.house+P.ind,NULL), 252s + subset=~phase2, 252s + data=simdata1,method='full') 252s > 252s > twophase.approx = twophase(id=list(~block+house+ind,~1), 252s + strata=list(~strat,NULL), 252s + probs=list(~P.block+P.house+P.ind,NULL), 252s + subset=~phase2, 252s + data=simdata1,method='approx') 252s > 252s > twophase.rep = twophase(id=list(~block,~1), 252s + strata=list(~strat,NULL), 252s + probs=list(~I(P.block*P.house*P.ind),NULL), 252s + subset=~phase2, 252s + data=simdata1,method='full') 252s > 252s > 252s > twophase.repapprox = twophase(id=list(~block,~1), 252s + strata=list(~strat,NULL), 252s + probs=list(~I(P.block*P.house*P.ind),NULL), 252s + subset=~phase2, 252s + data=simdata1,method='approx') 252s > 252s > 252s > svymean(~age, twophase.full) 252s mean SE 252s age 41.116 0.8114 252s > svymean(~age, twophase.approx) 252s mean SE 252s age 41.116 0.6693 252s > svymean(~age, twophase.rep) 252s mean SE 252s age 41.116 0.784 252s > svymean(~age, twophase.repapprox) 252s mean SE 252s age 41.116 0.6592 252s > 252s BEGIN TEST DBIcheck.R 252s 252s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 252s Copyright (C) 2024 The R Foundation for Statistical Computing 252s Platform: aarch64-unknown-linux-gnu (64-bit) 252s 252s R is free software and comes with ABSOLUTELY NO WARRANTY. 252s You are welcome to redistribute it under certain conditions. 252s Type 'license()' or 'licence()' for distribution details. 252s 252s R is a collaborative project with many contributors. 252s Type 'contributors()' for more information and 252s 'citation()' on how to cite R or R packages in publications. 252s 252s Type 'demo()' for some demos, 'help()' for on-line help, or 252s 'help.start()' for an HTML browser interface to help. 252s Type 'q()' to quit R. 252s 253s > 253s > library(survey) 253s Loading required package: grid 253s Loading required package: Matrix 254s Loading required package: survival 254s 254s Attaching package: 'survey' 254s 254s The following object is masked from 'package:graphics': 254s 254s dotchart 254s 254s > library(RSQLite) 255s > 255s > data(api) 255s > apiclus1$api_stu<-apiclus1$api.stu 255s > apiclus1$comp_imp<-apiclus1$comp.imp 255s > dclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,data=apiclus1) 255s > dbclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc, 255s + data="apiclus1",dbtype="SQLite", dbname=system.file("api.db",package="survey")) 255s > 255s > m<-svymean(~api00+stype,dclus1) 255s > m.db<-svymean(~api00+stype, dbclus1) 255s > all.equal(coef(m),coef(m.db)) 255s [1] TRUE 255s > all.equal(vcov(m), vcov(m.db)) 255s [1] TRUE 255s > 255s > r<-svyratio(~api_stu, ~enroll, design=dclus1) 255s > r.db<-svyratio(~api_stu, ~enroll, design=dbclus1) 255s > all.equal(coef(r), coef(r.db)) 255s [1] TRUE 255s > all.equal(SE(r), SE(r.db)) 255s [1] TRUE 255s > 255s > b<-svyby(~api99+api00,~stype, design=dclus1, svymean, deff=TRUE) 255s > b.db<-svyby(~api99+api00,~stype, design=dbclus1,svymean, deff=TRUE) 255s > all.equal(coef(b), coef(b.db)) 255s [1] TRUE 255s > all.equal(SE(b), SE(b.db)) 255s [1] TRUE 255s > all.equal(deff(b), deff(b.db)) 255s [1] TRUE 255s > 255s > l<-svyglm(api00~api99+mobility, design=dclus1) 255s > l.db<-svyglm(api00~api99+mobility, design=dbclus1) 255s > all.equal(coef(l),coef(l.db)) 255s [1] TRUE 255s > all.equal(vcov(l), vcov(l.db)) 255s [1] TRUE 255s > 255s > dclus1<-update(dclus1, apidiff=api00-api99) 255s > dclus1<-update(dclus1, apipct= apidiff/api99) 255s > dbclus1<-update(dbclus1, apidiff=api00-api99) 255s > dbclus1<-update(dbclus1, apipct= apidiff/api99) 255s > 255s > u<-svymean(~api00+apidiff+apipct, dclus1) 255s > u.db<-svymean(~api00+apidiff+apipct, dbclus1) 255s > all.equal(u, u.db) 255s [1] TRUE 255s > 255s > all.equal(nrow(dclus1),nrow(dbclus1)) 255s [1] TRUE 255s > all.equal(nrow(subset(dclus1,stype=="E")), 255s + nrow(subset(dbclus1,stype=="E"))) 255s [1] "Mean relative difference: 0.2708333" 255s > 255s > ## replicate weights 255s > rclus1<-as.svrepdesign(dclus1) 255s > db_rclus1<-svrepdesign(weights=~pw, repweights="wt[1-9]+", type="JK1", scale=(1-15/757)*14/15, 255s + data="apiclus1rep",dbtype="SQLite", dbname=system.file("api.db",package="survey"),combined.weights=FALSE) 255s > m<-svymean(~api00+api99,rclus1) 255s > m.db<-svymean(~api00+api99,db_rclus1) 255s > all.equal(m,m.db) 255s [1] TRUE 255s > 255s > summary(db_rclus1) 255s DB-backed replicate weight design 255s Call: svrepdesign(weights = ~pw, repweights = "wt[1-9]+", type = "JK1", 255s scale = (1 - 15/757) * 14/15, data = "apiclus1rep", dbtype = "SQLite", 255s dbname = system.file("api.db", package = "survey"), combined.weights = FALSE) 255s Unstratified cluster jacknife (JK1) with 15 replicates. 255s Variables: 255s [1] "row_names" "cds" "stype" "name" "sname" 255s [6] "snum" "dname" "dnum" "cname" "cnum" 255s [11] "flag" "pcttest" "api00" "api99" "target" 255s [16] "growth" "sch_wide" "comp_imp" "both" "awards" 255s [21] "meals" "ell" "yr_rnd" "mobility" "acs_k3" 255s [26] "acs_46" "acs_core" "pct_resp" "not_hsg" "hsg" 255s [31] "some_col" "col_grad" "grad_sch" "avg_ed" "full__1" 255s [36] "emer" "enroll" "api_stu" "fpc" "pw" 255s [41] "row_names:1" "wt1" "wt2" "wt3" "wt4" 255s [46] "wt5" "wt6" "wt7" "wt8" "wt9" 255s [51] "wt10" "wt11" "wt12" "wt13" "wt14" 255s [56] "wt15" 255s > 255s > s<-svymean(~api00, subset(rclus1, comp_imp=="Yes")) 255s > s.db<-svymean(~api00, subset(db_rclus1, comp_imp=="Yes")) 255s > all.equal(s,s.db) 255s [1] TRUE 255s > 256s BEGIN TEST anova-svycoxph.R 256s Loading required package: grid 256s Loading required package: Matrix 256s 256s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 256s Copyright (C) 2024 The R Foundation for Statistical Computing 256s Platform: aarch64-unknown-linux-gnu (64-bit) 256s 256s R is free software and comes with ABSOLUTELY NO WARRANTY. 256s You are welcome to redistribute it under certain conditions. 256s Type 'license()' or 'licence()' for distribution details. 256s 256s R is a collaborative project with many contributors. 256s Type 'contributors()' for more information and 256s 'citation()' on how to cite R or R packages in publications. 256s 256s Type 'demo()' for some demos, 'help()' for on-line help, or 256s 'help.start()' for an HTML browser interface to help. 256s Type 'q()' to quit R. 256s 256s > 256s > library(survey) 257s Loading required package: survival 257s 257s Attaching package: 'survey' 257s 257s > example(svycoxph, ask=FALSE) 257s The following object is masked from 'package:graphics': 257s 257s dotchart 257s 257s 257s svycxp> ## Somewhat unrealistic example of nonresponse bias. 257s svycxp> data(pbc, package="survival") 257s 257s svycxp> pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 257s 257s svycxp> biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 257s 257s svycxp> pbc$randprob<-fitted(biasmodel) 257s 257s svycxp> if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 257s 257s svycxp> dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 257s 257s svycxp> rpbc<-as.svrepdesign(dpbc) 257s 257s svycxp> (model<-svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=dpbc)) 257s Call: 257s svycoxph(formula = Surv(time, status > 0) ~ log(bili) + protime + 257s albumin, design = dpbc) 257s 257s coef exp(coef) se(coef) robust se z p 257s log(bili) 0.88592 2.42522 0.09140 0.09048 9.791 < 2e-16 257s protime 0.24487 1.27745 0.07825 0.08122 3.015 0.00257 257s albumin -1.04298 0.35240 0.21211 0.20454 -5.099 3.41e-07 257s 257s Likelihood ratio test= on 3 df, p= 257s n= 312, number of events= 144 257s 257s svycxp> svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=rpbc) 257s Call: 257s svycoxph.svyrep.design(formula = Surv(time, status > 0) ~ log(bili) + 257s protime + albumin, design = rpbc) 257s 257s coef exp(coef) se(coef) z p 257s log(bili) 0.88592 2.42522 0.09838 9.005 < 2e-16 257s protime 0.24487 1.27745 0.09373 2.612 0.00899 257s albumin -1.04298 0.35240 0.21966 -4.748 2.05e-06 257s 257s Likelihood ratio test=NA on 3 df, p=NA 257s n= 312, number of events= 144 257s 257s svycxp> s<-predict(model,se=TRUE, type="curve", 257s svycxp+ newdata=data.frame(bili=c(3,9), protime=c(10,10), albumin=c(3.5,3.5))) 257s 257s svycxp> plot(s[[1]],ci=TRUE,col="sienna") 258s 258s svycxp> lines(s[[2]], ci=TRUE,col="royalblue") 258s 258s svycxp> quantile(s[[1]], ci=TRUE) 258s 0.75 0.5 0.25 258s 1435 2503 3574 258s attr(,"ci") 258s 0.025 0.975 258s 0.75 1217 1786 258s 0.5 2256 3170 258s 0.25 3222 Inf 258s 258s svycxp> confint(s[[2]], parm=365*(1:5)) 258s 0.025 0.975 258s 365 0.8375139 0.9453781 258s 730 0.7382750 0.8999016 258s 1095 0.4784105 0.7478460 258s 1460 0.3192009 0.6206764 258s 1825 0.2149475 0.5292978 258s > m<-update(model, .~.+I(protime^2)) 258s > a<-anova(m,model) 258s > b<-anova(m, model,force=TRUE) 258s > stopifnot(isTRUE(all.equal(b[2:6],a[c(3,4,6,7,8)]))) 258s > 258s BEGIN TEST api.R 258s 258s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 258s Copyright (C) 2024 The R Foundation for Statistical Computing 258s Platform: aarch64-unknown-linux-gnu (64-bit) 258s 258s R is free software and comes with ABSOLUTELY NO WARRANTY. 258s You are welcome to redistribute it under certain conditions. 258s Type 'license()' or 'licence()' for distribution details. 258s 258s R is a collaborative project with many contributors. 258s Type 'contributors()' for more information and 258s 'citation()' on how to cite R or R packages in publications. 258s 258s Type 'demo()' for some demos, 'help()' for on-line help, or 258s 'help.start()' for an HTML browser interface to help. 258s Type 'q()' to quit R. 258s 258s > library(survey) 258s Loading required package: grid 258s Loading required package: Matrix 259s Loading required package: survival 259s > options(survey.replicates.mse=TRUE) 259s > example(api) 259s 259s api> library(survey) 259s 259s api> data(api) 259s 259s Attaching package: 'survey' 259s 259s The following object is masked from 'package:graphics': 259s 259s dotchart 259s 259s 259s api> mean(apipop$api00) 259s [1] 664.7126 259s 259s api> sum(apipop$enroll, na.rm=TRUE) 259s [1] 3811472 259s 259s api> #stratified sample 259s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 259s 259s api> summary(dstrat) 259s Stratified Independent Sampling design 259s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 259s Probabilities: 259s Min. 1st Qu. Median Mean 3rd Qu. Max. 259s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 259s Stratum Sizes: 259s E H M 259s obs 100 50 50 259s design.PSU 100 50 50 259s actual.PSU 100 50 50 259s Population stratum sizes (PSUs): 259s E H M 259s 4421 755 1018 259s Data variables: 259s [1] "cds" "stype" "name" "sname" "snum" "dname" 259s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 259s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 259s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 259s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 259s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 259s [37] "api.stu" "pw" "fpc" 259s 259s api> svymean(~api00, dstrat) 259s mean SE 259s api00 662.29 9.4089 259s 259s api> svytotal(~enroll, dstrat, na.rm=TRUE) 259s total SE 259s enroll 3687178 114642 259s 259s api> # one-stage cluster sample 259s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 259s 259s api> summary(dclus1) 259s 1 - level Cluster Sampling design 259s With (15) clusters. 259s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 259s Probabilities: 259s Min. 1st Qu. Median Mean 3rd Qu. Max. 259s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 259s Population size (PSUs): 757 259s Data variables: 259s [1] "cds" "stype" "name" "sname" "snum" "dname" 259s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 259s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 259s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 259s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 259s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 259s [37] "api.stu" "fpc" "pw" 259s 259s api> svymean(~api00, dclus1) 259s mean SE 259s api00 644.17 23.542 259s 259s api> svytotal(~enroll, dclus1, na.rm=TRUE) 259s total SE 259s enroll 3404940 932235 259s 259s api> # two-stage cluster sample 259s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 259s 259s api> summary(dclus2) 259s 2 - level Cluster Sampling design 259s With (40, 126) clusters. 259s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 259s Probabilities: 259s Min. 1st Qu. Median Mean 3rd Qu. Max. 259s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 259s Population size (PSUs): 757 259s Data variables: 259s [1] "cds" "stype" "name" "sname" "snum" "dname" 259s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 259s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 259s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 259s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 259s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 259s [37] "api.stu" "pw" "fpc1" "fpc2" 259s 259s api> svymean(~api00, dclus2) 259s mean SE 259s api00 670.81 30.099 259s 259s api> svytotal(~enroll, dclus2, na.rm=TRUE) 259s total SE 259s enroll 2639273 799638 259s 259s api> # two-stage `with replacement' 259s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 259s 259s api> summary(dclus2wr) 259s 2 - level Cluster Sampling design (with replacement) 259s With (40, 126) clusters. 259s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 259s Probabilities: 259s Min. 1st Qu. Median Mean 3rd Qu. Max. 259s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 259s Data variables: 259s [1] "cds" "stype" "name" "sname" "snum" "dname" 259s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 259s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 259s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 259s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 259s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 259s [37] "api.stu" "pw" "fpc1" "fpc2" 259s 259s api> svymean(~api00, dclus2wr) 259s mean SE 259s api00 670.81 30.712 259s 259s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 259s total SE 259s enroll 2639273 820261 259s 259s api> # convert to replicate weights 259s api> rclus1<-as.svrepdesign(dclus1) 259s 259s api> summary(rclus1) 259s Call: as.svrepdesign.default(dclus1) 259s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 259s Variables: 259s [1] "cds" "stype" "name" "sname" "snum" "dname" 259s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 259s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 259s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 259s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 259s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 259s [37] "api.stu" "fpc" "pw" 259s 259s api> svymean(~api00, rclus1) 259s mean SE 259s api00 644.17 26.335 259s 259s api> svytotal(~enroll, rclus1, na.rm=TRUE) 259s total SE 259s enroll 3404940 932235 259s 259s api> # post-stratify on school type 259s api> pop.types<-xtabs(~stype, data=apipop) 259s 259s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 259s 259s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 259s 259s api> summary(dclus1p) 259s 1 - level Cluster Sampling design 259s With (15) clusters. 259s dclus1p<-postStratify(dclus1, ~stype, pop.types) 259s Probabilities: 259s Min. 1st Qu. Median Mean 3rd Qu. Max. 259s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 259s Population size (PSUs): 757 259s Data variables: 259s [1] "cds" "stype" "name" "sname" "snum" "dname" 259s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 259s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 259s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 259s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 259s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 259s [37] "api.stu" "fpc" "pw" 259s 259s api> summary(rclus1p) 259s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 259s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 259s Variables: 259s [1] "cds" "stype" "name" "sname" "snum" "dname" 259s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 259s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 259s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 259s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 259s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 259s [37] "api.stu" "fpc" "pw" 259s 259s api> svymean(~api00, dclus1p) 259s mean SE 259s api00 642.31 23.921 259s 259s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 259s total SE 259s enroll 3680893 406293 259s 259s api> svymean(~api00, rclus1p) 259s mean SE 259s api00 642.31 26.936 259s 259s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 259s total SE 259s enroll 3680893 473434 259s > 259s > options(survey.replicates.mse=FALSE) 259s > example(api) 259s 259s api> library(survey) 259s 259s api> data(api) 260s 260s api> mean(apipop$api00) 260s [1] 664.7126 260s 260s api> sum(apipop$enroll, na.rm=TRUE) 260s [1] 3811472 260s 260s api> #stratified sample 260s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 260s 260s api> summary(dstrat) 260s Stratified Independent Sampling design 260s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 260s Probabilities: 260s Min. 1st Qu. Median Mean 3rd Qu. Max. 260s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 260s Stratum Sizes: 260s E H M 260s obs 100 50 50 260s design.PSU 100 50 50 260s actual.PSU 100 50 50 260s Population stratum sizes (PSUs): 260s E H M 260s 4421 755 1018 260s Data variables: 260s [1] "cds" "stype" "name" "sname" "snum" "dname" 260s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 260s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 260s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 260s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 260s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 260s [37] "api.stu" "pw" "fpc" 260s 260s api> svymean(~api00, dstrat) 260s mean SE 260s api00 662.29 9.4089 260s 260s api> svytotal(~enroll, dstrat, na.rm=TRUE) 260s total SE 260s enroll 3687178 114642 260s 260s api> # one-stage cluster sample 260s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 260s 260s api> summary(dclus1) 260s 1 - level Cluster Sampling design 260s With (15) clusters. 260s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 260s Probabilities: 260s Min. 1st Qu. Median Mean 3rd Qu. Max. 260s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 260s Population size (PSUs): 757 260s Data variables: 260s [1] "cds" "stype" "name" "sname" "snum" "dname" 260s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 260s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 260s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 260s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 260s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 260s [37] "api.stu" "fpc" "pw" 260s 260s api> svymean(~api00, dclus1) 260s mean SE 260s api00 644.17 23.542 260s 260s api> svytotal(~enroll, dclus1, na.rm=TRUE) 260s total SE 260s enroll 3404940 932235 260s 260s api> # two-stage cluster sample 260s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 260s 260s api> summary(dclus2) 260s 2 - level Cluster Sampling design 260s With (40, 126) clusters. 260s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 260s Probabilities: 260s Min. 1st Qu. Median Mean 3rd Qu. Max. 260s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 260s Population size (PSUs): 757 260s Data variables: 260s [1] "cds" "stype" "name" "sname" "snum" "dname" 260s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 260s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 260s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 260s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 260s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 260s [37] "api.stu" "pw" "fpc1" "fpc2" 260s 260s api> svymean(~api00, dclus2) 260s mean SE 260s api00 670.81 30.099 260s 260s api> svytotal(~enroll, dclus2, na.rm=TRUE) 260s total SE 260s enroll 2639273 799638 260s 260s api> # two-stage `with replacement' 260s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 260s 260s api> summary(dclus2wr) 260s 2 - level Cluster Sampling design (with replacement) 260s With (40, 126) clusters. 260s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 260s Probabilities: 260s Min. 1st Qu. Median Mean 3rd Qu. Max. 260s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 260s Data variables: 260s [1] "cds" "stype" "name" "sname" "snum" "dname" 260s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 260s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 260s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 260s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 260s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 260s [37] "api.stu" "pw" "fpc1" "fpc2" 260s 260s api> svymean(~api00, dclus2wr) 260s mean SE 260s api00 670.81 30.712 260s 260s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 260s total SE 260s enroll 2639273 820261 260s 260s api> # convert to replicate weights 260s api> rclus1<-as.svrepdesign(dclus1) 260s 260s api> summary(rclus1) 260s Call: as.svrepdesign.default(dclus1) 260s Unstratified cluster jacknife (JK1) with 15 replicates. 260s Variables: 260s [1] "cds" "stype" "name" "sname" "snum" "dname" 260s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 260s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 260s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 260s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 260s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 260s [37] "api.stu" "fpc" "pw" 260s 260s api> svymean(~api00, rclus1) 260s mean SE 260s api00 644.17 26.329 260s 260s api> svytotal(~enroll, rclus1, na.rm=TRUE) 260s total SE 260s enroll 3404940 932235 260s 260s api> # post-stratify on school type 260s api> pop.types<-xtabs(~stype, data=apipop) 260s 260s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 260s 260s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 260s 260s api> summary(dclus1p) 260s 1 - level Cluster Sampling design 260s With (15) clusters. 260s dclus1p<-postStratify(dclus1, ~stype, pop.types) 260s Probabilities: 260s Min. 1st Qu. Median Mean 3rd Qu. Max. 260s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 260s Population size (PSUs): 757 260s Data variables: 260s [1] "cds" "stype" "name" "sname" "snum" "dname" 260s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 260s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 260s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 260s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 260s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 260s [37] "api.stu" "fpc" "pw" 260s 260s api> summary(rclus1p) 260s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 260s Unstratified cluster jacknife (JK1) with 15 replicates. 