# revdeps

package: Gifi
version: 0.3-10
maintainer: Patrick Mair <mair@fas.harvard.edu>
status: ERROR
which: old
duration: 1.60686898231506
starttime: 2022-09-24 22:04:23
summary: {"class":["list"],"object":{"errors":[1],"warnings":[0],"notes":[0]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/old/Gifi.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘Gifi/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘Gifi’ version ‘0.3-10’\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘Gifi’ can be installed ... ERROR\nInstallation failed.\nSee ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/old/Gifi.Rcheck/00install.out’ for details.\n* DONE\n\nStatus: 1 ERROR\nSee\n  ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/old/Gifi.Rcheck/00check.log’\nfor details.\n\n\n"],"stderr":[""],"status":[1],"duration":[1.6072],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":["checking whether package ‘Gifi’ can be installed ... ERROR\nInstallation failed.\nSee ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/old/Gifi.Rcheck/00install.out’ for details."],"warnings":[],"notes":[],"description":["Package: Gifi\nType: Package\nTitle: Multivariate Analysis with Optimal Scaling\nVersion: 0.3-10\nDate: 2022-06-09\nAuthors@R: c(person(\"Patrick\", \"Mair\", role = c(\"aut\", \"cre\"), email = \"mair@fas.harvard.edu\"), person(\"Jan\", \"De Leeuw\", role = \"aut\"), person(\"Patrick J. F.\", \"Groenen\", role = \"ctb\"))\nDescription: Implements categorical principal component analysis ('PRINCALS'), multiple correspondence analysis ('HOMALS'), monotone regression analysis ('MORALS'). It replaces the 'homals' package. \nURL: https://r-forge.r-project.org/projects/psychor/\nImports: graphics, stats, colorspace\nDepends: R (>= 3.1.0)\nLicense: GPL-3\nSuggests: knitr, psych, psychTools\nLazyData: yes\nLazyLoad: yes\nByteCompile: yes\nNeedsCompilation: yes\nPackaged: 2022-06-09 15:18:16 UTC; patrick\nAuthor: Patrick Mair [aut, cre],\n  Jan De Leeuw [aut],\n  Patrick J. F. Groenen [ctb]\nMaintainer: Patrick Mair <mair@fas.harvard.edu>\nRepository: CRAN\nDate/Publication: 2022-06-10 16:33:26 UTC"],"package":["Gifi"],"version":["0.3-10"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/old/Gifi.Rcheck"],"test_fail":{},"test_output":{},"install_out":["* installing *source* package ‘Gifi’ ...\n** package ‘Gifi’ successfully unpacked and MD5 sums checked\n** using staged installation\n** libs\nclang -arch arm64 -I\"/Library/Frameworks/R.framework/Resources/include\" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c coding.c -o coding.o\nclang -arch arm64 -I\"/Library/Frameworks/R.framework/Resources/include\" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c gsC.c -o gsC.o\nclang -arch arm64 -I\"/Library/Frameworks/R.framework/Resources/include\" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o\n/opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c pava.f -o pava.o\nmake: /opt/R/arm64/bin/gfortran: No such file or directory\nmake: *** [pava.o] Error 1\nERROR: compilation failed for package ‘Gifi’\n* removing ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/old/Gifi.Rcheck/Gifi’\n"],"session_info":{"platform":{"version":["R version 4.2.1 (2022-06-23)"],"os":["macOS Monterey 12.6"],"system":["aarch64, darwin20"],"ui":["X11"],"language":["(EN)"],"collate":["C"],"ctype":["en_US.UTF-8"],"tz":["America/Chicago"],"date":["2022-09-24"],"pandoc":["2.19 @ /usr/local/bin/pandoc"]},"packages":[{"package":"Gifi","attached":false,"is_base":false,"_row":"Gifi"}]}}}


package: Gifi
version: 0.3-10
maintainer: Patrick Mair <mair@fas.harvard.edu>
status: ERROR
which: new
duration: 1