260s Variables: 260s [1] "cds" "stype" "name" "sname" "snum" "dname" 260s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 260s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 260s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 260s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 260s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 260s [37] "api.stu" "fpc" "pw" 260s 260s api> svymean(~api00, dclus1p) 260s mean SE 260s api00 642.31 23.921 260s 260s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 260s total SE 260s enroll 3680893 406293 260s 260s api> svymean(~api00, rclus1p) 260s mean SE 260s api00 642.31 26.934 260s 260s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 260s total SE 260s enroll 3680893 473431 260s > 260s BEGIN TEST badcal.R 260s 260s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 260s Copyright (C) 2024 The R Foundation for Statistical Computing 260s Platform: aarch64-unknown-linux-gnu (64-bit) 260s 260s R is free software and comes with ABSOLUTELY NO WARRANTY. 260s You are welcome to redistribute it under certain conditions. 260s Type 'license()' or 'licence()' for distribution details. 260s 260s R is a collaborative project with many contributors. 260s Type 'contributors()' for more information and 260s 'citation()' on how to cite R or R packages in publications. 260s 260s Type 'demo()' for some demos, 'help()' for on-line help, or 260s 'help.start()' for an HTML browser interface to help. 260s Type 'q()' to quit R. 260s 260s > ## 260s > ## Calibration with badly-scaled initial weights (bug report by Takahiro Tsuchiya) 260s > ## 260s > library(survey) 260s Loading required package: grid 260s Loading required package: Matrix 261s Loading required package: survival 261s 261s Attaching package: 'survey' 261s 261s The following object is masked from 'package:graphics': 261s 261s dotchart 261s 261s > data <- data.frame(x=c(1,1,1,1,2,2,2,2,2,2), w=rep(10,10)) 261s > des <- svydesign(ids=~1, weights=~w, data=data) 261s > des.c <- calibrate(des, ~factor(x), c(10000, 5000)) 261s > des.r <- calibrate(des, ~factor(x), c(10000, 5000), calfun='raking') 261s > stopifnot(all.equal(svytotal(~factor(x), des.c), svytotal(~factor(x), des.r))) 261s > 261s BEGIN TEST bycovmat.R 261s 261s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 261s Copyright (C) 2024 The R Foundation for Statistical Computing 261s Platform: aarch64-unknown-linux-gnu (64-bit) 261s 261s R is free software and comes with ABSOLUTELY NO WARRANTY. 261s You are welcome to redistribute it under certain conditions. 261s Type 'license()' or 'licence()' for distribution details. 261s 261s R is a collaborative project with many contributors. 261s Type 'contributors()' for more information and 261s 'citation()' on how to cite R or R packages in publications. 261s 261s Type 'demo()' for some demos, 'help()' for on-line help, or 261s 'help.start()' for an HTML browser interface to help. 261s Type 'q()' to quit R. 261s 261s > 261s > library(survey) 261s Loading required package: grid 262s Loading required package: Matrix 262s Loading required package: survival 263s 263s Attaching package: 'survey' 263s 263s The following object is masked from 'package:graphics': 263s 263s dotchart 263s 263s > data(api) 263s > options(survey.replicates.mse=TRUE) 263s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 263s > rclus1<-as.svrepdesign(dclus1) 263s > 263s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 263s + covmat=TRUE,drop.empty.groups=FALSE) 263s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 263s + covmat=TRUE,drop.empty.groups=TRUE) 263s > 263s > stopifnot(all.equal( 263s + as.vector(as.matrix(SE(a))),as.vector(sqrt(diag(vcov(a)))) 263s + )) 263s > stopifnot(all.equal( 263s + as.vector(as.matrix(SE(b))),as.vector(sqrt(diag(vcov(b)))) 263s + )) 263s > 263s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 263s > all <- svytotal(~ell+mobility+meals, dclus1) 263s > 263s > stopifnot(all(abs(vcov(svycontrast(all, 263s + list(quote(ell/mobility), 263s + quote(mobility/mobility), 263s + quote(ell/meals),quote(mobility/meals)))) 263s + -vcov(rat))<1e-10)) 263s > 263s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 263s > 263s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 263s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 263s > 263s > con<-svycontrast(all, 263s + list(quote(ell/mobility), 263s + quote(mobility/mobility), 263s + quote(ell/meals),quote(mobility/meals))) 263s > 263s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 263s > 263s > options(survey.replicates.mse=FALSE) 263s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 263s > rclus1<-as.svrepdesign(dclus1) 263s > 263s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 263s + covmat=TRUE,drop.empty.groups=FALSE) 263s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 263s + covmat=TRUE,drop.empty.groups=TRUE) 263s > 263s > stopifnot(all.equal( 263s + as.vector(as.matrix(SE(a))), as.vector(sqrt(diag(vcov(a)))) 263s + )) 263s > stopifnot(all.equal( 263s + as.vector(as.matrix(SE(b))), as.vector(sqrt(diag(vcov(b)))) 263s + )) 263s > 263s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 263s > all <- svytotal(~ell+mobility+meals, dclus1) 263s > 263s > stopifnot(all(abs(vcov(svycontrast(all, 263s + list(quote(ell/mobility), 263s + quote(mobility/mobility), 263s + quote(ell/meals),quote(mobility/meals)))) 263s + -vcov(rat))<1e-10)) 263s > 263s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 263s > 263s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 263s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 263s > 263s > con<-svycontrast(all, 263s + list(quote(ell/mobility), 263s + quote(mobility/mobility), 263s + quote(ell/meals),quote(mobility/meals))) 263s > 263s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 263s > 263s > 263s > 263s BEGIN TEST caleg.R 263s 263s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 263s Copyright (C) 2024 The R Foundation for Statistical Computing 263s Platform: aarch64-unknown-linux-gnu (64-bit) 263s 263s R is free software and comes with ABSOLUTELY NO WARRANTY. 263s You are welcome to redistribute it under certain conditions. 263s Type 'license()' or 'licence()' for distribution details. 263s 263s R is a collaborative project with many contributors. 263s Type 'contributors()' for more information and 263s 'citation()' on how to cite R or R packages in publications. 263s 263s Type 'demo()' for some demos, 'help()' for on-line help, or 263s 'help.start()' for an HTML browser interface to help. 263s Type 'q()' to quit R. 263s 263s > ## 263s > ## Calibration examples 263s > ## 263s > 263s > 263s > ## Example of calibration to first-stage clusters 263s > library(survey) 263s Loading required package: grid 263s Loading required package: Matrix 264s Loading required package: survival 264s 264s Attaching package: 'survey' 264s 264s The following object is masked from 'package:graphics': 264s 264s dotchart 264s 264s > data(api) 264s > 264s > clusters<-table(apiclus2$dnum) 264s > clusters<-clusters[clusters>1 & names(clusters)!="639"] 264s > apiclus2a<-subset(apiclus2, dnum %in% as.numeric(names(clusters))) 264s > 264s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2a) 264s > 264s > popclusters<-subset(apipop, dnum %in% as.numeric(names(clusters))) 264s > 264s > pop<-lapply(as.numeric(names(clusters)), function(cluster) { 264s + colSums(model.matrix(~api99, model.frame(~api99, subset(popclusters, dnum %in% cluster))))}) 264s > 264s > names(pop)<-names(clusters) 264s > 264s > dclus2g<-calibrate(dclus2, ~api99, pop,stage=1) 264s > 264s > svymean(~api99, dclus2) 264s mean SE 264s api99 642.14 31.434 264s > svymean(~api99, dclus2g) 264s mean SE 264s api99 654.49 29.82 264s > 264s > round(svyby(~api99, ~dnum, design=dclus2, svymean),4) 264s dnum api99 se 264s 83 83 694.3333 0.0000 264s 132 132 505.0000 0.0000 264s 152 152 574.0000 0.0000 264s 173 173 894.7500 0.0000 264s 198 198 533.7500 0.0000 264s 200 200 589.8000 6.8335 264s 228 228 477.0000 0.0000 264s 295 295 646.4000 0.0000 264s 302 302 903.5000 0.0000 264s 403 403 852.4000 0.0000 264s 452 452 533.0000 0.0000 264s 480 480 614.2000 0.0000 264s 523 523 580.5000 0.0000 264s 534 534 564.6000 0.0000 264s 549 549 896.2000 0.0000 264s 552 552 730.0000 0.0000 264s 570 570 518.4000 7.5478 264s 575 575 800.8000 4.2513 264s 596 596 785.6000 2.4155 264s 620 620 591.6000 10.5869 265s 638 638 560.2000 4.0954 265s 674 674 760.0000 0.0000 265s 679 679 610.2500 0.0000 265s 687 687 718.6667 0.0000 265s 701 701 651.5000 0.0000 265s 711 711 690.5000 0.0000 265s 731 731 702.0000 2.1744 265s 768 768 562.5000 0.0000 265s 781 781 854.4000 0.7456 265s > 265s > round(svyby(~api99, ~dnum, design=dclus2g, svymean),4) 265s dnum api99 se 265s 83 83 694.3333 0 265s 132 132 505.0000 0 265s 152 152 574.0000 0 265s 173 173 894.7500 0 265s 198 198 533.7500 0 265s 200 200 567.5455 0 265s 228 228 477.0000 0 265s 295 295 646.4000 0 265s 302 302 903.5000 0 265s 403 403 852.4000 0 265s 452 452 533.0000 0 265s 480 480 614.2000 0 265s 523 523 580.5000 0 265s 534 534 564.6000 0 265s 549 549 896.2000 0 265s 552 552 730.0000 0 265s 570 570 548.9444 0 265s 575 575 824.5357 0 265s 596 596 787.5714 0 265s 620 620 609.3750 0 265s 638 638 585.6429 0 265s 674 674 760.0000 0 265s 679 679 610.2500 0 265s 687 687 718.6667 0 265s 701 701 651.5000 0 265s 711 711 690.5000 0 265s 731 731 700.6667 0 265s 768 768 562.5000 0 265s 781 781 851.0000 0 265s > 265s > ## Averaging to first stage 265s > 265s > dclus1<- svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 265s > pop<-colSums(cbind(1,apipop$enroll),na.rm=TRUE) 265s > 265s > dclus1g<-calibrate(dclus1, ~enroll, pop, aggregate=1) 265s > 265s > svytotal(~enroll,dclus1g) 265s total SE 265s enroll 3811472 0 265s > svytotal(~api.stu,dclus1g) 265s total SE 265s api.stu 3242857 38967 265s > 265s > #variation within clusters should be zero 265s > all.equal(0, max(ave(weights(dclus1g),dclus1g$cluster,FUN=var),na.rm=TRUE)) 265s [1] TRUE 265s > 265s > ##bounded weights 265s > dclus1g<-calibrate(dclus1, ~enroll, pop) 265s > range(weights(dclus1g)/weights(dclus1)) 265s [1] 0.7906782 1.7891164 265s > dclus1gb<-calibrate(dclus1, ~enroll, pop, bounds=c(.6,1.5)) 265s > range(weights(dclus1gb)/weights(dclus1)) 265s [1] 0.7198751 1.5000000 265s > 265s > ## Ratio estimators 265s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 265s > svytotal(~api.stu,dstrat) 265s total SE 265s api.stu 3086009 99477 265s > common<-svyratio(~api.stu, ~enroll, dstrat, separate=FALSE) 265s > total.enroll<-sum(apipop$enroll,na.rm=TRUE) 265s > predict(common, total=total.enroll) 265s $total 265s enroll 265s api.stu 3190038 265s 265s $se 265s enroll 265s api.stu 29565.98 265s 265s > dstratg<-calibrate(dstrat,~enroll-1, total.enroll, variance=1) 265s > svytotal(~api.stu, dstratg) 265s total SE 265s api.stu 3190038 29566 265s > 265s > ## postStratify vs calibrate in stratified sample (Ben French) 265s > set.seed(17) 265s > dat<-data.frame(y=rep(0:1,each=100),x=rnorm(200)+2*rep(0:1,each=100), 265s + z=rbinom(200,1,.2), fpc=rep(c(100,10000),each=100)) 265s > dat$w<-ifelse(dat$y,dat$z,1-dat$z) 265s > popw<-data.frame(w=c("0","1"), Freq=c(2000,8000)) 265s > des<-svydesign(id=~1,fpc=~fpc, data=dat,strata=~y) 265s > postStratify(des,~w,popw)->dps 265s > dcal<-calibrate(des,~factor(w), pop=c(10000,8000)) 265s > 265s > all.equal(SE(svymean(~x,dcal)),SE(svymean(~x,dps))) 265s [1] TRUE 265s > 265s > ## missing data in calibrated design 265s > dps$variables$z[1]<-NA 265s > summary(svyglm(y~z+x,design=dps,family=quasibinomial)) 265s 265s Call: 265s svyglm(formula = y ~ z + x, design = dps, family = quasibinomial) 265s 265s Survey design: 265s postStratify(des, ~w, popw) 265s 265s Coefficients: 265s Estimate Std. Error t value Pr(>|t|) 265s (Intercept) -0.1203 0.3380 -0.356 0.722 265s z 6.2118 0.6451 9.630 <2e-16 *** 265s x 2.2602 0.2514 8.992 <2e-16 *** 265s --- 265s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 265s 265s (Dispersion parameter for quasibinomial family taken to be 1.919987) 265s 265s Number of Fisher Scoring iterations: 9 265s 265s > 265s > ## Ratio estimator using the heteroskedasticity parameter (Daniel Oehm) 265s > # should match the ratio estmate above 265s > dstratgh <- calibrate(dstrat,~enroll-1, total.enroll, variance=apistrat$enroll) 265s > svytotal(~api.stu, dstratgh) 265s total SE 265s api.stu 3190038 29566 265s > 265s > ## individual boundary constraints as multiplicative values (Daniel Oehm) 265s > bnds <- list( 265s + lower = c(1, 1, rep(-Inf, nrow(apistrat)-2)), 265s + upper = c(1, 1, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged the others are free to move 265s > lapply(bnds, head) 265s $lower 265s [1] 1 1 -Inf -Inf -Inf -Inf 265s 265s $upper 265s [1] 1 1 Inf Inf Inf Inf 265s 265s > dstratg1<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, variance=apistrat$enroll) 265s > svytotal(~api.stu, dstratg1) 265s total SE 265s api.stu 3190133 29561 265s > head(weights(dstrat)) 265s 1 2 3 4 5 6 265s 44.21 44.21 44.21 44.21 44.21 44.21 265s > head(weights(dstratg1)) 265s 1 2 3 4 5 6 265s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 265s > all.equal(weights(dstrat)[1:2], weights(dstratg1)[1:2]) 265s [1] TRUE 265s > 265s > ## individual boundary constraints as constant values (Daniel Oehm) 265s > bnds <- list( 265s + lower = c(44.21, 44.21, rep(-Inf, nrow(apistrat)-2)), 265s + upper = c(44.21, 44.21, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged 265s > lapply(bnds, head) 265s $lower 265s [1] 44.21 44.21 -Inf -Inf -Inf -Inf 265s 265s $upper 265s [1] 44.21 44.21 Inf Inf Inf Inf 265s 265s > dstratg2<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, bounds.const = TRUE, variance=apistrat$enroll) 265s > svytotal(~api.stu, dstratg2) 265s total SE 265s api.stu 3190133 29561 265s > head(weights(dstrat)) 265s 1 2 3 4 5 6 265s 44.21 44.21 44.21 44.21 44.21 44.21 265s > head(weights(dstratg2)) 265s 1 2 3 4 5 6 265s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 265s > all.equal(round(weights(dstrat)[1:2], 8), round(weights(dstratg2)[1:2]), 8) # minor rounding error but all good 265s [1] TRUE 265s > 265s > # sparse matrix support (Daniel Oehm) 265s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 265s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 265s > dclus1g<-calibrate(dclus1, ~stype, pop.totals) 265s > svymean(~api00, dclus1g) 265s mean SE 265s api00 642.31 23.921 265s > svytotal(~enroll, dclus1g) 265s total SE 265s enroll 3680893 406293 265s > 265s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 265s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE) 266s > svymean(~api00, dclus1g) 266s mean SE 266s api00 642.31 23.921 266s > svytotal(~enroll, dclus1g) 266s total SE 266s enroll 3680893 406293 266s > 266s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 266s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE, calfun = "raking") 266s > svymean(~api00, dclus1g) 266s mean SE 266s api00 642.31 23.921 266s > svytotal(~enroll, dclus1g) 266s total SE 266s enroll 3680893 406293 266s > 266s BEGIN TEST check.R 266s 266s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 266s Copyright (C) 2024 The R Foundation for Statistical Computing 266s Platform: aarch64-unknown-linux-gnu (64-bit) 266s 266s R is free software and comes with ABSOLUTELY NO WARRANTY. 266s You are welcome to redistribute it under certain conditions. 266s Type 'license()' or 'licence()' for distribution details. 266s 266s R is a collaborative project with many contributors. 266s Type 'contributors()' for more information and 266s 'citation()' on how to cite R or R packages in publications. 266s 266s Type 'demo()' for some demos, 'help()' for on-line help, or 266s 'help.start()' for an HTML browser interface to help. 266s Type 'q()' to quit R. 266s 266s > library(survey) 266s Loading required package: grid 266s Loading required package: Matrix 267s Loading required package: survival 267s 267s Attaching package: 'survey' 267s 267s The following object is masked from 'package:graphics': 267s 267s dotchart 267s 267s > data(fpc) 267s > ## test various possibilities for svydesign 267s > a<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 267s > a 267s Stratified Independent Sampling design (with replacement) 267s svydesign(weights = ~weight, ids = ~psuid, strata = ~stratid, 267s variables = ~x, data = fpc, nest = TRUE) 267s > svymean(~x,a) 267s mean SE 267s x 5.4481 0.7413 267s > a<-svydesign(weights=~weight, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 267s > a 267s Stratified Independent Sampling design (with replacement) 267s svydesign(weights = ~weight, ids = ~0, strata = ~stratid, variables = ~x, 267s data = fpc, nest = TRUE) 267s > svymean(~x,a) 267s mean SE 267s x 5.4481 0.7413 267s > a<-svydesign(weights=1, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 267s > a 267s Stratified Independent Sampling design (with replacement) 267s svydesign(weights = 1, ids = ~0, strata = ~stratid, variables = ~x, 267s data = fpc, nest = TRUE) 267s > svymean(~x,a) 267s mean SE 267s x 44.2 6.237 267s > a<-svydesign(ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 267s > a 267s Warning message: 267s In svydesign.default(ids = ~0, strata = ~stratid, variables = ~x, : 267s No weights or probabilities supplied, assuming equal probability 267s Warning message: 267s In svydesign.default(ids = ~psuid, strata = ~stratid, variables = ~x, : 267s No weights or probabilities supplied, assuming equal probability 267s Warning message: 267s In svydesign.default(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) : 267s No weights or probabilities supplied, assuming equal probability 267s Stratified Independent Sampling design (with replacement) 267s svydesign(ids = ~0, strata = ~stratid, variables = ~x, data = fpc, 267s nest = TRUE) 267s > svymean(~x,a) 267s mean SE 267s x 5.525 0.7796 267s > a<-svydesign(ids=~0, strata=~stratid, prob=~I(1/weight),variables=~x, data=fpc, nest=TRUE) 267s > a 267s Stratified Independent Sampling design (with replacement) 267s svydesign(ids = ~0, strata = ~stratid, prob = ~I(1/weight), variables = ~x, 267s data = fpc, nest = TRUE) 267s > svymean(~x,a) 267s mean SE 267s x 5.4481 0.7413 267s > a<-svydesign(ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 267s > a 267s Stratified Independent Sampling design (with replacement) 267s svydesign(ids = ~psuid, strata = ~stratid, variables = ~x, data = fpc, 267s nest = TRUE) 267s > svymean(~x,a) 267s mean SE 267s x 5.525 0.7796 267s > a<-svydesign(ids=~psuid, variables=~x, data=fpc, nest=TRUE) 267s > a 267s 1 - level Cluster Sampling design (with replacement) 267s With (5) clusters. 267s svydesign(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) 267s > svymean(~x,a) 267s mean SE 267s x 5.525 0.838 267s > a<-svydesign(ids=~psuid, weights=~weight, variables=~x, data=fpc, nest=TRUE) 267s > a 267s 1 - level Cluster Sampling design (with replacement) 267s With (5) clusters. 267s svydesign(ids = ~psuid, weights = ~weight, variables = ~x, data = fpc, 267s nest = TRUE) 267s > svymean(~x,a) 267s mean SE 267s x 5.4481 0.7938 267s > a<-svydesign(ids=~stratid+psuid, weights=~weight, variables=~x, data=fpc) 267s > a 267s 2 - level Cluster Sampling design (with replacement) 267s With (2, 8) clusters. 267s svydesign(ids = ~stratid + psuid, weights = ~weight, variables = ~x, 267s data = fpc) 267s > svymean(~x,a) 267s meanWarning message: 267s In svydesign.default(ids = ~stratid + psuid, variables = ~x, data = fpc) : 267s No weights or probabilities supplied, assuming equal probability 267s SE 267s x 5.4481 0.5465 267s > a<-svydesign(ids=~stratid+psuid, variables=~x, data=fpc) 267s > a 267s 2 - level Cluster Sampling design (with replacement) 267s With (2, 8) clusters. 267s svydesign(ids = ~stratid + psuid, variables = ~x, data = fpc) 267s > svymean(~x,a) 267s mean SE 267s x 5.525 0.5188 267s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,"x",drop=FALSE], nest=TRUE) 267s > a 267s Stratified Independent Sampling design (with replacement) 267s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 267s variables = fpc[, "x", drop = FALSE], nest = TRUE) 267s > svymean(~x,a) 267s mean SE 267s x 5.4481 0.7413 267s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,4:6], nest=TRUE) 267s > a 267s Stratified Independent Sampling design (with replacement) 267s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 267s variables = fpc[, 4:6], nest = TRUE) 267s > svymean(~x,a) 267s mean SE 267s x 5.4481 0.7413 267s > 267s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, variables=fpc[,4:6], fpc=rep(27,8)) 267s > a 267s 1 - level Cluster Sampling design 267s With (5) clusters. 267s svydesign(weights = fpc$weight, ids = fpc$psuid, variables = fpc[, 267s 4:6], fpc = rep(27, 8)) 267s > svymean(~x,a) 267s mean SE 267s x 5.4481 0.7165 267s > 267s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, nest=TRUE, variables=fpc[,4:6], fpc=fpc$Nh) 267s > a 267s Stratified Independent Sampling design 267s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 267s nest = TRUE, variables = fpc[, 4:6], fpc = fpc$Nh) 267s > svymean(~x,a) 267s mean SE 267s x 5.4481 0.616 267s > 267s BEGIN TEST contrast-replicates.R 267s 267s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 267s Copyright (C) 2024 The R Foundation for Statistical Computing 267s Platform: aarch64-unknown-linux-gnu (64-bit) 267s 267s R is free software and comes with ABSOLUTELY NO WARRANTY. 267s You are welcome to redistribute it under certain conditions. 267s Type 'license()' or 'licence()' for distribution details. 267s 267s R is a collaborative project with many contributors. 267s Type 'contributors()' for more information and 267s 'citation()' on how to cite R or R packages in publications. 267s 267s Type 'demo()' for some demos, 'help()' for on-line help, or 267s 'help.start()' for an HTML browser interface to help. 267s Type 'q()' to quit R. 267s 267s > ## test use of replicates in svyby, svycontrast 267s > library(survey) 267s Loading required package: grid 268s Loading required package: Matrix 268s Loading required package: survival 269s 269s Attaching package: 'survey' 269s 269s The following object is masked from 'package:graphics': 269s 269s dotchart 269s 269s > 269s > data(api) 269s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 269s > rclus1<-as.svrepdesign(dclus1) 269s > 269s > meanlogs_without<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE) 269s > c_without<-svycontrast(meanlogs_without, quote(exp(E-H))) 269s > vcov(c_without) 269s contrast 269s contrast 0.06862947 269s > 269s > meanlogs_with<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE,return.replicates=TRUE) 269s > 269s > c_with<-svycontrast(meanlogs_with, quote(exp(E-H))) 269s > 269s > v_with<- vcov(rclus1, c_with$replicates) 269s > 269s > r<- attr(meanlogs_with, "replicates") 269s > vr_with<-vcov(rclus1,exp(r[,1]-r[,2])) 269s > 269s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vr_with))) 269s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vcov(c_with)))) 269s > 269s BEGIN TEST coxph-termtest.R 269s 269s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 269s Copyright (C) 2024 The R Foundation for Statistical Computing 269s Platform: aarch64-unknown-linux-gnu (64-bit) 269s 269s R is free software and comes with ABSOLUTELY NO WARRANTY. 269s You are welcome to redistribute it under certain conditions. 269s Type 'license()' or 'licence()' for distribution details. 269s 269s R is a collaborative project with many contributors. 269s Type 'contributors()' for more information and 269s 'citation()' on how to cite R or R packages in publications. 269s 269s Type 'demo()' for some demos, 'help()' for on-line help, or 269s 'help.start()' for an HTML browser interface to help. 269s Type 'q()' to quit R. 269s 269s > library(survey) 269s Loading required package: grid 269s Loading required package: Matrix 270s Loading required package: survival 270s 270s Attaching package: 'survey' 270s 270s > library(survival) 270s > set.seed(2021-6-25) 270s > test1 <- list(time=c(4,3,1,1,2,2,3), 270s + status=c(1,1,1,0,1,1,0), 270s + x1=as.factor(rbinom(7, 2, 0.5)), 270s + x=c(0,2,1,1,1,0,0)) 270s > # Fit a stratified model 270s The following object is masked from 'package:graphics': 270s 270s dotchart 270s 270s > mod_c <- coxph(Surv(time, status) ~ x1 + x, test1) 270s > mod_d <- coxph(Surv(time, status) ~ x + x1, test1) 270s > stopifnot(all.equal(regTermTest(mod_c, ~x1, df = Inf)[c("chisq","df","test.terms","p")], 270s + regTermTest(mod_d, ~x1, df = Inf)[c("chisq","df","test.terms","p")])) 270s > 270s > data(pbc, package="survival") 270s > 270s > pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 270s > biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 270s > pbc$randprob<-fitted(biasmodel) 270s > if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 270s > 270s > dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 270s > library(splines) 270s > model<-svycoxph(formula = Surv(time, status > 0) ~ bili + protime + albumin+ns(bili,4)[,1:3], design = dpbc) 270s > test<-regTermTest(model, ~ns(bili,4)[,1:3],method="LRT") 270s > stopifnot(all.equal(test$chisq, 47.314, tolerance=1e-4)) 270s > stopifnot(all.equal(test$lambda, c(1.4764260, 1.0109836, 0.6923415),tolerance=1e-4)) 270s > 270s BEGIN TEST deff.R 270s 270s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 270s Copyright (C) 2024 The R Foundation for Statistical Computing 270s Platform: aarch64-unknown-linux-gnu (64-bit) 270s 270s R is free software and comes with ABSOLUTELY NO WARRANTY. 270s You are welcome to redistribute it under certain conditions. 270s Type 'license()' or 'licence()' for distribution details. 270s 270s R is a collaborative project with many contributors. 270s Type 'contributors()' for more information and 270s 'citation()' on how to cite R or R packages in publications. 270s 270s Type 'demo()' for some demos, 'help()' for on-line help, or 270s 'help.start()' for an HTML browser interface to help. 270s Type 'q()' to quit R. 270s 270s > ## from Takahiro Tsuchiya 270s > library(survey) 270s Loading required package: grid 270s Loading required package: Matrix 271s Loading required package: survival 271s 271s Attaching package: 'survey' 271s 271s The following object is masked from 'package:graphics': 271s 271s dotchart 271s 271s > kigyo<-read.table(tmp<-textConnection(" obs uriage srs.w pps.w 271s + 1 1 15 100 20 271s + 2 2 143 100 200 271s + 3 3 21 100 11 271s + 4 4 51 100 25 271s + 5 5 337 100 550 271s + 6 6 50 100 30 271s + 7 7 274 100 250 271s + 8 8 145 100 100 271s + 9 9 15 100 10 271s + 10 10 86 100 55 271s + ",open="r"),header=TRUE) 271s > close(tmp) 271s > des.srs <- svydesign(ids=~1, weights=~srs.w, data=kigyo) 271s > (res.srs <- svymean(~uriage, des.srs, deff=TRUE)) 271s mean SE DEff 271s uriage 113.700 35.626 1.0101 271s > (SE(res.srs)^2) / ((1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 271s uriage 271s uriage 1.010101 271s > 271s > (tres.srs <- svytotal(~uriage, des.srs, deff=TRUE)) 271s total SE DEff 271s uriage 113700 35626 1.0101 271s > (SE(tres.srs)^2) / (1000^2 * (1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 271s uriage 271s uriage 1.010101 271s > 271s > 271s > des.pps <- svydesign(ids=~1, weights=~pps.w, data=kigyo) 271s > (res.pps <- svymean(~uriage, des.pps, deff='replace')) 271s mean SE DEff 271s uriage 243.914 48.752 1.9741 271s > (SE(res.pps)^2) / (coef(svyvar(~uriage, des.pps)) / 10) 271s uriage 271s uriage 1.974067 271s > (tres.pps <- svytotal(~uriage, des.pps, deff='replace')) 271s total SE DEff 271s uriage 305136 184965 18.157 271s > (N.hat <- sum(weights(des.pps))) 271s [1] 1251 271s > (SE(tres.pps)^2) / (N.hat^2 * coef(svyvar(~uriage, des.pps)) / 10) 271s uriage 271s uriage 18.15669 271s > 271s BEGIN TEST defftest.R 271s 271s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 271s Copyright (C) 2024 The R Foundation for Statistical Computing 271s Platform: aarch64-unknown-linux-gnu (64-bit) 271s 271s R is free software and comes with ABSOLUTELY NO WARRANTY. 271s You are welcome to redistribute it under certain conditions. 271s Type 'license()' or 'licence()' for distribution details. 271s 271s R is a collaborative project with many contributors. 271s Type 'contributors()' for more information and 271s 'citation()' on how to cite R or R packages in publications. 271s 271s Type 'demo()' for some demos, 'help()' for on-line help, or 271s 'help.start()' for an HTML browser interface to help. 271s Type 'q()' to quit R. 271s 271s > library(survey) 271s Loading required package: grid 271s Loading required package: Matrix 272s Loading required package: survival 272s 272s Attaching package: 'survey' 272s 272s > 272s > data(api) 272s The following object is masked from 'package:graphics': 272s 272s dotchart 272s 272s > 272s > ## one-stage cluster sample 272s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 272s > 272s > # svyglm model 272s > mod <- svyglm(api99 ~ enroll + api.stu, design = dclus1, deff = TRUE) 273s > 273s > #deffs returned from svyglm model - implausibly high 273s > deff(mod) 273s (Intercept) enroll api.stu 273s 1.919945 2.500983 2.686102 273s > #> (Intercept) enroll api.stu 273s > #> 351.3500 457.6799 491.5567 273s > 273s > # run mod with same data and glm() 273s > srs_mod <- glm(api99 ~ enroll + api.stu, data = apiclus1) 273s > 273s > # manually calculate deffs 273s > 273s > clust_se <- summary(mod)$coefficients[,2] 273s > srs_se <- summary(srs_mod)$coefficients[,2] 273s > 273s > deffs <- clust_se^2 / srs_se^2 273s > stopifnot(all.equal(deffs, deff(mod))) 273s > 273s > 273s BEGIN TEST domain.R 273s 273s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 273s Copyright (C) 2024 The R Foundation for Statistical Computing 273s Platform: aarch64-unknown-linux-gnu (64-bit) 273s 273s R is free software and comes with ABSOLUTELY NO WARRANTY. 273s You are welcome to redistribute it under certain conditions. 273s Type 'license()' or 'licence()' for distribution details. 273s 273s R is a collaborative project with many contributors. 273s Type 'contributors()' for more information and 273s 'citation()' on how to cite R or R packages in publications. 273s 273s Type 'demo()' for some demos, 'help()' for on-line help, or 273s 'help.start()' for an HTML browser interface to help. 273s Type 'q()' to quit R. 273s 273s > ## 273s > ## Domain means can be written as ratio estimators or as regression coefficients 273s > ## 273s > ## This code checks that subsetting the design object gives the same results as 273s > ## these approaches. 273s > ## 273s > 273s > 273s > library(survey) 273s Loading required package: grid 273s Loading required package: Matrix 274s Loading required package: survival 274s 274s Attaching package: 'survey' 274s 274s The following object is masked from 'package:graphics': 274s 274s dotchart 274s 274s > data(fpc) 274s > dfpc<-svydesign(id=~psuid,strat=~stratid,weight=~weight,data=fpc,nest=TRUE) 274s > dsub<-subset(dfpc,x>4) 274s > (m1<-svymean(~x,design=dsub)) 274s mean SE 274s x 6.195 0.7555 274s > 274s > ## These should give the same domain estimates and standard errors 274s > (m2<-svyby(~x,~I(x>4),design=dfpc, svymean,keep.var=TRUE)) 274s I(x > 4) x se 274s FALSE FALSE 3.314286 0.3117042 274s TRUE TRUE 6.195000 0.7555129 274s > m3<-svyglm(x~I(x>4)+0,design=dfpc) 274s > summary(m3) 274s 274s Call: 274s svyglm(formula = x ~ I(x > 4) + 0, design = dfpc) 274s 274s Survey design: 274s svydesign(id = ~psuid, strat = ~stratid, weight = ~weight, data = fpc, 274s nest = TRUE) 274s 274s Coefficients: 274s Estimate Std. Error t value Pr(>|t|) 274s I(x > 4)FALSE 3.3143 0.3117 10.63 0.000127 *** 274s I(x > 4)TRUE 6.1950 0.7555 8.20 0.000439 *** 274s --- 274s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 274s 274s (Dispersion parameter for gaussian family taken to be 2.557379) 274s 274s Number of Fisher Scoring iterations: 2 274s 274s > (m4<-svyratio(~I(x*(x>4)),~as.numeric(x>4), dfpc)) 274s Ratio estimator: svyratio.survey.design2(~I(x * (x > 4)), ~as.numeric(x > 4), 274s dfpc) 274s Ratios= 274s as.numeric(x > 4) 274s I(x * (x > 4)) 6.195 274s SEs= 274s as.numeric(x > 4) 274s I(x * (x > 4)) 0.7555129 274s > stopifnot(isTRUE(all.equal(SE(m2), as.vector(SE(m3))))) 274s > stopifnot(isTRUE(all.equal(SE(m2)[2], as.vector(SE(m4))))) 274s > 274s > ## with strata 274s > data(api) 274s > dstrat<-svydesign(id=~1, strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 274s > m1<-svymean(~enroll, subset(dstrat, comp.imp=="Yes")) 274s > m2<-svyglm(enroll~comp.imp-1, dstrat) 274s > m3<- svyratio(~I(enroll*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dstrat) 274s > stopifnot(isTRUE(all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 274s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 274s > 274s > ## with calibration 274s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 274s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 274s > (dclus1g3 <- calibrate(dclus1, ~stype+api99, c(pop.totals, api99=3914069))) 274s 1 - level Cluster Sampling design 274s With (15) clusters. 274s calibrate(dclus1, ~stype + api99, c(pop.totals, api99 = 3914069)) 274s > 274s > m1<-svymean(~api00, subset(dclus1g3, comp.imp=="Yes")) 274s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1g3) 274s > m2<-svyglm(api00~comp.imp-1, dclus1g3) 274s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 274s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 274s > 274s > ## with raking 274s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 274s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 274s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 274s > m1<-svymean(~api00, subset(dclus1r, comp.imp=="Yes")) 274s > m2<-svyglm(api00~comp.imp-1, dclus1r) 274s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1r) 274s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 274s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 274s > 274s > 274s > 274s > ## 274s > ## based on bug report from Takahiro Tsuchiya for version 3.4 274s > ## 274s > rei<-read.table(tmp<-textConnection( 274s + " id N n.a h n.ah n.h sub y 274s + 1 1 300 20 1 12 5 TRUE 1 274s + 2 2 300 20 1 12 5 TRUE 2 274s + 3 3 300 20 1 12 5 TRUE 3 274s + 4 4 300 20 1 12 5 TRUE 4 274s + 5 5 300 20 1 12 5 TRUE 5 274s + 6 6 300 20 1 12 5 FALSE NA 274s + 7 7 300 20 1 12 5 FALSE NA 274s + 8 8 300 20 1 12 5 FALSE NA 274s + 9 9 300 20 1 12 5 FALSE NA 274s + 10 10 300 20 1 12 5 FALSE NA 274s + 11 11 300 20 1 12 5 FALSE NA 274s + 12 12 300 20 1 12 5 FALSE NA 274s + 13 13 300 20 2 8 3 TRUE 6 274s + 14 14 300 20 2 8 3 TRUE 7 274s + 15 15 300 20 2 8 3 TRUE 8 274s + 16 16 300 20 2 8 3 FALSE NA 274s + 17 17 300 20 2 8 3 FALSE NA 274s + 18 18 300 20 2 8 3 FALSE NA 274s + 19 19 300 20 2 8 3 FALSE NA 274s + 20 20 300 20 2 8 3 FALSE NA 274s + "), header=TRUE) 274s > close(tmp) 274s > 274s > 274s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 274s + fpc=list(~N,NULL), subset=~sub, data=rei, method="full") 274s > tot2<- svytotal(~y, subset(des.rei2, y>3)) 274s > 274s > rei$y<-rei$y*(rei$y>3) 274s > ## based on Sarndal et al (9.4.14) 274s > rei$w.ah <- rei$n.ah / rei$n.a 274s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 274s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 274s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 274s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h)) 274s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 274s > 274s > a.rei$f.h<-with(a.rei, n.h/n.ah) 274s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 274s > 274s > a.rei$f<-with(a.rei, n.a/N) 274s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 274s > 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))) 274s > 274s > V 274s [1] 70761.47 274s > Vphase1 274s [1] 44325.47 274s > Vphase2 274s [1] 26436 274s > vcov(tot2) 274s [,1] 274s [1,] 70761.47 274s attr(,"phases") 274s attr(,"phases")$phase1 274s [,1] 274s [1,] 44325.47 274s 274s attr(,"phases")$phase2 274s [,1] 274s [1,] 26436 274s 274s > 274s > ## comparing to regression 274s > reg<-svyglm(y~I(y<4), design=des.rei2) 274s > mn<-svymean(~y, subset(des.rei2,y>3)) 274s > all.equal(as.vector(coef(reg))[1],as.vector(coef(mn))) 274s [1] TRUE 274s > all.equal(as.vector(SE(reg))[1],as.vector(SE(mn))) 274s [1] TRUE 274s > vcov(mn) 274s [,1] 274s [1,] 0.3292258 274s attr(,"phases") 274s attr(,"phases")$phase1 274s [,1] 274s [1,] 0.1599264 274s 274s attr(,"phases")$phase2 274s [,1] 274s [1,] 0.1692994 274s 274s > vcov(reg) 274s (Intercept) I(y < 4)TRUE 274s (Intercept) 0.3292258 -0.3292258 274s I(y < 4)TRUE -0.3292258 0.5901907 274s attr(,"phases") 274s attr(,"phases")$phase1 274s (Intercept) I(y < 4)TRUE 274s (Intercept) 0.1599264 -0.1599264 274s I(y < 4)TRUE -0.1599264 0.2588542 274s 274s attr(,"phases")$phase2 274s (Intercept) I(y < 4)TRUE 274s (Intercept) 0.1692994 -0.1692994 274s I(y < 4)TRUE -0.1692994 0.3313365 274s 274s > 274s > 274s BEGIN TEST fpc.R 274s 274s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 274s Copyright (C) 2024 The R Foundation for Statistical Computing 274s Platform: aarch64-unknown-linux-gnu (64-bit) 274s 274s R is free software and comes with ABSOLUTELY NO WARRANTY. 274s You are welcome to redistribute it under certain conditions. 274s Type 'license()' or 'licence()' for distribution details. 274s 274s R is a collaborative project with many contributors. 274s Type 'contributors()' for more information and 274s 'citation()' on how to cite R or R packages in publications. 274s 274s Type 'demo()' for some demos, 'help()' for on-line help, or 274s 'help.start()' for an HTML browser interface to help. 274s Type 'q()' to quit R. 274s 274s > library(survey) 274s Loading required package: grid 274s Loading required package: Matrix 275s Loading required package: survival 275s 275s Attaching package: 'survey' 275s 275s The following object is masked from 'package:graphics': 275s 275s dotchart 275s 275s > ## check many permutations of fpc specification 275s > example(fpc) 275s 275s fpc> data(fpc) 275s 275s fpc> fpc 275s stratid psuid weight nh Nh x 275s 1 1 1 3 5 15 2.8 275s 2 1 2 3 5 15 4.1 275s 3 1 3 3 5 15 6.8 275s 4 1 4 3 5 15 6.8 275s 5 1 5 3 5 15 9.2 275s 6 2 1 4 3 12 3.7 275s 7 2 2 4 3 12 6.6 275s 8 2 3 4 3 12 4.2 275s 275s fpc> withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 275s fpc+ data=fpc, nest=TRUE) 275s 275s fpc> withoutfpc 275s Stratified Independent Sampling design (with replacement) 275s withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 275s data=fpc, nest=TRUE) 275s 275s fpc> svymean(~x, withoutfpc) 275s mean SE 275s x 5.4481 0.7413 275s 275s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 275s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 275s 275s fpc> withfpc 275s Stratified Independent Sampling design 275s withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 275s fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 275s 275s fpc> svymean(~x, withfpc) 275s mean SE 275s x 5.4481 0.616 275s 275s fpc> ## Other equivalent forms 275s fpc> withfpc<-svydesign(prob=~I(1/weight), ids=~psuid, strata=~stratid, 275s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 275s 275s fpc> svymean(~x, withfpc) 275s mean SE 275s x 5.4481 0.616 275s 275s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 275s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 275s 275s fpc> svymean(~x, withfpc) 275s mean SE 275s x 5.4481 0.616 275s 275s fpc> withfpc<-svydesign(weights=~weight, ids=~interaction(stratid,psuid), 275s fpc+ strata=~stratid, fpc=~I(nh/Nh), variables=~x, data=fpc) 275s 275s fpc> svymean(~x, withfpc) 275s mean SE 275s x 5.4481 0.616 275s 275s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, fpc=~Nh, 275s fpc+ variables=~x,data=fpc,nest=TRUE) 275s 275s fpc> svymean(~x, withfpc) 275s mean SE 275s x 5.4481 0.616 275s 275s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, 275s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 275s 275s fpc> svymean(~x, withfpc) 275s mean SE 275s x 5.4481 0.616 275s > 275s > 276s BEGIN TEST glm-scoping.R 276s 276s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 276s Copyright (C) 2024 The R Foundation for Statistical Computing 276s Platform: aarch64-unknown-linux-gnu (64-bit) 276s 276s R is free software and comes with ABSOLUTELY NO WARRANTY. 276s You are welcome to redistribute it under certain conditions. 276s Type 'license()' or 'licence()' for distribution details. 276s 276s R is a collaborative project with many contributors. 276s Type 'contributors()' for more information and 276s 'citation()' on how to cite R or R packages in publications. 276s 276s Type 'demo()' for some demos, 'help()' for on-line help, or 276s 'help.start()' for an HTML browser interface to help. 276s Type 'q()' to quit R. 276s 276s > ## bug report from Thomas Leeper, fixed in version 3.32-3 276s > 276s > library("survey") 276s Loading required package: grid 276s Loading required package: Matrix 277s Loading required package: survival 277s 277s Attaching package: 'survey' 277s 277s The following object is masked from 'package:graphics': 277s 277s dotchart 277s 277s > data(api) 277s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 277s > 277s > # pass `family` directly (WORKS!) 277s > svyglm(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 277s Stratified Independent Sampling design 277s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 277s fpc = ~fpc) 277s 277s Call: svyglm(formula = api00 ~ ell + meals + mobility, design = dstrat, 277s family = gaussian()) 277s 277s Coefficients: 277s (Intercept) ell meals mobility 277s 820.8873 -0.4806 -3.1415 0.2257 277s 277s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 277s Null Deviance: 3023000 277s Residual Deviance: 1029000 AIC: 2308 277s > 277s > # passing `family` via ... (WORKS!) 277s > myfun1 <- function(formula, design, ...) { 277s + svyglm(formula, design = design, ...) 277s + } 277s > myfun1(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 277s Stratified Independent Sampling design 277s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 277s fpc = ~fpc) 277s 277s Call: svyglm(formula = formula, design = design, family = ..1) 277s 277s Coefficients: 277s (Intercept) ell meals mobility 277s 820.8873 -0.4806 -3.1415 0.2257 277s 277s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 277s Null Deviance: 3023000 277s Residual Deviance: 1029000 AIC: 2308 277s > 277s > # passing `family` via default argument (DOES NOT WORK!) 277s > myfun2 <- function(formula, design, family = gaussian()) { 277s + svyglm(formula, design = design, family = family) 277s + } 277s > myfun2(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 277s Stratified Independent Sampling design 277s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 277s fpc = ~fpc) 277s 277s Call: svyglm(formula = formula, design = design, family = family) 277s 277s Coefficients: 277s (Intercept) ell meals mobility 277s 820.8873 -0.4806 -3.1415 0.2257 277s 277s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 277s Null Deviance: 3023000 277s Residual Deviance: 1029000 AIC: 2308 277s > 277s BEGIN TEST kalton.R 277s 277s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 277s Copyright (C) 2024 The R Foundation for Statistical Computing 277s Platform: aarch64-unknown-linux-gnu (64-bit) 277s 277s R is free software and comes with ABSOLUTELY NO WARRANTY. 277s You are welcome to redistribute it under certain conditions. 277s Type 'license()' or 'licence()' for distribution details. 277s 277s R is a collaborative project with many contributors. 277s Type 'contributors()' for more information and 277s 'citation()' on how to cite R or R packages in publications. 277s 277s Type 'demo()' for some demos, 'help()' for on-line help, or 277s 'help.start()' for an HTML browser interface to help. 277s Type 'q()' to quit R. 277s 277s > library(survey) 277s Loading required package: grid 277s Loading required package: Matrix 278s Loading required package: survival 278s 278s Attaching package: 'survey' 278s 278s The following object is masked from 'package:graphics': 278s 278s dotchart 278s 278s > 278s > ab<-expand.grid(a=factor(1:4),b=factor(1:3)) 278s > 278s > kaltonsample<-ab[rep(1:12,c(20,50,100,30,40,140,50,100,40,310,50,70)),] 278s > 278s > kaltonpop<-ab[rep(1:12,c(80,60,170,55,40,150,60,165,55,340,200,125)),] 278s > 278s > jointpop<-colSums(model.matrix(~a*b,kaltonpop)) 278s > marginalpop<-colSums(model.matrix(~a+b,kaltonpop)) 278s > gregpop<-colSums(model.matrix(~as.numeric(a)+as.numeric(b),kaltonpop)) 278s > 278s > dkalton<-svydesign(id=~1,data=kaltonsample) 278s Warning message: 278s In svydesign.default(id = ~1, data = kaltonsample) : 278s No weights or probabilities supplied, assuming equal probability 278s > 278s > dps<-postStratify(dkalton,~a+b,xtabs(~a+b,kaltonpop)) 278s > 278s > drake<-rake(dkalton, list(~a,~b),list(xtabs(~a,kaltonpop),xtabs(~b,kaltonpop)),control=list(epsilon=0.0001)) 278s > 278s > dcalps<-calibrate(dkalton, ~a*b, jointpop) 278s > dcalrake<-calibrate(dkalton,~a+b, marginalpop, calfun="raking") 278s > dlinear<-calibrate(dkalton, ~a+b, marginalpop) 278s > 278s > dtrunclinear<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2)) 278s > 278s > dlogit<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2),calfun="logit") 278s > 278s > dgreg<-calibrate(dkalton,~as.numeric(a)+as.numeric(b), gregpop) 278s > 278s > 278s > #table A 278s > round(svytable(~a+b,dps)/xtabs(~a+b,kaltonsample),2) 278s b 278s a 1 2 3 278s 1 4.00 1.00 1.38 278s 2 1.20 1.07 1.10 278s 3 1.70 1.20 4.00 278s 4 1.83 1.65 1.79 278s > round(svytable(~a+b,dcalps)/xtabs(~a+b,kaltonsample),2) 278s b 278s a 1 2 3 278s 1 4.00 1.00 1.37 278s 2 1.20 1.07 1.10 278s 3 1.70 1.20 4.00 278s 4 1.83 1.65 1.79 278s > 278s > #table B 278s > round(svytable(~a+b,drake)/xtabs(~a+b,kaltonsample),2) 278s b 278s a 1 2 3 278s 1 1.81 1.45 2.02 278s 2 1.08 0.87 1.21 278s 3 2.20 1.76 2.45 278s 4 1.83 1.47 2.04 278s > round(svytable(~a+b,dcalrake)/xtabs(~a+b,kaltonsample),2) 278s b 278s a 1 2 3 278s 1 1.81 1.45 2.02 278s 2 1.08 0.87 1.21 278s 3 2.20 1.76 2.45 278s 4 1.83 1.47 2.04 278s > 278s > #table C 278s > round(svytable(~a+b,dlinear)/xtabs(~a+b,kaltonsample),2) 278s b 278s a 1 2 3 278s 1 1.82 1.50 1.97 278s 2 1.09 0.78 1.24 278s 3 2.19 1.88 2.34 278s 4 1.83 1.52 1.98 278s > 278s > #table D 278s > round(svytable(~a+b,dgreg)/xtabs(~a+b,kaltonsample),2) 278s b 278s a 1 2 3 278s 1 1.21 1.17 1.14 278s 2 1.43 1.40 1.36 278s 3 1.66 1.62 1.59 278s 4 1.88 1.85 1.81 278s > 278s > #table G 278s > round(svytable(~a+b,dlogit)/xtabs(~a+b,kaltonsample),2) 278s b 278s a 1 2 3 278s 1 1.87 1.46 1.98 278s 2 1.08 0.74 1.27 278s 3 2.17 2.09 2.18 278s 4 1.89 1.49 1.99 278s > 278s > #table G 278s > round(svytable(~a+b,dtrunclinear)/xtabs(~a+b,kaltonsample),2) 278s b 278s a 1 2 3 278s 1 1.81 1.48 1.99 278s 2 1.08 0.75 1.26 278s 3 2.20 2.00 2.20 278s 4 1.83 1.50 2.00 278s > 278s BEGIN TEST logranktest.R 278s 278s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 278s Copyright (C) 2024 The R Foundation for Statistical Computing 278s Platform: aarch64-unknown-linux-gnu (64-bit) 278s 278s R is free software and comes with ABSOLUTELY NO WARRANTY. 278s You are welcome to redistribute it under certain conditions. 278s Type 'license()' or 'licence()' for distribution details. 278s 278s R is a collaborative project with many contributors. 278s Type 'contributors()' for more information and 278s 'citation()' on how to cite R or R packages in publications. 278s 278s Type 'demo()' for some demos, 'help()' for on-line help, or 278s 'help.start()' for an HTML browser interface to help. 278s Type 'q()' to quit R. 278s 278s > ## StackOverflow 63333282 278s > 278s > library(survey) 278s Loading required package: grid 278s Loading required package: Matrix 279s Loading required package: survival 279s > D = data.frame(unique_id = 1:135, 279s + 279s + weights = rep(1,135), 279s + 279s + 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 , 279s + 279s + 6.53631154, 6.31914568, 7.00146597, 9.67616088, 7.94212358, 9.70693890, 10.67575835, 10.06764688, 12.29175616, 13.60092871, 13.12508566, 14.66417522, 279s + 279s + 15.35250691, 0.93368707, 0.19087611, 3.15533767, 4.40821633, 17.54334957, 17.95177642, 15.50903946, 16.48376185, 20.87956697, 21.24571398, 22.34297263, 279s + 279s + 23.36042629, 21.01760215, 23.84785038, 26.06105822, 4.16866350, 1.96922485, 0.66199008, 6.76987830, 1.55617685, 0.19095871, 3.13291784, 5.43159409, 279s + 279s + 9.55805671, 4.31437322, 0.78259860, 5.26415156, 3.45095686, 1.69128712, 8.41942426, 3.33748695, 6.08516173, 2.72897404, 0.22789783, 0.86348009, 279s 279s Attaching package: 'survey' 279s 279s The following object is masked from 'package:graphics': 279s 279s dotchart 279s 280s + 280s + 2.35707587, 2.97477615, 12.33273800, 0.58532123, 0.14586238, 10.67948547, 4.07655972, 3.94405136, 0.37226898, 1.42558725, 1.47680658, 4.22506540, 280s + 280s + 1.56703478, 8.37484756, 12.54015087, 1.80994787, 3.66453633, 1.02834532, 1.99065652, 1.23577436, 16.21981618, 14.35039798, 4.15321606, 2.79740679, 280s + 280s + 0.35538726, 7.46823358, 1.66329088, 7.46525382, 2.62734831, 3.19057957, 0.33317193, 0.09122886, 9.14616245, 2.48542578, 2.37569263, 5.48499630, 280s + 280s + 2.22749399, 2.64816296, 0.97101545, 1.42468625, 1.27668904, 0.03692447, 1.98783210, 5.47692729, 3.88316178, 0.32921277, 1.77225345, 9.33268901, 280s + 280s + 2.44517775, 1.49813702, 2.56059172, 3.43194832, 1.22955630, 3.56263947, 9.07060099, 3.58312362, 2.22755370, 4.24783776, 3.46364804, 1.61671354, 280s + 280s + 11.10973565, 7.18764270, 1.80400046, 6.39833474, 6.72825192, 6.46063344, 5.76855531, 5.27157807, 4.66154734, 3.50019718, 2.27156678, 3.28531594, 280s + 280s + 2.35699896, 2.94956000, 8.85381736), 280s + 280s + 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, 280s + 280s + 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, 280s + 280s + 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), 280s + 280s + group = c(rep("group1", 40), rep("group2", 95))) 280s > 280s > 280s > 280s > svykm_formula = as.formula("Surv(event_time, event_flag) ~ group") 280s > 280s > svy_design = svydesign( ids = ~unique_id , weights = ~weights, data = D ) 280s > 280s > a<-svylogrank(formula = svykm_formula, design = svy_design) 280s > 280s > ii<-with(D, order(event_time, event_flag)) 280s > 280s > svy_design2 = svydesign( ids = ~unique_id , weights = ~weights, data = D[ii,] ) 280s > 280s > b<-svylogrank(formula = svykm_formula, design = svy_design2) 280s > d<-svylogrank(formula = svykm_formula, design = svy_design, method = "large") 280s > 280s > f<- svylogrank(formula = svykm_formula, design = svy_design, method = "score") 280s > 280s > 280s > stopifnot(all.equal(a[[2]],b[[2]])) 280s > 280s > stopifnot(all.equal(a[[2]],d[[2]])) 280s > 280s > stopifnot(all.equal(a[[2]],f[-1])) 280s > 280s > 280s BEGIN TEST lonely.psu.R 280s 280s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 280s Copyright (C) 2024 The R Foundation for Statistical Computing 280s Platform: aarch64-unknown-linux-gnu (64-bit) 280s 280s R is free software and comes with ABSOLUTELY NO WARRANTY. 280s You are welcome to redistribute it under certain conditions. 280s Type 'license()' or 'licence()' for distribution details. 280s 280s R is a collaborative project with many contributors. 280s Type 'contributors()' for more information and 280s 'citation()' on how to cite R or R packages in publications. 280s 280s Type 'demo()' for some demos, 'help()' for on-line help, or 280s 'help.start()' for an HTML browser interface to help. 280s Type 'q()' to quit R. 280s 280s > 280s > ## lonely PSUs by design 280s > library(survey) 280s Loading required package: grid 280s Loading required package: Matrix 281s Loading required package: survival 281s 281s Attaching package: 'survey' 281s 281s The following object is masked from 'package:graphics': 281s 281s dotchart 281s 281s > data(api) 281s > ## not certainty PSUs by fpc 281s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 281s > summary(ds) 281s Stratified Independent Sampling design (with replacement) 281s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 281s Probabilities: 281s Min. 1st Qu. Median Mean 3rd Qu. Max. 281s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 281s Stratum Sizes: 281s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 281s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 281s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 281s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 281s Data variables: 281s [1] "cds" "stype" "name" "sname" "snum" "dname" 281s Error in onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1], : 281s Stratum (413) has only one PSU at stage 1 281s Error in jknweights(design$strata[, 1], design$cluster[, 1], fpc = fpc, : 281s Stratum413has only one PSU 281s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 281s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 281s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 281s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 281s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 281s [37] "api.stu" "fpc" "pw" 281s > 281s > options(survey.lonely.psu="fail") 281s > try(svymean(~api00,ds)) 281s > try(svymean(~api00, as.svrepdesign(ds))) 281s > options(survey.lonely.psu="remove") 281s > svymean(~api00,ds) 281s mean SE 281s api00 644.17 5.8058 281s > svymean(~api00, as.svrepdesign(ds)) 281s mean SE 281s api00 644.17 5.8058 281s > options(survey.lonely.psu="certainty") 281s > svymean(~api00,ds) 281s mean SE 281s api00 644.17 5.8058 281s > svymean(~api00, as.svrepdesign(ds)) 281s mean SE 281s api00 644.17 5.8058 281s > options(survey.lonely.psu="adjust") 281s > svymean(~api00,ds) 281s mean SE 281s api00 644.17 5.8281 281s > svymean(~api00, as.svrepdesign(ds)) 281s mean SE 281s api00 644.17 5.8267 281s > options(survey.lonely.psu="average") 281s > svymean(~api00,ds) 281s mean SE 281s api00 644.17 6.0096 281s > svymean(~api00, as.svrepdesign(ds)) 281s mean SE 281s api00 644.17 5.8217 281s > 281s > ## fpc specified 281s > fpc<-ifelse(apiclus1$dnum==413, 1,1000) 281s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1,fpc=fpc) 281s > summary(ds) 281s Stratified Independent Sampling design 281s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1, 281s fpc = fpc) 281s Probabilities: 281s Min. 1st Qu. Median Mean 3rd Qu. Max. 281s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 281s Stratum Sizes: 281s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 281s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 281s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 281s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 281s Population stratum sizes (PSUs): 281s 135 178 197 255 406 413 437 448 510 568 61 637 716 778 815 281s 1000 1000 1000 1000 1000 1 1000 1000 1000 1000 1000 1000 1000 1000 1000 281s Data variables: 281s [1] "cds" "stype" "name" "sname" "snum" "dname" 281s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 281s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 281s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 281s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 281s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 281s [37] "api.stu" "fpc" "pw" 281s > 281s > options(survey.lonely.psu="fail") 281s > try(svymean(~api00,ds)) 281s mean SE 281s api00 644.17 5.7344 281s > svymean(~api00, as.svrepdesign(ds)) 281s mean SE 281s api00 644.17 5.7344 281s > options(survey.lonely.psu="remove") 281s > svymean(~api00,ds) 281s mean SE 281s api00 644.17 5.7344 281s > svymean(~api00, as.svrepdesign(ds)) 281s mean SE 281s api00 644.17 5.7344 281s > options(survey.lonely.psu="certainty") 281s > svymean(~api00,ds) 281s mean SE 281s api00 644.17 5.7344 281s > svymean(~api00, as.svrepdesign(ds)) 281s mean SE 281s api00 644.17 5.7344 281s > options(survey.lonely.psu="adjust") 281s > svymean(~api00,ds) 281s mean SE 281s api00 644.17 5.7344 281s > svymean(~api00, as.svrepdesign(ds)) 281s mean SE 281s api00 644.17 5.7344 281s > options(survey.lonely.psu="average") 281s > svymean(~api00,ds) 281s mean SE 281s api00 644.17 5.7344 281s > svymean(~api00, as.svrepdesign(ds)) 281s mean SE 281s api00 644.17 5.7501 281s > 281s > rs<-as.svrepdesign(ds) 281s > svytotal(~api00,rs) 281s total SE 281s api00 3989986 35616 281s > SE(svytotal(~api00,subset(rs, dnum==413)))==0 281s [1] TRUE 281s > 281s > ## lonely PSUs after subsetting 281s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 281s > ds1<-ds[-31,] 281s > summary(ds1) 281s Stratified Independent Sampling design (with replacement) 281s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 281s dnum != 413)) 281s Probabilities: 281s Min. 1st Qu. Median Mean 3rd Qu. Max. 281s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 281s Stratum Sizes: 281s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 281s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 281s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 281s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 281s Data variables: 281s [1] "cds" "stype" "name" "sname" "snum" "dname" 281s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 281s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 281s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 281s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 281s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 281s [37] "api.stu" "fpc" "pw" 281s > 281s > options(survey.lonely.psu="fail") 281s > svymean(~api00,ds1) 281s mean SE 281s api00 645.14 5.8909 281s > options(survey.lonely.psu="remove") 281s > svymean(~api00,ds1) 281s mean SE 281s api00 645.14 5.8909 281s > options(survey.lonely.psu="certainty") 281s > svymean(~api00,ds1) 281s mean SE 281s api00 645.14 5.8909 281s > options(survey.lonely.psu="adjust") 281s > svymean(~api00,ds1) 281s mean SE 281s api00 645.14 5.8909 281s > options(survey.lonely.psu="average") 281s > svymean(~api00,ds1) 281s mean SE 281s api00 645.14 5.8909 281s > 281s > ## with adjustment 281s > options(survey.adjust.domain.lonely=TRUE) 281s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 281s > ds1<-ds[-31,] 281s > summary(ds1) 281s Stratified Independent Sampling design (with replacement) 281s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 281s dnum != 413)) 281s Probabilities: 281s Min. 1st Qu. Median Mean 3rd Qu. Max. 281s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 281s Stratum Sizes: 281s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 281s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 281s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 281s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 281s Data variables: 281s [1] "cds" "stype" "name" "sname" "snum" "dname" 281s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 281s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 281s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 281s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 281s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 281s [37] "api.stu" "fpc" "pw" 281s > 281s > options(survey.lonely.psu="fail") 281s > try(svymean(~api00,ds1)) 281s Warning message: 281s In onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1], : mean SE 281s api00 645.14 5.8909 281s 281s Stratum (406) has only one PSU at stage 1 281s > options(survey.lonely.psu="remove") 281s > svymean(~api00,ds1) 281s Warning message: 281s In onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1], : 281s Stratum (406) has only one PSU at stage 1 281s mean SE 281s api00 645.14 5.8909 281s > Warning message: 281s In onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1], : 281s Stratum (406) has only one PSU at stage 1 281s Warning message: 281s In onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1], : 281s Stratum (406) has only one PSU at stage 1 281s Warning message: 281s In onestrat(x[index, , drop = FALSE], clusters[index], nPSU[index][1], : 281s Stratum (406) has only one PSU at stage 1 281s options(survey.lonely.psu="certainty") 281s > svymean(~api00,ds1) 281s mean SE 281s api00 645.14 5.8909 281s > options(survey.lonely.psu="adjust") 281s > svymean(~api00,ds1) 281s mean SE 281s api00 645.14 5.9119 281s > options(survey.lonely.psu="average") 281s > svymean(~api00,ds1) 281s mean SE 281s api00 645.14 6.0914 281s > 281s BEGIN TEST mtcars-var.R 281s 281s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 281s Copyright (C) 2024 The R Foundation for Statistical Computing 281s Platform: aarch64-unknown-linux-gnu (64-bit) 281s 281s R is free software and comes with ABSOLUTELY NO WARRANTY. 281s You are welcome to redistribute it under certain conditions. 281s Type 'license()' or 'licence()' for distribution details. 281s 281s R is a collaborative project with many contributors. 281s Type 'contributors()' for more information and 281s 'citation()' on how to cite R or R packages in publications. 281s 281s Type 'demo()' for some demos, 'help()' for on-line help, or 281s 'help.start()' for an HTML browser interface to help. 281s Type 'q()' to quit R. 281s 281s > library(survey) 281s Loading required package: grid 281s Loading required package: Matrix 282s Loading required package: survival 282s 282s Attaching package: 'survey' 282s 282s > 282s > # don't throw an error on domains of size 1, just return NA 282s > input <- mtcars 282s The following object is masked from 'package:graphics': 282s 282s dotchart 282s 282s > input$carb <- factor(input$carb) 282s > design <- svydesign(ids = ~0, weights = NULL, data = input) 282s > svyby( 282s + ~mpg, 282s + ~carb, 282s + design, 282s + svyvar 282s + ) 282s carb mpg se 282s 1 1 36.01619 11.2823286 282s 2 2 29.94444 9.0030898 282s 3 3 1.11000 0.4604066 282s 4 4 15.29656 4.3174617 282s 6 6 NA NA 282s 8 8 NA NA 282s > 282s > 282s > ## same n with na.rm=TRUE as subset(, !is.na) 282s > input$mpg[1]<-NA 282s > design <- svydesign(ids = ~0, weights = NULL, data = input) 282s > stopifnot(all.equal(svyvar(~mpg, design, na.rm=TRUE), 282s + svyvar(~mpg, subset(design, !is.na(mpg))))) 282s > 282s BEGIN TEST multistage.R 282s 282s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 282s Copyright (C) 2024 The R Foundation for Statistical Computing 282s Platform: aarch64-unknown-linux-gnu (64-bit) 282s 282s R is free software and comes with ABSOLUTELY NO WARRANTY. 282s You are welcome to redistribute it under certain conditions. 282s Type 'license()' or 'licence()' for distribution details. 282s 282s R is a collaborative project with many contributors. 282s Type 'contributors()' for more information and 282s 'citation()' on how to cite R or R packages in publications. 282s 282s Type 'demo()' for some demos, 'help()' for on-line help, or 282s 'help.start()' for an HTML browser interface to help. 282s Type 'q()' to quit R. 282s 283s > ## 283s > ## Check that multistage samples still work 283s > ## 283s > library(survey) 283s Loading required package: grid 283s Loading required package: Matrix 283s Loading required package: survival 284s 284s Attaching package: 'survey' 284s 284s > example(mu284) 284s The following object is masked from 'package:graphics': 284s 284s dotchart 284s 284s 284s mu284> data(mu284) 284s 284s mu284> (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 284s 2 - level Cluster Sampling design 284s With (5, 15) clusters. 284s (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 284s 284s mu284> (ytotal<-svytotal(~y1, dmu284)) 284s total SE 284s y1 15080 2274.3 284s 284s mu284> vcov(ytotal) 284s y1 284s y1 5172234 284s > 284s > 284s BEGIN TEST na_action.R 284s 284s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 284s Copyright (C) 2024 The R Foundation for Statistical Computing 284s Platform: aarch64-unknown-linux-gnu (64-bit) 284s 284s R is free software and comes with ABSOLUTELY NO WARRANTY. 284s You are welcome to redistribute it under certain conditions. 284s Type 'license()' or 'licence()' for distribution details. 284s 284s R is a collaborative project with many contributors. 284s Type 'contributors()' for more information and 284s 'citation()' on how to cite R or R packages in publications. 284s 284s Type 'demo()' for some demos, 'help()' for on-line help, or 284s 'help.start()' for an HTML browser interface to help. 284s Type 'q()' to quit R. 284s 284s > ## from Terry Therneau 284s > library(survey) 284s Loading required package: grid 284s Loading required package: Matrix 285s Loading required package: survival 285s 285s Attaching package: 'survey' 285s 285s The following object is masked from 'package:graphics': 285s 285s dotchart 285s 285s > load("naa.rda") 285s > 285s > fit1e <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s,na.action=na.exclude) 285s > fit1o <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s) 285s > all.equal(coef(fit1e),coef(fit1o)) 285s [1] TRUE 285s > all.equal(vcov(fit1e),vcov(fit1o)) 285s [1] TRUE 285s > 285s BEGIN TEST newquantile.R 285s 285s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 285s Copyright (C) 2024 The R Foundation for Statistical Computing 285s Platform: aarch64-unknown-linux-gnu (64-bit) 285s 285s R is free software and comes with ABSOLUTELY NO WARRANTY. 285s You are welcome to redistribute it under certain conditions. 285s Type 'license()' or 'licence()' for distribution details. 285s 285s R is a collaborative project with many contributors. 285s Type 'contributors()' for more information and 285s 'citation()' on how to cite R or R packages in publications. 285s 285s Type 'demo()' for some demos, 'help()' for on-line help, or 285s 'help.start()' for an HTML browser interface to help. 285s Type 'q()' to quit R. 285s 285s > ## quantiles with equal weights 285s > 285s > library(survey) 285s Loading required package: grid 285s Loading required package: Matrix 286s Loading required package: survival 286s 286s Attaching package: 'survey' 286s 286s > The following object is masked from 'package:graphics': 286s 286s dotchart 286s 286s data(api) 286s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 286s > 286s > 286s > for(i in 1:9){ 286s + print(i) 286s + all.equal( 286s + as.vector(coef(svyquantile(~ell, dclus1, c(0.2,0.5,0.9), qrule=paste0("hf",i)))), 286s + as.vector(quantile(apiclus1$ell, c(0.2,0.5,0.9), type=i)) 286s + ) 286s + 286s + } 286s [1] 1 286s [1] 2 286s [1] 3 286s [1] 4 286s [1] 5 286s [1] 6 286s [1] 7 286s [1] 8 286s [1] 9 286s > 286s BEGIN TEST nwts-cch.R 287s 287s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 287s Copyright (C) 2024 The R Foundation for Statistical Computing 287s Platform: aarch64-unknown-linux-gnu (64-bit) 287s 287s R is free software and comes with ABSOLUTELY NO WARRANTY. 287s You are welcome to redistribute it under certain conditions. 287s Type 'license()' or 'licence()' for distribution details. 287s 287s R is a collaborative project with many contributors. 287s Type 'contributors()' for more information and 287s 'citation()' on how to cite R or R packages in publications. 287s 287s Type 'demo()' for some demos, 'help()' for on-line help, or 287s 'help.start()' for an HTML browser interface to help. 287s Type 'q()' to quit R. 287s 287s > library(survey) 287s Loading required package: grid 287s Loading required package: Matrix 287s Loading required package: survival 288s 288s Attaching package: 'survey' 288s 288s The following object is masked from 'package:graphics': 288s 288s dotchart 288s 288s > library(survival) 288s > data(nwtco) 288s > 288s > ntwco<-subset(nwtco, !is.na(edrel)) 288s > 288s > load("nwtco-subcohort.rda") 288s > nwtco$subcohort<-subcohort 288s > 288s > d_BorganII <- twophase(id=list(~seqno,~seqno), 288s + strata=list(NULL,~interaction(instit,rel)), 288s + data=nwtco, subset=~I(rel |subcohort)) 288s > 288s > ##Coefficient results same as Splus with code from 288s > ## http://faculty.washington.edu/norm/software.html 288s > ## SE slightly larger due to using sandwich variance. 288s > 288s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganII) 288s Call: 288s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 288s I(age/12), design = d_BorganII) 288s 288s coef exp(coef) se(coef) robust se z p 288s factor(stage)2 0.46286 1.58861 0.23762 0.18087 2.559 0.01049 288s factor(stage)3 0.58309 1.79156 0.23965 0.17848 3.267 0.00109 288s factor(stage)4 1.05967 2.88541 0.26182 0.20524 5.163 2.43e-07 288s factor(histol)2 1.59744 4.94035 0.17688 0.13342 11.973 < 2e-16 288s I(age/12) 0.02994 1.03039 0.02942 0.03337 0.897 0.36972 288s 288s Likelihood ratio test= on 5 df, p= 288s n= 1062, number of events= 571 288s > 288s > ## 288s > ## This gives higher standard errors. calibrate() does not recompute the 288s > ## finite population correction if a calibration variable happens to predict 288s > ## sampling perfectly. It probably should. 288s > ## 288s > d_BorganIIps<-calibrate(twophase(id=list(~seqno,~seqno), 288s + strata=list(NULL,~rel), 288s + data=nwtco, subset=~I(rel |subcohort)), 288s + phase=2, formula=~interaction(instit,rel), 288s + epsilon=1e-10) 288s > 288s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganIIps) 289s Call: 289s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 289s I(age/12), design = d_BorganIIps) 289s 289s coef exp(coef) se(coef) robust se z p 289s factor(stage)2 0.46286 1.58861 0.23762 0.18076 2.561 0.01045 289s factor(stage)3 0.58309 1.79156 0.23965 0.17838 3.269 0.00108 289s factor(stage)4 1.05967 2.88541 0.26182 0.20513 5.166 2.39e-07 289s factor(histol)2 1.59744 4.94035 0.17688 0.13044 12.246 < 2e-16 289s I(age/12) 0.02994 1.03039 0.02942 0.03331 0.899 0.36876 289s 289s Likelihood ratio test= on 5 df, p= 289s n= 1062, number of events= 571 289s > 289s BEGIN TEST nwts.R 289s 289s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 289s Copyright (C) 2024 The R Foundation for Statistical Computing 289s Platform: aarch64-unknown-linux-gnu (64-bit) 289s 289s R is free software and comes with ABSOLUTELY NO WARRANTY. 289s You are welcome to redistribute it under certain conditions. 289s Type 'license()' or 'licence()' for distribution details. 289s 289s R is a collaborative project with many contributors. 289s Type 'contributors()' for more information and 289s 'citation()' on how to cite R or R packages in publications. 289s 289s Type 'demo()' for some demos, 'help()' for on-line help, or 289s 'help.start()' for an HTML browser interface to help. 289s Type 'q()' to quit R. 289s 289s > 289s > ## examples from Breslow & Chatterjee: Applied Statistics 1999 No. 4, p458 289s > ## data from Norman Breslow's web page. 289s > library(survey) 289s Loading required package: grid 289s Loading required package: Matrix 290s Loading required package: survival 290s 290s Attaching package: 'survey' 290s 290s The following object is masked from 'package:graphics': 290s 290s dotchart 290s 290s > load("nwts.rda") 290s > nwtsnb<-nwts 290s > nwtsnb$case<-nwts$case-nwtsb$case 290s > nwtsnb$control<-nwts$control-nwtsb$control 290s > 290s > a<-rbind(nwtsb,nwtsnb) 290s > a$in.ccs<-rep(c(TRUE,FALSE),each=16) 290s > 290s > b<-rbind(a,a) 290s > b$rel<-rep(c(1,0),each=32) 290s > b$n<-ifelse(b$rel,b$case,b$control) 290s > 290s > index<-rep(1:64,b$n) 290s > 290s > nwt.exp<-b[index,c(1:3,6,7)] 290s > nwt.exp$id<-1:4088 290s > 290s > dccs2<-twophase(id=list(~id,~id),subset=~in.ccs, 290s + strata=list(NULL,~interaction(instit,rel)),data=nwt.exp) 290s > 290s > dccs8<-twophase(id=list(~id,~id),subset=~in.ccs, 290s + strata=list(NULL,~interaction(instit,stage,rel)),data=nwt.exp) 290s > 290s > gccs8<-calibrate(dccs2,phase=2,formula=~interaction(instit,stage,rel)) 290s > 290s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs2)) 291s 291s Call: 291s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs2, 291s family = quasibinomial) 291s 291s Survey design: 291s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 291s subset = subset, data = data) 291s 291s Coefficients: 291s Estimate Std. Error t value Pr(>|t|) 291s (Intercept) -2.5701 0.1288 -19.955 < 2e-16 *** 291s factor(stage)2 0.5482 0.1979 2.769 0.005708 ** 291s factor(stage)3 0.4791 0.2032 2.359 0.018515 * 291s factor(stage)4 1.0037 0.2592 3.872 0.000114 *** 291s factor(histol)2 1.3505 0.3107 4.346 1.51e-05 *** 291s factor(stage)2:factor(histol)2 0.1152 0.4410 0.261 0.793876 291s factor(stage)3:factor(histol)2 0.5066 0.4241 1.194 0.232548 291s factor(stage)4:factor(histol)2 0.9785 0.6214 1.575 0.115615 291s --- 291s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 291s 291s (Dispersion parameter for quasibinomial family taken to be 1.000876) 291s 291s Number of Fisher Scoring iterations: 4 291s 291s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs8)) 291s 291s Call: 291s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs8, 291s family = quasibinomial) 291s 291s Survey design: 291s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 291s subset = subset, data = data) 291s 291s Coefficients: 291s Estimate Std. Error t value Pr(>|t|) 291s (Intercept) -2.71604 0.10827 -25.085 < 2e-16 *** 291s factor(stage)2 0.78141 0.14726 5.306 1.35e-07 *** 291s factor(stage)3 0.80093 0.15250 5.252 1.80e-07 *** 291s factor(stage)4 1.07293 0.17817 6.022 2.33e-09 *** 291s factor(histol)2 1.45836 0.31780 4.589 4.96e-06 *** 291s factor(stage)2:factor(histol)2 -0.04743 0.43495 -0.109 0.913 291s factor(stage)3:factor(histol)2 0.28064 0.41298 0.680 0.497 291s factor(stage)4:factor(histol)2 0.90983 0.63774 1.427 0.154 291s --- 291s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 291s 291s (Dispersion parameter for quasibinomial family taken to be 1.000876) 291s 291s Number of Fisher Scoring iterations: 4 291s 291s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=gccs8)) 291s 291s Call: 291s svyglm(formula = rel ~ factor(stage) * factor(histol), design = gccs8, 291s family = quasibinomial) 291s 291s Survey design: 291s calibrate(dccs2, phase = 2, formula = ~interaction(instit, stage, 291s rel)) 291s 291s Coefficients: 291s Estimate Std. Error t value Pr(>|t|) 291s (Intercept) -2.71604 0.10878 -24.968 < 2e-16 *** 291s factor(stage)2 0.78141 0.14729 5.305 1.35e-07 *** 291s factor(stage)3 0.80093 0.15212 5.265 1.68e-07 *** 291s factor(stage)4 1.07293 0.17905 5.993 2.77e-09 *** 291s factor(histol)2 1.45836 0.31757 4.592 4.88e-06 *** 291s factor(stage)2:factor(histol)2 -0.04743 0.43432 -0.109 0.913 291s factor(stage)3:factor(histol)2 0.28064 0.41231 0.681 0.496 291s factor(stage)4:factor(histol)2 0.90983 0.63187 1.440 0.150 291s --- 291s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 291s 291s (Dispersion parameter for quasibinomial family taken to be 1.000876) 291s 291s Number of Fisher Scoring iterations: 4 291s 291s > 291s > ## check subsets of calibrated designs. 291s > summary(svyglm(rel~factor(stage), 291s + family=quasibinomial,design=subset(dccs8,histol==1))) 291s 291s Call: 291s svyglm(formula = rel ~ factor(stage), design = subset(dccs8, 291s histol == 1), family = quasibinomial) 291s 291s Survey design: 291s subset(dccs8, histol == 1) 291s 291s Coefficients: 291s Estimate Std. Error t value Pr(>|t|) 291s (Intercept) Warning messages: 291s 1: In `[.twophase2`(x, r, ) : 1 strata have only one PSU in this subset. 291s 2: In summary.glm(g) : -2.7160 0.1083 -25.085 < 2e-16 *** 291s factor(stage)2 0.7814 0.1473 5.306 1.48e-07 *** 291s factor(stage)3 0.8009 0.1525 5.252 1.97e-07 *** 291s factor(stage)4 1.0729 0.1782 6.022 2.73e-09 *** 291s --- 291s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 291s 291s (Dispersion parameter for quasibinomial family taken to be 1.001333) 291s 291s Number of Fisher Scoring iterations: 4 291s 291s 291s observations with zero weight not used for calculating dispersion 291s 3: In summary.glm(glm.object) : 291s observations with zero weight not used for calculating dispersion 291s > summary(svyglm(rel~factor(stage), 291s + family=quasibinomial,design=subset(gccs8,histol==1))) 291s 4: In `[.twophase2`(design, nas == 0, ) : 291s 1 strata have only one PSU in this subset. 291s 5: In `[.twophase2`(design, nas == 0, ) : 291s 1 strata have only one PSU in this subset. 291s 291s Call: 291s Warning messages: 291s 1: In summary.glm(g) : 291s observations with zero weight not used for calculating dispersion 291s 2: In summary.glm(glm.object) : 291s observations with zero weight not used for calculating dispersion 291s svyglm(formula = rel ~ factor(stage), design = subset(gccs8, 291s histol == 1), family = quasibinomial) 291s 291s Survey design: 291s subset(gccs8, histol == 1) 291s 291s Coefficients: 291s Estimate Std. Error t value Pr(>|t|) 291s (Intercept) -2.7160 0.1082 -25.105 < 2e-16 *** 291s factor(stage)2 0.7814 0.1457 5.363 1.10e-07 *** 291s factor(stage)3 0.8009 0.1504 5.324 1.34e-07 *** 291s factor(stage)4 1.0729 0.1759 6.101 1.70e-09 *** 291s --- 291s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 291s 291s (Dispersion parameter for quasibinomial family taken to be 1.001333) 291s 291s Number of Fisher Scoring iterations: 4 291s 291s > 291s > 291s BEGIN TEST poisson.R 291s 291s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 291s Copyright (C) 2024 The R Foundation for Statistical Computing 291s Platform: aarch64-unknown-linux-gnu (64-bit) 291s 291s R is free software and comes with ABSOLUTELY NO WARRANTY. 291s You are welcome to redistribute it under certain conditions. 291s Type 'license()' or 'licence()' for distribution details. 291s 291s R is a collaborative project with many contributors. 291s Type 'contributors()' for more information and 291s 'citation()' on how to cite R or R packages in publications. 291s 291s Type 'demo()' for some demos, 'help()' for on-line help, or 291s 'help.start()' for an HTML browser interface to help. 291s Type 'q()' to quit R. 291s 291s > ## check poisson sampling 291s > library(survey) 291s Loading required package: grid 291s Loading required package: Matrix 292s Loading required package: survival 292s > data(api) 292s 292s Attaching package: 'survey' 292s 292s The following object is masked from 'package:graphics': 292s 292s dotchart 292s 292s > set.seed(2021-7-15) 292s > apipop$prob<-apipop$api00/1000 292s > insample<-rbinom(nrow(apipop),1,apipop$prob) 292s > apipois<-apipop[insample,] 292s > des<-svydesign(id=~1, prob=~prob, pps=poisson_sampling(apipois$prob), data=apipois) 292s > 292s > stopifnot(isTRUE(all.equal( 292s + as.vector(SE(svytotal(~api00,design=des))), 292s + as.vector(sqrt(sum( (apipois$api00*weights(des))^2*(1-apipois$prob)))) 292s + ))) 292s > 292s > 292s BEGIN TEST pps.R 292s 292s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 292s Copyright (C) 2024 The R Foundation for Statistical Computing 292s Platform: aarch64-unknown-linux-gnu (64-bit) 292s 292s R is free software and comes with ABSOLUTELY NO WARRANTY. 292s You are welcome to redistribute it under certain conditions. 292s Type 'license()' or 'licence()' for distribution details. 292s 292s R is a collaborative project with many contributors. 292s Type 'contributors()' for more information and 292s 'citation()' on how to cite R or R packages in publications. 292s 292s Type 'demo()' for some demos, 'help()' for on-line help, or 292s 'help.start()' for an HTML browser interface to help. 292s Type 'q()' to quit R. 292s 292s Loading required package: grid 292s > library(survey) 292s Loading required package: Matrix 293s Loading required package: survival 293s > data(election) 293s 293s Attaching package: 'survey' 293s 293s The following object is masked from 'package:graphics': 293s 293s dotchart 293s 293s > 293s > dpps<- svydesign(id=~1, weights=~wt, fpc=~p, data=election_pps, pps="brewer") 293s > dppswr <-svydesign(id=~1, weights=~wt, data=election_pps) 293s > svytotal(~Bush+Kerry+Nader, dpps) 293s total SE 293s Bush 64518472 2447629 293s Kerry 51202102 2450787 293s Nader 478530 102420 293s > svytotal(~Bush+Kerry+Nader, dppswr) 293s total SE 293s Bush 64518472 2671455 293s Kerry 51202102 2679433 293s Nader 478530 105303 293s > 293s > ##subsets 293s > svytotal(~Bush+Kerry+Nader, subset(dpps, Nader>0)) 293s total SE 293s Bush 34944285 5399833 293s Kerry 25581714 4028434 293s Nader 478530 102420 293s > 293s > ##multistage: should agree with STRS analysis 293s > data(api) 293s > dclus2<-svydesign(id = ~dnum + snum, fpc = ~fpc1 + fpc2, data = apiclus2) 293s > dclus2pps<-svydesign(id = ~dnum + snum, fpc = ~I(40/fpc1) + I(pmin(1,5/fpc2)), data = apiclus2) 293s > 293s > all.equal(svytotal(~sch.wide,dclus2), svytotal(~sch.wide,dclus2pps)) 293s [1] TRUE 293s > all.equal(svymean(~sch.wide,dclus2), svymean(~sch.wide,dclus2pps)) 293s [1] TRUE 293s > all.equal(svytotal(~enroll,dclus2), svytotal(~enroll,dclus2pps)) 294s [1] TRUE 294s > 294s > ## the new without-replacement methods 294s > data(election) 294s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 294s > dpps_ov<- svydesign(id=~1, fpc=~p, data=election_pps, pps="overton") 294s > dpps_hr<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40)) 294s > dpps_hr1<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR()) 294s > dpps_ht<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob)) 294s > ## Yates-Grundy type 294s > dpps_yg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob),variance="YG") 294s > dpps_hryg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40),variance="YG") 294s > 294s > ## The with-replacement approximation 294s > svytotal(~Bush+Kerry+Nader, dpps_ht) 294s total SE 294s Bush 64518472 2604404 294s Kerry 51202102 2523712 294s Nader 478530 102326 294s > svytotal(~Bush+Kerry+Nader, dpps_yg) 294s total SE 294s Bush 64518472 2406526 294s Kerry 51202102 2408091 294s Nader 478530 101664 294s > svytotal(~Bush+Kerry+Nader, dpps_hr) 294s total SE 294s Bush 64518472 2624662 294s Kerry 51202102 2525222 294s Nader 478530 102793 294s > svytotal(~Bush+Kerry+Nader, dpps_hryg) 294s total SE 294s Bush 64518472 2436738 294s Kerry 51202102 2439845 294s Nader 478530 102016 294s > svytotal(~Bush+Kerry+Nader, dpps_hr1) 294s total SE 294s Bush 64518472 2472753 294s Kerry 51202102 2426842 294s Nader 478530 102595 294s > svytotal(~Bush+Kerry+Nader, dpps_br) 294s total SE 294s Bush 64518472 2447629 294s Kerry 51202102 2450787 294s Nader 478530 102420 294s > svytotal(~Bush+Kerry+Nader, dpps_ov) 294s total SE 294s Bush 64518472 2939608 294s Kerry 51202102 1964632 294s Nader 478530 104373 294s > 294s > ## subsets 294s > svytotal(~Bush+Kerry+Nader, subset(dpps_ht, Nader>0)) 294s total SE 294s Bush 34944285 5406348 294s Kerry 25581714 4047741 294s Nader 478530 102326 294s > svytotal(~Bush+Kerry+Nader, subset(dpps_hryg, Nader>0)) 294s total SE 294s Bush 34944285 5377659 294s Kerry 25581714 4010908 294s Nader 478530 102016 294s > 294s > ## counts 294s > svyby(~Bush+Kerry+Nader,~I(Nader>0), unwtd.count,design=dpps_ht) 294s I(Nader > 0) counts se 294s FALSE FALSE 19 0 294s TRUE TRUE 21 0 294s > 294s BEGIN TEST quantile.R 294s 294s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 294s Copyright (C) 2024 The R Foundation for Statistical Computing 294s Platform: aarch64-unknown-linux-gnu (64-bit) 294s 294s R is free software and comes with ABSOLUTELY NO WARRANTY. 294s You are welcome to redistribute it under certain conditions. 294s Type 'license()' or 'licence()' for distribution details. 294s 294s R is a collaborative project with many contributors. 294s Type 'contributors()' for more information and 294s 'citation()' on how to cite R or R packages in publications. 294s 294s Type 'demo()' for some demos, 'help()' for on-line help, or 294s 'help.start()' for an HTML browser interface to help. 294s Type 'q()' to quit R. 294s 294s > library(survey) 294s Loading required package: grid 294s Loading required package: Matrix 295s Loading required package: survival 295s > set.seed(42) 295s 295s Attaching package: 'survey' 295s 295s The following object is masked from 'package:graphics': 295s 295s dotchart 295s 295s > 295s > df<-data.frame(x=exp(rnorm(1000))) 295s > df$y<-round(df$x,1) 295s > ddf<-svydesign(id=~1,data=df) 295s Warning message: 295s In svydesign.default(id = ~1, data = df) : 295s No weights or probabilities supplied, assuming equal probability 295s > rdf<-as.svrepdesign(ddf) 295s > 295s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 295s 0.01 0.1 0.5 0.9 0.99 295s 0.01543792 0.01264453 0.03386225 0.16131948 2.10605799 295s > 295s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 296s x 296s q0.01 0.01554946 296s q0.1 0.01425828 296s q0.5 0.03428012 296s q0.9 0.16457488 296s q0.99 1.88672412 296s > 296s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 296s 0.01 0.1 0.5 0.9 0.99 296s 0.01545209 0.01265608 0.03388011 0.16145776 2.10061576 296s > 296s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 296s x 296s q0.01 0.01556240 296s q0.1 0.01420086 296s q0.5 0.03430175 296s q0.9 0.16461019 296s q0.99 1.88818131 296s > 296s > 296s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 296s $quantiles 296s 0.01 0.1 0.5 0.9 0.99 296s y 0.02352941 0.2230769 0.9340909 3.55 9.4 296s 296s $CIs 296s , , y 296s 296s 0.01 0.1 0.5 0.9 0.99 296s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 296s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 296s 296s 296s > 296s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 296s Statistic: 296s y 296s q0.01 0.1 296s q0.1 0.3 296s q0.5 1.0 296s q0.9 3.6 296s q0.99 9.4 296s SE: 296s y 296s q0.01 0.02547977 296s q0.1 0.02547977 296s q0.5 0.02547977 296s q0.9 0.15287859 296s q0.99 1.88302540 296s > 296s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 296s $quantiles 296s 0.01 0.1 0.5 0.9 0.99 296s y 0.02352941 0.2230769 0.9340909 3.55 9.4 296s 296s $CIs 296s , , y 296s 296s 0.01 0.1 0.5 0.9 0.99 296s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 296s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 296s 296s 296s > 296s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 296s Statistic: 296s y 296s q0.01 0.1 296s q0.1 0.3 296s q0.5 1.0 296s q0.9 3.6 296s q0.99 9.4 296s SE: 296s y 296s q0.01 0.02551067 296s q0.1 0.02551067 296s q0.5 0.02551067 296s q0.9 0.15306404 296s q0.99 1.88450896 296s > 296s > 296s > 296s > df<-data.frame(x=exp(rnorm(20))) 296s > df$y<-round(df$x,1) 296s > ddf<-svydesign(id=~1,data=df) 296s Warning message: 296s In svydesign.default(id = ~1, data = df) : 296s No weights or probabilities supplied, assuming equal probability 296s > rdf<-as.svrepdesign(ddf) 296s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 296s 0.01 0.1 0.5 0.9 0.99 296s 0.03576771 0.07329496 0.30149917 2.03440784 1.88468597 296s > 296s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 296s x 296s q0.01 0.00000000 296s q0.1 0.04598541 296s q0.5 0.25943731 296s q0.9 2.12343073 296s q0.99 1.91998924 296s > 296s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 296s 0.01 0.1 0.5 0.9 0.99 296s 0.03637398 0.07470310 0.29938115 2.16381289 2.00708994 296s > 296s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 296s x 296s q0.01 0.00000000 296s q0.1 0.04732818 296s q0.5 0.24957966 296s q0.9 2.25211815 296s q0.99 2.04043154 296s > 296s > 296s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 296s $quantiles 296s 0.01 0.1 0.5 0.9 0.99 296s y 0.1 0.15 0.75 2.4 8.68 296s 296s $CIs 296s , , y 296s 296s 0.01 0.1 0.5 0.9 0.99 296s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 296s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 296s 296s 296s > 296s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 296s Statistic: 296s y 296s q0.01 0.10 296s q0.1 0.20 296s q0.5 0.80 296s q0.9 2.40 296s q0.99 8.68 296s SE: 296s y 296s q0.01 0.00000000 296s q0.1 0.02611112 296s q0.5 0.26542051 296s q0.9 2.10908603 296s q0.99 1.91777710 296s > 296s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 296s $quantiles 296s 0.01 0.1 0.5 0.9 0.99 296s y 0.1 0.15 0.75 2.4 8.68 296s 296s $CIs 296s , , y 296s 296s 0.01 0.1 0.5 0.9 0.99 296s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 296s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 296s 296s 296s > 296s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 296s Statistic: 296s y 296s q0.01 0.10 296s q0.1 0.20 296s q0.5 0.80 296s q0.9 2.40 296s q0.99 8.68 296s SE: 296s y 296s q0.01 0.00000000 296s q0.1 0.02551067 296s q0.5 0.25244616 296s q0.9 2.23558589 296s q0.99 2.03881114 296s > 296s BEGIN TEST quantiles-chile.R 296s 296s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 296s Copyright (C) 2024 The R Foundation for Statistical Computing 296s Platform: aarch64-unknown-linux-gnu (64-bit) 296s 296s R is free software and comes with ABSOLUTELY NO WARRANTY. 296s You are welcome to redistribute it under certain conditions. 296s Type 'license()' or 'licence()' for distribution details. 296s 296s R is a collaborative project with many contributors. 296s Type 'contributors()' for more information and 296s 'citation()' on how to cite R or R packages in publications. 296s 296s Type 'demo()' for some demos, 'help()' for on-line help, or 296s 'help.start()' for an HTML browser interface to help. 296s Type 'q()' to quit R. 296s 296s > library(survey) 296s Loading required package: grid 296s Loading required package: Matrix 297s Loading required package: survival 298s 298s Attaching package: 'survey' 298s 298s > datos <- readRDS("datos_ejemplo.rds") 298s The following object is masked from 'package:graphics': 298s 298s dotchart 298s 298s > 298s > design <- svydesign(id = ~id_directorio, strata = ~estrato, weights = ~f_pers, check.strata = TRUE, data = datos) 298s > set.seed(234262762) 298s > repdesign <- as.svrepdesign(design, type = "subbootstrap", replicates=20) 298s > options(survey.lonely.psu="remove") 298s > 298s > values<-datos$ing_t_p[datos$CL_GRUPO_OCU_08=="ISCO08_6"] 298s > 298s > suppressWarnings({ 298s + f0<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 298s + f0.5<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 298s + }) 298s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 298s [1] TRUE 298s > 298s > suppressWarnings({ 298s + f0<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 298s + f0.5<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 298s + }) 298s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 298s [1] TRUE 298s > 298s BEGIN TEST rakecheck.R 298s 298s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 298s Copyright (C) 2024 The R Foundation for Statistical Computing 298s Platform: aarch64-unknown-linux-gnu (64-bit) 298s 298s R is free software and comes with ABSOLUTELY NO WARRANTY. 298s You are welcome to redistribute it under certain conditions. 298s Type 'license()' or 'licence()' for distribution details. 298s 298s R is a collaborative project with many contributors. 298s Type 'contributors()' for more information and 298s 'citation()' on how to cite R or R packages in publications. 298s 298s Type 'demo()' for some demos, 'help()' for on-line help, or 298s 'help.start()' for an HTML browser interface to help. 298s Type 'q()' to quit R. 298s 298s > library(survey) 298s Loading required package: grid 298s Loading required package: Matrix 299s Loading required package: survival 299s 299s Attaching package: 'survey' 299s 299s > The following object is masked from 'package:graphics': 299s 299s dotchart 299s 299s 299s > data(api) 299s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 299s > rclus1 <- as.svrepdesign(dclus1) 299s > 299s > ## population marginal totals for each stratum 299s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 299s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 299s > 299s > rclus1r <- rake(rclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 299s > 299s > svymean(~api00, rclus1r) 299s mean SE 299s api00 641.23 26.873 299s > svytotal(~enroll, rclus1r) 299s total SE 299s enroll 3647300 463511 299s > 299s > ff<-~stype+sch.wide 299s > poptotals<-colSums(model.matrix(ff,model.frame(ff,apipop))) 299s > rclus1g<-calibrate(rclus1, ~stype+sch.wide, poptotals,calfun="raking") 299s > 299s > svymean(~api00,rclus1g) 299s mean SE 299s api00 641.23 26.874 299s > svytotal(~enroll,rclus1g) 299s total SE 299s enroll 3647280 463582 299s > 299s > summary(weights(rclus1g)/weights(rclus1r)) 299s V1 V2 V3 V4 V5 V6 299s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 299s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 299s Median :1 Median :1 Median :1 Median :1 Median :1 Median :1 299s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 299s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 299s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 299s NA's :11 NA's :4 NA's :2 NA's :13 NA's :2 NA's :4 299s V7 V8 V9 V10 V11 299s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 299s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 299s Median :1 Median :1 Median :1 Median :1 Median :1 299s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 299s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 299s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 299s NA's :4 NA's :16 NA's :9 NA's :34 NA's :21 299s V12 V13 V14 V15 299s Min. :0.9997 Min. :1 Min. :1 Min. :1 299s 1st Qu.:1.0001 1st Qu.:1 1st Qu.:1 1st Qu.:1 299s Median :1.0001 Median :1 Median :1 Median :1 299s Mean :1.0000 Mean :1 Mean :1 Mean :1 299s 3rd Qu.:1.0001 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 299s Max. :1.0002 Max. :1 Max. :1 Max. :1 299s NA's :37 NA's :13 NA's :1 NA's :12 299s > 299s > 299s > ## Do it for a design without replicate weights 299s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 299s > 299s > svymean(~api00, dclus1r) 299s mean SE 299s api00 641.23 23.704 299s > svytotal(~enroll, dclus1r) 299s total SE 299s enroll 3647300 400603 299s > 299s > dclus1g<-calibrate(dclus1, ~stype+sch.wide, poptotals,calfun="raking") 299s > 299s > svymean(~api00,dclus1g) 299s mean SE 299s api00 641.23 23.704 299s > svytotal(~enroll,dclus1g) 299s total SE 299s enroll 3647280 400603 299s > 299s > summary(weights(dclus1g)/weights(dclus1r)) 299s Min. 1st Qu. Median Mean 3rd Qu. Max. 299s 1 1 1 1 1 1 299s > 299s > 299s > 299s > ## Example of raking with partial joint distributions 299s > pop.table <- xtabs(~stype+sch.wide,apipop) 299s > pop.imp<-data.frame(comp.imp=c("No","Yes"),Freq=c(1712,4482)) 299s > dclus1r2<-rake(dclus1, list(~stype+sch.wide, ~comp.imp), 299s + list(pop.table, pop.imp)) 299s > svymean(~api00, dclus1r2) 299s mean SE 299s api00 642.62 22.732 299s > 299s > ff1 <-~stype*sch.wide+comp.imp 299s > 299s > poptotals1<-colSums(model.matrix(ff1,model.frame(ff1,apipop))) 299s > dclus1g2<-calibrate(dclus1, ~stype*sch.wide+comp.imp, poptotals1, calfun="raking") 299s > 299s > svymean(~api00, dclus1g2) 299s mean SE 299s api00 642.61 22.731 299s > 299s > summary(weights(dclus1r2)/weights(dclus1g2)) 299s Min. 1st Qu. Median Mean 3rd Qu. Max. 299s 0.999 1.000 1.000 1.000 1.000 1.002 299s > 299s BEGIN TEST raowuboot.R 299s 299s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 299s Copyright (C) 2024 The R Foundation for Statistical Computing 299s Platform: aarch64-unknown-linux-gnu (64-bit) 299s 299s R is free software and comes with ABSOLUTELY NO WARRANTY. 299s You are welcome to redistribute it under certain conditions. 299s Type 'license()' or 'licence()' for distribution details. 299s 299s R is a collaborative project with many contributors. 299s Type 'contributors()' for more information and 299s 'citation()' on how to cite R or R packages in publications. 299s 299s Type 'demo()' for some demos, 'help()' for on-line help, or 299s 'help.start()' for an HTML browser interface to help. 299s Type 'q()' to quit R. 299s 299s > ## regression test for bug reported by Richard Valliant 299s > library(survey) 299s Loading required package: grid 299s Loading required package: Matrix 300s Loading required package: survival 300s 300s Attaching package: 'survey' 300s 300s The following object is masked from 'package:graphics': 300s 300s dotchart 300s 300s > s<-subbootweights(c(1,1),1:2, 50) 300s > stopifnot(all(s$repweights$weights %in% c(0,2))) 300s > 300s BEGIN TEST regTermTest-missing.R 301s 301s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 301s Copyright (C) 2024 The R Foundation for Statistical Computing 301s Platform: aarch64-unknown-linux-gnu (64-bit) 301s 301s R is free software and comes with ABSOLUTELY NO WARRANTY. 301s You are welcome to redistribute it under certain conditions. 301s Type 'license()' or 'licence()' for distribution details. 301s 301s R is a collaborative project with many contributors. 301s Type 'contributors()' for more information and 301s 'citation()' on how to cite R or R packages in publications. 301s 301s Type 'demo()' for some demos, 'help()' for on-line help, or 301s 'help.start()' for an HTML browser interface to help. 301s Type 'q()' to quit R. 301s 301s > library(survey) 301s Loading required package: grid 301s Loading required package: Matrix 301s Loading required package: survival 302s 302s Attaching package: 'survey' 302s 302s The following object is masked from 'package:graphics': 302s 302s dotchart 302s 302s > data(nhanes) 302s > design <- svydesign(id=~SDMVPSU, strata=~SDMVSTRA, weights=~WTMEC2YR, nest=TRUE,data=nhanes) 302s > 302s > a<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design = subset(design,!is.na(HI_CHOL)), family=quasibinomial) 302s > b<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design =design , family=quasibinomial) 302s > 302s > ta<-regTermTest(a, ~HI_CHOL) 302s > tb<-regTermTest(b, ~HI_CHOL) 302s > 302s > stopifnot(isTRUE(all.equal(ta$chisq, tb$chisq))) 302s > stopifnot(isTRUE(all.equal(ta$lambda, tb$lambda))) 302s > 302s BEGIN TEST regpredict.R 302s 302s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 302s Copyright (C) 2024 The R Foundation for Statistical Computing 302s Platform: aarch64-unknown-linux-gnu (64-bit) 302s 302s R is free software and comes with ABSOLUTELY NO WARRANTY. 302s You are welcome to redistribute it under certain conditions. 302s Type 'license()' or 'licence()' for distribution details. 302s 302s R is a collaborative project with many contributors. 302s Type 'contributors()' for more information and 302s 'citation()' on how to cite R or R packages in publications. 302s 302s Type 'demo()' for some demos, 'help()' for on-line help, or 302s 'help.start()' for an HTML browser interface to help. 302s Type 'q()' to quit R. 302s 302s > library(survey) 302s Loading required package: grid 302s Loading required package: Matrix 303s Loading required package: survival 303s 303s Attaching package: 'survey' 303s 303s The following object is masked from 'package:graphics': 303s 303s dotchart 303s 303s > data(api) 303s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 303s > 303s > 303s > ## regression estimator of total, three ways 303s > pop<-data.frame(enroll=sum(apipop$enroll, na.rm=TRUE)) 303s > npop <- sum(!is.na(apipop$enroll)) 303s > 303s > api.reg <- svyglm(api.stu~enroll, design=dstrat) 303s > a <- predict(api.reg, newdata=pop, total=npop) 303s > b <- svytotal(~api.stu, calibrate(dstrat, ~enroll, pop=c(npop, pop$enroll))) 303s > 303s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 303s [1] TRUE 303s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 303s [1] TRUE 303s > if(!is.null(getOption("DEBUG"))){ ## uses 6194x6194 matrix 303s + d <- predict(api.reg, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 303s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 303s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 303s + } 303s > 303s > ## classical ratio estimator, four ways. 303s > api.reg2 <- svyglm(api.stu~enroll-1, design=dstrat, 303s + family=quasi(link="identity", var="mu")) 303s > 303s > a <- predict(api.reg2, newdata=pop, total=npop) 303s > b <- svytotal(~api.stu, 303s + calibrate(dstrat, ~enroll-1, pop= pop$enroll, variance=2)) 303s > e <- predict(svyratio(~api.stu, ~enroll, dstrat),total=pop$enroll) 303s > 303s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 303s [1] TRUE 303s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 303s [1] TRUE 303s > all.equal(as.vector(coef(a)),as.vector(e$total)) 303s [1] TRUE 303s > all.equal(as.vector(SE(a)), as.vector(e$se)) 303s [1] TRUE 303s > if(!is.null(getOption("DEBUG"))){## uses 6194x6194 matrix 303s + d <- predict(api.reg2, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 303s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 303s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 303s + } 303s > 303s BEGIN TEST rss_scores.R 303s 303s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 303s Copyright (C) 2024 The R Foundation for Statistical Computing 303s Platform: aarch64-unknown-linux-gnu (64-bit) 303s 303s R is free software and comes with ABSOLUTELY NO WARRANTY. 303s You are welcome to redistribute it under certain conditions. 303s Type 'license()' or 'licence()' for distribution details. 303s 303s R is a collaborative project with many contributors. 303s Type 'contributors()' for more information and 303s 'citation()' on how to cite R or R packages in publications. 303s 303s Type 'demo()' for some demos, 'help()' for on-line help, or 303s 'help.start()' for an HTML browser interface to help. 303s Type 'q()' to quit R. 303s 303s > ## Example from Rao, Scott, and Skinner 1998 Statistica Sinica 303s > library(survey) 303s Loading required package: grid 303s Loading required package: Matrix 304s Loading required package: survival 304s 304s Attaching package: 'survey' 304s 304s The following object is masked from 'package:graphics': 304s 304s dotchart 304s 304s > data(myco) 304s > dmyco<-svydesign(id=~1, strata=~interaction(Age,leprosy),weights=~wt,data=myco) 304s > m_full<-svyglm(leprosy~I((Age+7.5)^-2)+Scar, family=quasibinomial, design=dmyco) 304s > m_null<-svyglm(leprosy~I((Age+7.5)^-2), family=quasibinomial, design=dmyco) 304s > 304s > stopifnot(isTRUE(all.equal(coef(m_null), c(`(Intercept)`=-4.6, `I((Age + 7.5)^-2)`=-427),tol=1e-2))) 304s > 304s > s<-svyscoretest(m_full, ~Scar) 304s > stopifnot(abs(s[1]-10.73)<0.05) 304s > 304s > t<-svyscoretest(m_full,~Scar,method="individual") 304s > stopifnot(abs(coef(t)- -32.61)<0.1) 304s > stopifnot(abs(vcov(t)-99.1)<0.1) 304s > 304s > 304s BEGIN TEST scoping.R 305s 305s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 305s Copyright (C) 2024 The R Foundation for Statistical Computing 305s Platform: aarch64-unknown-linux-gnu (64-bit) 305s 305s R is free software and comes with ABSOLUTELY NO WARRANTY. 305s You are welcome to redistribute it under certain conditions. 305s Type 'license()' or 'licence()' for distribution details. 305s 305s R is a collaborative project with many contributors. 305s Type 'contributors()' for more information and 305s 'citation()' on how to cite R or R packages in publications. 305s 305s Type 'demo()' for some demos, 'help()' for on-line help, or 305s 'help.start()' for an HTML browser interface to help. 305s Type 'q()' to quit R. 305s 305s Loading required package: grid 305s Loading required package: Matrix 305s > 305s > ## regression test for testing regression 305s > 305s > library(survey) 306s Loading required package: survival 306s 306s Attaching package: 'survey' 306s 306s The following object is masked from 'package:graphics': 306s 306s dotchart 306s 306s > data(api) 306s > 306s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 306s > 306s > 306s > f<-function(){ 306s + form<-acs.46~stype 306s + svyglm(formula=form, design = dstrat) 306s + } 306s > 306s > g<-function(form){ 306s + svyglm(formula=form, design = dstrat) 306s + } 306s > f() 306s Stratified Independent Sampling design 306s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 306s fpc = ~fpc) 306s 306s Call: svyglm(formula = form, design = dstrat) 306s 306s Coefficients: 306s (Intercept) stypeH stypeM 306s 28.7449 0.7551 0.4022 306s 306s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 306s (66 observations deleted due to missingness) 306s Null Deviance: 1838 306s Residual Deviance: 1835 AIC: 719.8 306s > g(acs.46~stype) 306s Stratified Independent Sampling design 306s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 306s fpc = ~fpc) 306s 306s Call: svyglm(formula = form, design = dstrat) 306s 306s Coefficients: 306s (Intercept) stypeH stypeM 306s 28.7449 0.7551 0.4022 306s 306s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 306s (66 observations deleted due to missingness) 306s Null Deviance: 1838 306s Residual Deviance: 1835 AIC: 719.8 306s > 306s > f<-function(){ 306s + form<-Surv(acs.46)~stype 306s + svycoxph(formula=form, design = dstrat) 306s + } 306s > 306s > g<-function(form){ 306s + svycoxph(formula=form, design = dstrat) 306s + } 306s > 306s > f() 306s Call: 306s svycoxph(formula = form, design = dstrat) 306s 306s coef exp(coef) se(coef) robust se z p 306s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 306s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 306s 306s Likelihood ratio test= on 2 df, p= 306s n= 134, number of events= 134 306s (66 observations deleted due to missingness) 306s > g(Surv(acs.46)~stype) 306s Call: 306s svycoxph(formula = form, design = dstrat) 306s 306s coef exp(coef) se(coef) robust se z p 306s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 306s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 306s 306s Likelihood ratio test= on 2 df, p= 306s n= 134, number of events= 134 306s (66 observations deleted due to missingness) 306s > 306s > ## check coxph for a single predictor 306s > svycoxph(Surv(acs.46)~api00,design=dstrat) 306s Call: 306s svycoxph(formula = Surv(acs.46) ~ api00, design = dstrat) 306s 306s coef exp(coef) se(coef) robust se z p 306s api00 6.060e-06 1.000e+00 6.244e-04 7.492e-04 0.008 0.994 306s 306s Likelihood ratio test= on 1 df, p= 306s n= 134, number of events= 134 306s (66 observations deleted due to missingness) 306s > 306s BEGIN TEST survcurve.R 306s 306s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 306s Copyright (C) 2024 The R Foundation for Statistical Computing 306s Platform: aarch64-unknown-linux-gnu (64-bit) 306s 306s R is free software and comes with ABSOLUTELY NO WARRANTY. 306s You are welcome to redistribute it under certain conditions. 306s Type 'license()' or 'licence()' for distribution details. 306s 306s R is a collaborative project with many contributors. 306s Type 'contributors()' for more information and 306s 'citation()' on how to cite R or R packages in publications. 306s 306s Type 'demo()' for some demos, 'help()' for on-line help, or 306s 'help.start()' for an HTML browser interface to help. 306s Type 'q()' to quit R. 306s 306s > library(survey) 306s Loading required package: grid 306s Loading required package: Matrix 307s Loading required package: survival 307s 307s Attaching package: 'survey' 307s 307s > library(survival) 307s The following object is masked from 'package:graphics': 307s 307s dotchart 307s 307s > 307s > pbc2<-rbind(pbc,pbc) 307s > pbc2$id<-rep(1:418,2) 307s > 307s > dpbc1<-svydesign(id=~1, data=pbc) 307s Warning message: 307s In svydesign.default(id = ~1, data = pbc) :> dpbc2<-svydesign(id=~id, data=pbc2) 307s > 307s > s1<-svykm(Surv(time,status>0)~1, subset(dpbc1, bili>6), se=TRUE) 307s > s2<-svykm(Surv(time,status>0)~1, subset(dpbc2, bili>6), se=TRUE) 307s 307s No weights or probabilities supplied, assuming equal probability 307s Warning message: 307s In svydesign.default(id = ~id, data = pbc2) : 307s No weights or probabilities supplied, assuming equal probability 307s > 307s > (c1<-confint(s1,(1:5)*365)) 307s 0.025 0.975 307s 365 0.6446215 0.8594153 307s 730 0.5410938 0.7766848 307s 1095 0.2683127 0.5103356 307s 1460 0.1444731 0.3722001 307s 1825 0.1009672 0.3204713 307s > (c2<-confint(s2,(1:5)*365)) 307s 0.025 0.975 307s 365 0.6446215 0.8594153 307s 730 0.5410938 0.7766848 307s 1095 0.2683127 0.5103356 307s 1460 0.1444731 0.3722001 307s 1825 0.1009672 0.3204713 307s > all.equal(c1, c2) 307s [1] TRUE 307s > 307s > m1<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc1) 307s > m2<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc2) 307s > 307s > d<-data.frame(bili=c(5,10)) 307s > p1<-predict(m1, se=TRUE, newdata=d,type="curve") 308s > p2<-predict(m2, se=TRUE, newdata=d,type="curve") 309s > 309s > (pc1<-confint(p1[[1]],(1:5)*365)) 309s 0.025 0.975 309s 365 0.8410027 0.9266263 309s 730 0.7371114 0.8548312 309s 1095 0.5517779 0.7018583 309s 1460 0.4335073 0.5992819 309s 1825 0.3260899 0.5046241 309s > (pc2<-confint(p2[[1]],(1:5)*365)) 309s 0.025 0.975 309s 365 0.8409490 0.9267054 309s 730 0.7370152 0.8549432 309s 1095 0.5515848 0.7019513 309s 1460 0.4332252 0.5992968 309s 1825 0.3257172 0.5045795 309s > all.equal(pc1, pc2) 309s [1] "Mean relative difference: 0.0002070722" 309s > 309s > (q1<-quantile(p1[[2]])) 309s 0.75 0.5 0.25 309s 489 930 1492 309s > (q2<-quantile(p2[[2]])) 309s 0.75 0.5 0.25 309s 489 930 1492 309s > all.equal(q1,q2) 309s [1] TRUE 309s > 309s BEGIN TEST svyby-strings.R 309s 309s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 309s Copyright (C) 2024 The R Foundation for Statistical Computing 309s Platform: aarch64-unknown-linux-gnu (64-bit) 309s 309s R is free software and comes with ABSOLUTELY NO WARRANTY. 309s You are welcome to redistribute it under certain conditions. 309s Type 'license()' or 'licence()' for distribution details. 309s 309s R is a collaborative project with many contributors. 309s Type 'contributors()' for more information and 309s 'citation()' on how to cite R or R packages in publications. 309s 309s Type 'demo()' for some demos, 'help()' for on-line help, or 309s 'help.start()' for an HTML browser interface to help. 309s Type 'q()' to quit R. 309s 310s > 310s > ## check that stringsAsFactors fixes the string levels problem 310s > data(api, package = "survey") 310s > des <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 311s > est0 <- 311s + survey::svyby(design=des, formula=~cname, by=~both, FUN=survey::svymean, keep.var=TRUE, stringsAsFactors=TRUE) 311s > 311s > stopifnot(isTRUE(all(dim(est0)==c(2,23)))) 311s > 311s BEGIN TEST svyby_bug.R 311s 311s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 311s Copyright (C) 2024 The R Foundation for Statistical Computing 311s Platform: aarch64-unknown-linux-gnu (64-bit) 311s 311s R is free software and comes with ABSOLUTELY NO WARRANTY. 311s You are welcome to redistribute it under certain conditions. 311s Type 'license()' or 'licence()' for distribution details. 311s 311s R is a collaborative project with many contributors. 311s Type 'contributors()' for more information and 311s 'citation()' on how to cite R or R packages in publications. 311s 311s Type 'demo()' for some demos, 'help()' for on-line help, or 311s 'help.start()' for an HTML browser interface to help. 311s Type 'q()' to quit R. 311s 311s > library(survey) 311s Loading required package: grid 311s Loading required package: Matrix 312s Loading required package: survival 312s 312s Attaching package: 'survey' 312s 312s > options(warn=2) 312s > 312s > ## Caused warnings and unhelpful results in 4.1_1 (Guilherme Jacob) 312s > data(api) 312s The following object is masked from 'package:graphics': 312s 312s dotchart 312s 312s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 312s > svyby(~api99, ~stype, dclus1, svymean ) 312s stype api99 se 312s E E 607.7917 22.81660 312s H H 595.7143 41.76400 312s M M 608.6000 32.56064 312s > 312s > set.seed(123) 312s > apiclus1$api99[ sample.int( nrow(apiclus1) , 5 ) ] <- NA 312s > dclus1.na <-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 312s > 312s > # subsetting w/ na.rm = FALSE... 312s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = FALSE ) 312s mean SE 312s api99 NA NaN 312s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = FALSE ) 312s mean SE 312s api99 595.71 41.764 312s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = FALSE ) 312s mean SE 312s api99 NA NaN 312s > 312s > # ... looks like this: 312s > svyby(~api99, ~stype, dclus1.na , svymean ) 312s stype api99 se 312s E E NA NaN 312s H H 595.7143 41.764 312s M M NA NaN 312s > 312s > # subsetting w/ na.rm = TRUE... 312s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = TRUE ) 312s mean SE 312s api99 606.53 22.901 312s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = TRUE ) 312s mean SE 312s api99 595.71 41.764 312s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = TRUE ) 312s mean SE 312s api99 613.39 33.224 312s > 312s > # ... looks like this 312s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE ) 312s stype api99 se 312s E E 606.5319 22.90084 312s H H 595.7143 41.76400 312s M M 613.3913 33.22358 312s > 312s > # Without missing values, this works: 312s > svyby(~api99, ~stype, dclus1 , svymean , na.rm = TRUE , covmat = TRUE ) 312s stype api99 se 312s E E 607.7917 22.81660 312s H H 595.7143 41.76400 312s M M 608.6000 32.56064 312s > 312s > # ... but this breaks! 312s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE , covmat = TRUE ) 312s stype api99 se 312s E E 606.5319 22.90084 312s H H 595.7143 41.76400 312s M M 613.3913 33.22358 312s > 312s > # ... and i don't think this is the expected behavior 312s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , covmat = TRUE ) 312s stype api99 se 312s E E NA NaN 312s H H 595.7143 41.764 312s M M NA NaN 312s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , na.rm = TRUE , covmat = TRUE ) 312s stype api99 se 312s E E 606.5319 22.90084 312s H H 595.7143 41.76400 312s M M 613.3913 33.22358 312s > 312s > 312s > ## Now some more as tests 312s > svyby(~api99, ~stype, dclus1.na , svytotal , na.rm = TRUE , covmat = TRUE ) 312s stype api99 se 312s E E 2894629.0 792809.8 312s H H 282283.9 101492.9 312s M M 477513.4 107555.5 312s > svyby(~api99, ~stype, dclus1.na , svyratio , na.rm = TRUE , denominator=~api00, covmat = TRUE ) 312s stype api99/api00 se.api99/api00 312s E E 0.9367750 0.006365702 312s H H 0.9630485 0.010520785 312s M M 0.9682246 0.009390982 312s > 312s > ff<-function(f,d,...,na.rm=TRUE) svyglm(f,d,...) 312s > svyby(api99~1, ~stype, dclus1.na , ff , na.rm = TRUE , covmat = TRUE ) 312s stype (Intercept) se.(Intercept) 312s E E 606.5319 22.90084 312s H H 595.7143 41.76400 312s M M 613.3913 33.22358 312s > 312s BEGIN TEST svyby_se.R 312s 312s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 312s Copyright (C) 2024 The R Foundation for Statistical Computing 312s Platform: aarch64-unknown-linux-gnu (64-bit) 312s 312s R is free software and comes with ABSOLUTELY NO WARRANTY. 312s You are welcome to redistribute it under certain conditions. 312s Type 'license()' or 'licence()' for distribution details. 312s 312s R is a collaborative project with many contributors. 312s Type 'contributors()' for more information and 312s 'citation()' on how to cite R or R packages in publications. 312s 312s Type 'demo()' for some demos, 'help()' for on-line help, or 312s 'help.start()' for an HTML browser interface to help. 312s Type 'q()' to quit R. 312s 312s > library(survey) 312s Loading required package: grid 312s Loading required package: Matrix 313s Loading required package: survival 313s 313s Attaching package: 'survey' 313s 313s The following object is masked from 'package:graphics': 313s 313s dotchart 313s 313s > data(api) 313s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 313s > 313s > a<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("ci","se")) 313s > b<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("se","ci")) 313s > 313s > 313s > stopifnot(all.equal(SE(a),SE(b))) 313s > 314s BEGIN TEST svycontrast.R 314s 314s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 314s Copyright (C) 2024 The R Foundation for Statistical Computing 314s Platform: aarch64-unknown-linux-gnu (64-bit) 314s 314s R is free software and comes with ABSOLUTELY NO WARRANTY. 314s You are welcome to redistribute it under certain conditions. 314s Type 'license()' or 'licence()' for distribution details. 314s 314s R is a collaborative project with many contributors. 314s Type 'contributors()' for more information and 314s 'citation()' on how to cite R or R packages in publications. 314s 314s Type 'demo()' for some demos, 'help()' for on-line help, or 314s 'help.start()' for an HTML browser interface to help. 314s Type 'q()' to quit R. 314s 314s > library(survey) 314s Loading required package: grid 314s Loading required package: Matrix 315s Loading required package: survival 315s 315s Attaching package: 'survey' 315s 315s > data(api) 315s The following object is masked from 'package:graphics': 315s 315s dotchart 315s 315s > dclus2<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 315s > rclus2<-as.svrepdesign(dclus2) 315s > model<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2) 315s > svycontrast(model, c(ell=1,meals=0)) 315s contrast SE 315s contrast -2.0592 1.6177 315s > a<-svycontrast(model, c(0,1,0,0)) 315s > 315s > model2<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2,return.replicates=TRUE) 315s > svycontrast(model2, c(ell=1,meals=0)) 315s contrast SE 315s contrast -2.0592 1.6177 315s > a2<-svycontrast(model2, c(0,1,0,0)) 315s > stopifnot(!is.null(a2$replicates)) 315s > 315s BEGIN TEST svyivreg-var.R 315s 315s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 315s Copyright (C) 2024 The R Foundation for Statistical Computing 315s Platform: aarch64-unknown-linux-gnu (64-bit) 315s 315s R is free software and comes with ABSOLUTELY NO WARRANTY. 315s You are welcome to redistribute it under certain conditions. 315s Type 'license()' or 'licence()' for distribution details. 315s 315s R is a collaborative project with many contributors. 315s Type 'contributors()' for more information and 315s 'citation()' on how to cite R or R packages in publications. 315s 315s Type 'demo()' for some demos, 'help()' for on-line help, or 315s 'help.start()' for an HTML browser interface to help. 315s Type 'q()' to quit R. 315s 315s > 315s > library(survey) 315s Loading required package: grid 315s Loading required package: Matrix 316s Loading required package: survival 316s 316s Attaching package: 'survey' 316s 316s > data(api) 316s The following object is masked from 'package:graphics': 316s 316s dotchart 316s 316s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 316s > a<-summary(svyglm(api00~ell+meals+mobility, design=dstrat)) 316s > b<- summary(svyivreg(api00~ell+meals+mobility, design=dstrat)) 316s > stopifnot(isTRUE(all.equal(a$cov.scaled, b$vcov))) 316s > 316s BEGIN TEST svyivreg.R 316s 316s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 316s Copyright (C) 2024 The R Foundation for Statistical Computing 316s Platform: aarch64-unknown-linux-gnu (64-bit) 316s 316s R is free software and comes with ABSOLUTELY NO WARRANTY. 316s You are welcome to redistribute it under certain conditions. 316s Type 'license()' or 'licence()' for distribution details. 316s 316s R is a collaborative project with many contributors. 316s Type 'contributors()' for more information and 316s 'citation()' on how to cite R or R packages in publications. 316s 316s Type 'demo()' for some demos, 'help()' for on-line help, or 316s 'help.start()' for an HTML browser interface to help. 316s Type 'q()' to quit R. 316s 317s > library(survey) 317s Loading required package: grid 317s Loading required package: Matrix 317s Loading required package: survival 318s > library(AER) 318s 318s Attaching package: 'survey' 318s 318s The following object is masked from 'package:graphics': 318s 318s dotchart 318s 318s Loading required package: car 318s Loading required package: carData 318s Loading required package: lmtest 318s Loading required package: zoo 318s 318s Attaching package: 'zoo' 318s 318s The following objects are masked from 'package:base': 318s 318s as.Date, as.Date.numeric 318s 318s Loading required package: sandwich 318s > 318s > load("cigsw.rda") 318s > 318s > des<-svydesign(id=~1, weights=~wt, data=cigsw) 318s > m<-svyivreg(log(packs) ~ log(rprice) + log(rincome) | log(rincome) + tdiff + I(tax/cpi), design=des) 318s > 318s > all.equal(as.vector(coef(m)), c(10.42009 , -1.588135, 0.6140887),tolerance=1e-6) 318s [1] TRUE 318s > all.equal(as.vector(SE(m)), c( 1.047699, .3394232, .3614382 ),tolerance=1e-6) 318s [1] TRUE 318s > 318s BEGIN TEST svyolr-rake-subset.R 318s 318s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 318s Copyright (C) 2024 The R Foundation for Statistical Computing 318s Platform: aarch64-unknown-linux-gnu (64-bit) 318s 318s R is free software and comes with ABSOLUTELY NO WARRANTY. 318s You are welcome to redistribute it under certain conditions. 318s Type 'license()' or 'licence()' for distribution details. 318s 318s R is a collaborative project with many contributors. 318s Type 'contributors()' for more information and 318s 'citation()' on how to cite R or R packages in publications. 318s 318s Type 'demo()' for some demos, 'help()' for on-line help, or 318s 'help.start()' for an HTML browser interface to help. 318s Type 'q()' to quit R. 318s 318s > library(survey) 318s Loading required package: grid 318s Loading required package: Matrix 319s Loading required package: survival 319s 319s Attaching package: 'survey' 319s 319s The following object is masked from 'package:graphics': 319s 319s dotchart 319s 319s > data(api) 319s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 319s > 319s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 319s > 319s > ## population marginal totals for each stratum 319s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 319s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 319s > 319s > 319s > ## rake with the population totals 319s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 319s > 319s > # works 319s > m <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 319s > 319s > # fails in 4.1 (should work because svyolr's default na.action is na.omit) 319s > m2 <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1r) 319s > 319s > # fails in 4.1 (should work because NA values are subsetted out) 319s > m3 <- svyolr(mealcat~avg.ed+mobility+stype, design=subset( dclus1r , !is.na( avg.ed ) ) ) 319s > 319s BEGIN TEST svyolr.R 319s 319s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 319s Copyright (C) 2024 The R Foundation for Statistical Computing 319s Platform: aarch64-unknown-linux-gnu (64-bit) 319s 319s R is free software and comes with ABSOLUTELY NO WARRANTY. 319s You are welcome to redistribute it under certain conditions. 319s Type 'license()' or 'licence()' for distribution details. 319s 319s R is a collaborative project with many contributors. 319s Type 'contributors()' for more information and 319s 'citation()' on how to cite R or R packages in publications. 319s 319s Type 'demo()' for some demos, 'help()' for on-line help, or 319s 'help.start()' for an HTML browser interface to help. 319s Type 'q()' to quit R. 319s 319s > library(survey) 319s Loading required package: grid 319s Loading required package: Matrix 320s Loading required package: survival 320s 320s Attaching package: 'survey' 320s 320s > 320s > ################################################################################ 320s > # Example from svyolr: runs OK 320s > data(api) 320s The following object is masked from 'package:graphics': 320s 320s dotchart 320s 320s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 320s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 320s > 320s > m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 320s > m 320s Call: 320s svyolr(mealcat ~ avg.ed + mobility + stype, design = dclus1) 320s 320s Coefficients: 320s avg.ed mobility stypeH stypeM 320s -2.6999217 0.0325042 -1.7574715 -0.6191463 320s 320s Intercepts: 320s (0,25]|(25,50] (25,50]|(50,75] (50,75]|(75,100] 320s -8.857919 -6.586464 -4.924938 320s > 320s > ## Use regTermTest for testing multiple parameters 320s > test<-regTermTest(m, ~avg.ed+stype, method="LRT") 320s > ################################################################################ 320s > 320s > ################################################################################ 320s > # If we wrap everything into a function: error b/c it looks for design variable 320s > # dclus1 in .GlobalEnv 320s > 320s > foo <- function(x){ 320s + dclus1<-svydesign(id=~dnum, weights=~pw, data=x, fpc=~fpc) 320s + dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 320s + 320s + m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 320s + ## Use regTermTest for testing multiple parameters 320s + regTermTest(m, ~avg.ed+stype, method="LRT") 320s + } 320s > 320s > # OK 320s > foo(apiclus1) 320s Working (Rao-Scott+F) LRT for avg.ed stype 320s in svyolr(formula = mealcat ~ avg.ed + mobility + stype, design = dclus1) 320s Working 2logLR = 0.6580304 p= 0.73257 320s (scale factors: 2.7 0.22 0.11 ); denominator df= 10 320s > 320s > # Clean-up everything but apiclus1 and foo 320s > rm(list = setdiff(ls(),c('apiclus1','foo','test'))) 320s > 320s > # Error 320s > test2<-foo(apiclus1) 320s > ################################################################################ 320s > all.equal(test,test2) 320s [1] TRUE 320s > 320s > 320s BEGIN TEST toy_example_for_postStratify.R 321s 321s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 321s Copyright (C) 2024 The R Foundation for Statistical Computing 321s Platform: aarch64-unknown-linux-gnu (64-bit) 321s 321s R is free software and comes with ABSOLUTELY NO WARRANTY. 321s You are welcome to redistribute it under certain conditions. 321s Type 'license()' or 'licence()' for distribution details. 321s 321s R is a collaborative project with many contributors. 321s Type 'contributors()' for more information and 321s 'citation()' on how to cite R or R packages in publications. 321s 321s Type 'demo()' for some demos, 'help()' for on-line help, or 321s 'help.start()' for an HTML browser interface to help. 321s Type 'q()' to quit R. 321s 321s > library(survey) 321s Loading required package: grid 321s Loading required package: Matrix 322s Loading required package: survival 322s 322s Attaching package: 'survey' 322s 322s The following object is masked from 'package:graphics': 322s 322s dotchart 322s 322s > 322s > # Dummy data for testing nonresponse adjustments 322s > toy <- data.frame(id = 1:10, 322s + dummy = 1, 322s + class = c(rep("A", 5), rep("B", 5)), 322s + responded = c(rep(TRUE, 8), FALSE, FALSE), 322s + weight = rep(100, 10)) 322s > 322s > # With jackknife replicate weights 322s > toy_repweights <- matrix(rep(1000/9, 100), nrow = 10) 322s > diag(toy_repweights) <- rep(0, 10) 322s > 322s > # Scramble up which person is in which jackknife group 322s > toy_repweights <- toy_repweights[sample(1:10, size = 10), ] 322s > 322s > toy_design <- svrepdesign(variables = toy[, 1:4], 322s + weights = toy$weight, 322s + repweights = toy_repweights, 322s + type = "JK1", 322s + scale = 0.9) 322s > 322s > # Get the sum of the weights for the full sample 322s > poptotals <- as.data.frame(svyby(formula = ~dummy, 322s + by = ~class, 322s + design = toy_design, 322s + FUN = survey::svytotal)) 322s > 322s > poptotals$Freq <- poptotals$dummy 322s > poptotals$dummy <- NULL 322s > poptotals$se <- NULL 322s > 322s > # Adjust the weights of the responding sample to match to the full sample 322s > adjusted <- postStratify(design = subset(toy_design, responded), 322s + strata = ~class, 322s + population = poptotals) 322s > 322s > # This works for the weights... 322s > svyby(formula = ~dummy, 322s + by = ~class, 322s + design = adjusted, 322s + FUN = survey::svytotal) 322s class dummy se 322s A A 500 0 322s B B 500 0 322s > 322s > # ...and some, but not all, the replicate weights 322s > stopifnot(all.equal(colSums(toy_design$repweights), colSums(adjusted$repweights))) 322s > 322s > 322s > 322s BEGIN TEST twophase.R 322s 322s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 322s Copyright (C) 2024 The R Foundation for Statistical Computing 322s Platform: aarch64-unknown-linux-gnu (64-bit) 322s 322s R is free software and comes with ABSOLUTELY NO WARRANTY. 322s You are welcome to redistribute it under certain conditions. 322s Type 'license()' or 'licence()' for distribution details. 322s 322s R is a collaborative project with many contributors. 322s Type 'contributors()' for more information and 322s 'citation()' on how to cite R or R packages in publications. 322s 322s Type 'demo()' for some demos, 'help()' for on-line help, or 322s 'help.start()' for an HTML browser interface to help. 322s Type 'q()' to quit R. 322s 322s > library(survey) 322s Loading required package: grid 322s Loading required package: Matrix 323s Loading required package: survival 323s 323s Attaching package: 'survey' 323s 323s > 323s > ## two-phase simple random sampling. 323s > data(pbc, package="survival") 323s The following object is masked from 'package:graphics': 323s 323s dotchart 323s 323s > pbc$id<-1:nrow(pbc) 323s > pbc$randomized<-with(pbc, !is.na(trt) & trt>-9) 323s > (d2pbc<-twophase(id=list(~id,~id), data=pbc, subset=~I(!randomized))) 323s Two-phase sparse-matrix design: 323s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 323s subset = subset, data = data) 323s Phase 1: 323s Independent Sampling design (with replacement) 323s svydesign(ids = ~id) 323s Phase 2: 323s Independent Sampling design 323s svydesign(ids = ~id, fpc = `*phase1*`) 323s > m<-svymean(~bili, d2pbc) 323s > all.equal(as.vector(coef(m)),with(pbc, mean(bili[!randomized]))) 323s [1] TRUE 323s > all.equal(as.vector(SE(m)), 323s + with(pbc, sd(bili[!randomized])/sqrt(sum(!randomized))), 323s + tolerance=0.002) 323s [1] TRUE 323s > 323s > ## two-stage sampling as two-phase 323s > data(mu284) 323s > ii<-with(mu284, c(1:15, rep(1:5,n2[1:5]-3))) 323s > mu284.1<-mu284[ii,] 323s > mu284.1$id<-1:nrow(mu284.1) 323s > mu284.1$sub<-rep(c(TRUE,FALSE),c(15,34-15)) 323s > dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284) 323s > ## first phase cluster sample, second phase stratified within cluster 323s > (d2mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 323s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="approx")) 323s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 323s NULL), data = mu284.1, subset = ~sub, method = "approx") 323s Phase 1: 323s 1 - level Cluster Sampling design 323s With (5) clusters. 323s svydesign(ids = ~id1, fpc = ~n1) 323s Phase 2: 323s Stratified Independent Sampling design 323s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 323s > (d22mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 323s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="full")) 323s Two-phase sparse-matrix design: 323s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 323s subset = subset, data = data) 323s Phase 1: 323s 1 - level Cluster Sampling design 323s With (5) clusters. 323s svydesign(ids = ~id1, fpc = ~n1) 323s Phase 2: 323s Stratified Independent Sampling design 323s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 323s > summary(d2mu284) 323s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 323s NULL), data = mu284.1, subset = ~sub, method = "approx") 323s Phase 1: 323s 1 - level Cluster Sampling design 323s With (5) clusters. 323s svydesign(ids = ~id1, fpc = ~n1) 323s Probabilities: 323s Min. 1st Qu. Median Mean 3rd Qu. Max. 323s 0.1 0.1 0.1 0.1 0.1 0.1 323s Population size (PSUs): 50 323s Phase 2: 323s Stratified Independent Sampling design 323s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 323s Probabilities: 323s Min. 1st Qu. Median Mean 3rd Qu. Max. 323s 0.3333 0.3750 0.4286 0.4674 0.6000 0.6000 323s Stratum Sizes: 323s 19 31 45 47 50 323s obs 3 3 3 3 3 323s design.PSU 3 3 3 3 3 323s actual.PSU 3 3 3 3 3 323s Population stratum sizes (PSUs): 323s 19 31 45 47 50 323s 5 7 8 5 9 323s Data variables: 323s [1] "id1" "n1" "id2" "y1" "n2" "id" "sub" 323s > t1<-svytotal(~y1, dmu284) 323s > t2<-svytotal(~y1, d2mu284) 323s > t22<-svytotal(~y1,d22mu284) 323s > m1<-svymean(~y1, dmu284) 323s > m2<-svymean(~y1, d2mu284) 323s > m22<-svymean(~y1, d22mu284) 323s > all.equal(coef(t1),coef(t2)) 323s [1] TRUE 323s > all.equal(coef(t1),coef(t22)) 323s [1] TRUE 323s > all.equal(coef(m1),coef(m2)) 323s [1] TRUE 323s > all.equal(coef(m1),coef(m22)) 323s [1] TRUE 323s > all.equal(as.vector(SE(m1)),as.vector(SE(m2))) 323s [1] TRUE 323s > all.equal(as.vector(SE(m1)),as.vector(SE(m22))) 323s [1] TRUE 323s > all.equal(as.vector(SE(t1)),as.vector(SE(t2))) 323s [1] TRUE 323s > all.equal(as.vector(SE(t1)),as.vector(SE(t22))) 323s [1] TRUE 323s > 323s > ## case-cohort design 323s > ##this example requires R 2.3.1 or later for cch and data. 323s > library("survival") 323s > data(nwtco, package="survival") 323s > ## unstratified, equivalent to Lin & Ying (1993) 323s > print(dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 323s + subset=~I(in.subcohort | rel), data=nwtco)) 324s Two-phase sparse-matrix design: 324s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 324s subset = subset, data = data) 324s Phase 1: 324s Independent Sampling design (with replacement) 324s svydesign(ids = ~seqno) 324s Phase 2: 324s Stratified Independent Sampling design 324s svydesign(ids = ~seqno, strata = ~rel, fpc = `*phase1*`) 324s > cch1<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 324s + design=dcchs) 324s > dcchs2<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 324s + subset=~I(in.subcohort | rel), data=nwtco,method="approx") 324s > cch1.2<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 324s + design=dcchs) 324s > all.equal(coef(cch1),coef(cch1.2)) 324s [1] TRUE 324s > all.equal(SE(cch1),SE(cch1.2)) 324s [1] TRUE 324s > ## Using survival::cch 324s > subcoh <- nwtco$in.subcohort 324s > selccoh <- with(nwtco, rel==1|subcoh==1) 324s > ccoh.data <- nwtco[selccoh,] 324s > ccoh.data$subcohort <- subcoh[selccoh] 324s > cch2<-cch(Surv(edrel, rel) ~ factor(stage) + factor(histol) + I(age/12), 324s + data =ccoh.data, subcoh = ~subcohort, id=~seqno, 324s + cohort.size=4028, method="LinYing", robust=TRUE) 324s > 324s > print(all.equal(as.vector(coef(cch1)),as.vector(coef(cch2)))) 324s [1] TRUE 324s > ## cch has smaller variances by a factor of 1.0005 because 324s > ## there is a (n/(n-1)) in the survey phase1 varianace 324s > print(all.equal(as.vector(SE(cch1)), as.vector(SE(cch2)),tolerance=0.0006)) 324s [1] TRUE 324s > 324s > 324s > ## bug report from Takahiro Tsuchiya for version 3.4 324s > ## We used to not match Sarndal exactly, because our old phase-one 324s > ## estimator had a small bias for finite populations 324s > rei<-read.table(tmp<-textConnection( 324s + " id N n.a h n.ah n.h sub y 324s + 1 1 300 20 1 12 5 TRUE 1 324s + 2 2 300 20 1 12 5 TRUE 2 324s + 3 3 300 20 1 12 5 TRUE 3 324s + 4 4 300 20 1 12 5 TRUE 4 324s + 5 5 300 20 1 12 5 TRUE 5 324s + 6 6 300 20 1 12 5 FALSE NA 324s + 7 7 300 20 1 12 5 FALSE NA 324s + 8 8 300 20 1 12 5 FALSE NA 324s + 9 9 300 20 1 12 5 FALSE NA 324s + 10 10 300 20 1 12 5 FALSE NA 324s + 11 11 300 20 1 12 5 FALSE NA 324s + 12 12 300 20 1 12 5 FALSE NA 324s + 13 13 300 20 2 8 3 TRUE 6 324s + 14 14 300 20 2 8 3 TRUE 7 324s + 15 15 300 20 2 8 3 TRUE 8 324s + 16 16 300 20 2 8 3 FALSE NA 324s + 17 17 300 20 2 8 3 FALSE NA 324s + 18 18 300 20 2 8 3 FALSE NA 324s + 19 19 300 20 2 8 3 FALSE NA 324s + 20 20 300 20 2 8 3 FALSE NA 324s + "), header=TRUE) 324s > close(tmp) 324s > 324s > des.rei <- twophase(id=list(~id,~id), strata=list(NULL,~h), 324s + fpc=list(~N,NULL), subset=~sub, data=rei, method="approx") 324s > tot<- svytotal(~y, des.rei) 324s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 324s + fpc=list(~N,NULL), subset=~sub, data=rei) 324s > tot2<- svytotal(~y, des.rei2) 324s > 324s > ## based on Sarndal et al (9.4.14) 324s > rei$w.ah <- rei$n.ah / rei$n.a 324s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 324s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 324s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 324s > 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)) 324s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 324s > 324s > a.rei$f.h<-with(a.rei, n.h/n.ah) 324s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 324s > 324s > a.rei$f<-with(a.rei, n.a/N) 324s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 324s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2))) 324s > 324s > V 324s [1] 36522.63 324s > Vphase1 324s [1] 24072.63 324s > Vphase2 324s [1] 12450 324s > vcov(tot) 324s y 324s y 35911.05 324s attr(,"phases") 324s attr(,"phases")$phase1 324s [,1] 324s [1,] 23461.05 324s 324s attr(,"phases")$phase2 324s y 324s y 12450 324s 324s > vcov(tot2) 324s [,1] 324s [1,] 36522.63 324s attr(,"phases") 324s attr(,"phases")$phase1 324s [,1] 324s [1,] 24072.63 324s 324s attr(,"phases")$phase2 324s [,1] 324s [1,] 12450 324s 324s > ## phase 2 identical 324s > all.equal(Vphase2,drop(attr(vcov(tot),"phases")$phase2)) 324s [1] TRUE 324s > all.equal(Vphase2,drop(attr(vcov(tot2),"phases")$phase2)) 324s [1] TRUE 324s > ## phase 1 differs by 2.6% for old twophase estimator 324s > Vphase1/attr(vcov(tot),"phases")$phase1 324s [,1] 324s [1,] 1.026068 324s > all.equal(Vphase1,as.vector(attr(vcov(tot2),"phases")$phase1)) 324s [1] TRUE 324s > 324s > 325s autopkgtest [20:25:49]: test run-unit-test: -----------------------] 325s autopkgtest [20:25:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 325s run-unit-test PASS 326s autopkgtest [20:25:50]: test pkg-r-autopkgtest: preparing testbed 327s Reading package lists... 327s Building dependency tree... 327s Reading state information... 327s Starting pkgProblemResolver with broken count: 0 327s Starting 2 pkgProblemResolver with broken count: 0 327s Done 328s The following additional packages will be installed: 328s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 328s dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 328s gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 328s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 328s libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 328s libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 libicu-dev libisl23 328s libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 328s liblzma-dev libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 328s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 328s libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config 328s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-hexbin rpcsvc-proto 328s zlib1g-dev 328s Suggested packages: 328s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 328s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 328s gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 328s liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc 328s libstdc++-13-doc texlive-base texlive-latex-base texlive-plain-generic 328s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 328s texlive-latex-recommended texlive-latex-extra texinfo r-bioc-affy 328s r-bioc-biobase r-bioc-limma 328s Recommended packages: 328s bzip2-doc manpages manpages-dev libc-devtools libpng-tools 328s The following NEW packages will be installed: 328s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 328s cpp-aarch64-linux-gnu dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu 328s g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu 328s gcc-aarch64-linux-gnu gfortran gfortran-13 gfortran-13-aarch64-linux-gnu 328s gfortran-aarch64-linux-gnu icu-devtools libasan8 libatomic1 libblas-dev 328s libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev 328s libgfortran-13-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 328s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 328s libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 328s libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev libstdc++-13-dev 328s libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config pkg-r-autopkgtest 328s pkgconf pkgconf-bin r-base-dev r-cran-hexbin rpcsvc-proto zlib1g-dev 328s 0 upgraded, 63 newly installed, 0 to remove and 0 not upgraded. 328s Need to get 94.4 MB/94.4 MB of archives. 328s After this operation, 345 MB of additional disk space will be used. 328s Get:1 /tmp/autopkgtest.8gUBgk/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [768 B] 328s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 328s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 329s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 329s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [201 kB] 329s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 329s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 329s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 329s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 329s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 329s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 329s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 329s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 329s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 329s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 329s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 329s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 329s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 329s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 329s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 330s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 330s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 330s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 330s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 330s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 330s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 330s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 330s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 330s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 330s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 330s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 330s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 330s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 330s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB] 330s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] 330s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] 331s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] 331s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] 331s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] 331s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] 331s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] 331s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 331s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] 331s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] 331s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 331s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 331s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] 331s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] 331s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] 331s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB] 331s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B] 331s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB] 331s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 331s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 331s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-3 [267 kB] 331s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline-dev arm64 8.2-3.1 [177 kB] 331s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 331s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 331s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 331s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 331s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-dev all 4.3.3-2build1 [4334 B] 331s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 331s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-hexbin arm64 1.28.3-1 [1576 kB] 332s Fetched 94.4 MB in 3s (30.3 MB/s) 332s Selecting previously unselected package libc-dev-bin. 332s (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 ... 96002 files and directories currently installed.) 332s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 332s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 332s Selecting previously unselected package linux-libc-dev:arm64. 332s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_arm64.deb ... 332s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 332s Selecting previously unselected package libcrypt-dev:arm64. 332s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 332s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 332s Selecting previously unselected package libtirpc-dev:arm64. 332s Preparing to unpack .../03-libtirpc-dev_1.3.4+ds-1.1_arm64.deb ... 332s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 332s Selecting previously unselected package libnsl-dev:arm64. 332s Preparing to unpack .../04-libnsl-dev_1.3.0-3_arm64.deb ... 332s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 332s Selecting previously unselected package rpcsvc-proto. 332s Preparing to unpack .../05-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 332s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 332s Selecting previously unselected package libc6-dev:arm64. 332s Preparing to unpack .../06-libc6-dev_2.39-0ubuntu2_arm64.deb ... 332s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 333s Selecting previously unselected package libisl23:arm64. 333s Preparing to unpack .../07-libisl23_0.26-3_arm64.deb ... 333s Unpacking libisl23:arm64 (0.26-3) ... 333s Selecting previously unselected package libmpc3:arm64. 333s Preparing to unpack .../08-libmpc3_1.3.1-1_arm64.deb ... 333s Unpacking libmpc3:arm64 (1.3.1-1) ... 333s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 333s Preparing to unpack .../09-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 333s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 333s Selecting previously unselected package cpp-13. 333s Preparing to unpack .../10-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 333s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 333s Selecting previously unselected package cpp-aarch64-linux-gnu. 333s Preparing to unpack .../11-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 333s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 333s Selecting previously unselected package cpp. 333s Preparing to unpack .../12-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 333s Unpacking cpp (4:13.2.0-7ubuntu1) ... 333s Selecting previously unselected package libcc1-0:arm64. 333s Preparing to unpack .../13-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 333s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 333s Selecting previously unselected package libitm1:arm64. 334s Preparing to unpack .../14-libitm1_14-20240303-1ubuntu1_arm64.deb ... 334s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 334s Selecting previously unselected package libatomic1:arm64. 334s Preparing to unpack .../15-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 334s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 334s Selecting previously unselected package libasan8:arm64. 334s Preparing to unpack .../16-libasan8_14-20240303-1ubuntu1_arm64.deb ... 334s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 334s Selecting previously unselected package liblsan0:arm64. 334s Preparing to unpack .../17-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 334s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 334s Selecting previously unselected package libtsan2:arm64. 334s Preparing to unpack .../18-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 334s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 334s Selecting previously unselected package libubsan1:arm64. 334s Preparing to unpack .../19-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 334s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 334s Selecting previously unselected package libhwasan0:arm64. 334s Preparing to unpack .../20-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 334s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 334s Selecting previously unselected package libgcc-13-dev:arm64. 334s Preparing to unpack .../21-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 334s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 334s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 334s Preparing to unpack .../22-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 334s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 334s Selecting previously unselected package gcc-13. 335s Preparing to unpack .../23-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 335s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 335s Selecting previously unselected package gcc-aarch64-linux-gnu. 335s Preparing to unpack .../24-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 335s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 335s Selecting previously unselected package gcc. 336s Preparing to unpack .../25-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 336s Unpacking gcc (4:13.2.0-7ubuntu1) ... 336s Selecting previously unselected package libstdc++-13-dev:arm64. 336s Preparing to unpack .../26-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 336s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 336s Selecting previously unselected package g++-13-aarch64-linux-gnu. 337s Preparing to unpack .../27-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 337s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 337s Selecting previously unselected package g++-13. 337s Preparing to unpack .../28-g++-13_13.2.0-17ubuntu2_arm64.deb ... 337s Unpacking g++-13 (13.2.0-17ubuntu2) ... 337s Selecting previously unselected package g++-aarch64-linux-gnu. 337s Preparing to unpack .../29-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 337s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 337s Selecting previously unselected package g++. 337s Preparing to unpack .../30-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 337s Unpacking g++ (4:13.2.0-7ubuntu1) ... 337s Selecting previously unselected package build-essential. 337s Preparing to unpack .../31-build-essential_12.10ubuntu1_arm64.deb ... 337s Unpacking build-essential (12.10ubuntu1) ... 337s Selecting previously unselected package dctrl-tools. 337s Preparing to unpack .../32-dctrl-tools_2.24-3build2_arm64.deb ... 337s Unpacking dctrl-tools (2.24-3build2) ... 337s Selecting previously unselected package libgfortran-13-dev:arm64. 337s Preparing to unpack .../33-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ... 337s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 337s Selecting previously unselected package gfortran-13-aarch64-linux-gnu. 337s Preparing to unpack .../34-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 337s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 338s Selecting previously unselected package gfortran-13. 338s Preparing to unpack .../35-gfortran-13_13.2.0-17ubuntu2_arm64.deb ... 338s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 338s Selecting previously unselected package gfortran-aarch64-linux-gnu. 338s Preparing to unpack .../36-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 338s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 338s Selecting previously unselected package gfortran. 338s Preparing to unpack .../37-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ... 338s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 338s Selecting previously unselected package icu-devtools. 338s Preparing to unpack .../38-icu-devtools_74.2-1ubuntu1_arm64.deb ... 338s Unpacking icu-devtools (74.2-1ubuntu1) ... 338s Selecting previously unselected package libblas-dev:arm64. 338s Preparing to unpack .../39-libblas-dev_3.12.0-3_arm64.deb ... 338s Unpacking libblas-dev:arm64 (3.12.0-3) ... 338s Selecting previously unselected package libbz2-dev:arm64. 338s Preparing to unpack .../40-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 338s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 338s Selecting previously unselected package libicu-dev:arm64. 338s Preparing to unpack .../41-libicu-dev_74.2-1ubuntu1_arm64.deb ... 338s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ... 339s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 339s Preparing to unpack .../42-libjpeg-turbo8-dev_2.1.5-2ubuntu1_arm64.deb ... 339s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 339s Selecting previously unselected package libjpeg8-dev:arm64. 339s Preparing to unpack .../43-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 339s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 339s Selecting previously unselected package libjpeg-dev:arm64. 339s Preparing to unpack .../44-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 339s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 339s Selecting previously unselected package liblapack-dev:arm64. 339s Preparing to unpack .../45-liblapack-dev_3.12.0-3_arm64.deb ... 339s Unpacking liblapack-dev:arm64 (3.12.0-3) ... 339s Selecting previously unselected package libncurses-dev:arm64. 339s Preparing to unpack .../46-libncurses-dev_6.4+20240113-1ubuntu1_arm64.deb ... 339s Unpacking libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 339s Selecting previously unselected package libpcre2-16-0:arm64. 339s Preparing to unpack .../47-libpcre2-16-0_10.42-4ubuntu1_arm64.deb ... 339s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 339s Selecting previously unselected package libpcre2-32-0:arm64. 339s Preparing to unpack .../48-libpcre2-32-0_10.42-4ubuntu1_arm64.deb ... 339s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 339s Selecting previously unselected package libpcre2-posix3:arm64. 339s Preparing to unpack .../49-libpcre2-posix3_10.42-4ubuntu1_arm64.deb ... 339s Unpacking libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 339s Selecting previously unselected package libpcre2-dev:arm64. 339s Preparing to unpack .../50-libpcre2-dev_10.42-4ubuntu1_arm64.deb ... 339s Unpacking libpcre2-dev:arm64 (10.42-4ubuntu1) ... 339s Selecting previously unselected package libpkgconf3:arm64. 339s Preparing to unpack .../51-libpkgconf3_1.8.1-2_arm64.deb ... 339s Unpacking libpkgconf3:arm64 (1.8.1-2) ... 339s Selecting previously unselected package zlib1g-dev:arm64. 340s Preparing to unpack .../52-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 340s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 340s Selecting previously unselected package libpng-dev:arm64. 340s Preparing to unpack .../53-libpng-dev_1.6.43-3_arm64.deb ... 340s Unpacking libpng-dev:arm64 (1.6.43-3) ... 340s Selecting previously unselected package libreadline-dev:arm64. 340s Preparing to unpack .../54-libreadline-dev_8.2-3.1_arm64.deb ... 340s Unpacking libreadline-dev:arm64 (8.2-3.1) ... 340s Selecting previously unselected package pkgconf-bin. 340s Preparing to unpack .../55-pkgconf-bin_1.8.1-2_arm64.deb ... 340s Unpacking pkgconf-bin (1.8.1-2) ... 340s Selecting previously unselected package pkgconf:arm64. 340s Preparing to unpack .../56-pkgconf_1.8.1-2_arm64.deb ... 340s Unpacking pkgconf:arm64 (1.8.1-2) ... 340s Selecting previously unselected package pkg-config:arm64. 340s Preparing to unpack .../57-pkg-config_1.8.1-2_arm64.deb ... 340s Unpacking pkg-config:arm64 (1.8.1-2) ... 340s Selecting previously unselected package liblzma-dev:arm64. 340s Preparing to unpack .../58-liblzma-dev_5.4.5-0.3_arm64.deb ... 340s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ... 340s Selecting previously unselected package r-base-dev. 340s Preparing to unpack .../59-r-base-dev_4.3.3-2build1_all.deb ... 340s Unpacking r-base-dev (4.3.3-2build1) ... 340s Selecting previously unselected package pkg-r-autopkgtest. 340s Preparing to unpack .../60-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 340s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 340s Selecting previously unselected package r-cran-hexbin. 340s Preparing to unpack .../61-r-cran-hexbin_1.28.3-1_arm64.deb ... 340s Unpacking r-cran-hexbin (1.28.3-1) ... 340s Selecting previously unselected package autopkgtest-satdep. 340s Preparing to unpack .../62-2-autopkgtest-satdep.deb ... 340s Unpacking autopkgtest-satdep (0) ... 340s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 340s Setting up libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 340s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 340s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 340s Setting up libpkgconf3:arm64 (1.8.1-2) ... 340s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 340s Setting up libmpc3:arm64 (1.3.1-1) ... 340s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 340s Setting up icu-devtools (74.2-1ubuntu1) ... 340s Setting up pkgconf-bin (1.8.1-2) ... 340s Setting up r-cran-hexbin (1.28.3-1) ... 340s Setting up liblzma-dev:arm64 (5.4.5-0.3) ... 340s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 340s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 340s Setting up libnsl-dev:arm64 (1.3.0-3) ... 340s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 340s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 340s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 340s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 340s Setting up libisl23:arm64 (0.26-3) ... 340s Setting up libc-dev-bin (2.39-0ubuntu2) ... 340s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 340s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 340s Setting up libblas-dev:arm64 (3.12.0-3) ... 340s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 340s Setting up dctrl-tools (2.24-3build2) ... 340s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 340s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 340s Setting up pkgconf:arm64 (1.8.1-2) ... 340s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 340s Setting up liblapack-dev:arm64 (3.12.0-3) ... 340s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 340s Setting up pkg-config:arm64 (1.8.1-2) ... 340s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 340s Setting up libc6-dev:arm64 (2.39-0ubuntu2) ... 340s Setting up libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 340s Setting up libicu-dev:arm64 (74.2-1ubuntu1) ... 340s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 340s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 340s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 340s Setting up libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 340s Setting up libpcre2-dev:arm64 (10.42-4ubuntu1) ... 340s Setting up cpp-13 (13.2.0-17ubuntu2) ... 340s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 340s Setting up libreadline-dev:arm64 (8.2-3.1) ... 340s Setting up gcc-13 (13.2.0-17ubuntu2) ... 340s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 340s Setting up cpp (4:13.2.0-7ubuntu1) ... 340s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 340s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 340s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 340s Setting up g++-13 (13.2.0-17ubuntu2) ... 340s Setting up libpng-dev:arm64 (1.6.43-3) ... 340s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 340s Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 340s Setting up gcc (4:13.2.0-7ubuntu1) ... 340s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 340s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 340s Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 340s Setting up gfortran (4:13.2.0-7ubuntu1) ... 340s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 340s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 340s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 340s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist 340s Setting up g++ (4:13.2.0-7ubuntu1) ... 340s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 340s Setting up build-essential (12.10ubuntu1) ... 340s Setting up r-base-dev (4.3.3-2build1) ... 340s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 340s Setting up autopkgtest-satdep (0) ... 340s Processing triggers for man-db (2.12.0-3) ... 341s Processing triggers for install-info (7.1-3) ... 342s Processing triggers for libc-bin (2.39-0ubuntu2) ... 345s (Reading database ... 99613 files and directories currently installed.) 345s Removing autopkgtest-satdep (0) ... 346s autopkgtest [20:26:10]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 346s autopkgtest [20:26:10]: test pkg-r-autopkgtest: [----------------------- 346s Test: Try to load the R library survey 346s 346s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 346s Copyright (C) 2024 The R Foundation for Statistical Computing 346s Platform: aarch64-unknown-linux-gnu (64-bit) 346s 346s R is free software and comes with ABSOLUTELY NO WARRANTY. 346s You are welcome to redistribute it under certain conditions. 346s Type 'license()' or 'licence()' for distribution details. 346s 346s R is a collaborative project with many contributors. 346s Type 'contributors()' for more information and 346s 'citation()' on how to cite R or R packages in publications. 346s 346s Type 'demo()' for some demos, 'help()' for on-line help, or 346s 'help.start()' for an HTML browser interface to help. 346s Type 'q()' to quit R. 346s 347s > library('survey') 347s Loading required package: grid 347s Loading required package: Matrix 348s Loading required package: survival 348s 348s Attaching package: ‘survey’ 348s 348s > 348s > 348s The following object is masked from ‘package:graphics’: 348s 348s dotchart 348s 348s Other tests are currently unsupported! 348s They will be progressively added. 348s autopkgtest [20:26:12]: test pkg-r-autopkgtest: -----------------------] 349s pkg-r-autopkgtest PASS 349s autopkgtest [20:26:13]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 349s autopkgtest [20:26:13]: @@@@@@@@@@@@@@@@@@@@ summary 349s run-unit-test PASS 349s pkg-r-autopkgtest PASS 360s Creating nova instance adt-noble-arm64-r-cran-survey-20240316-202024-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...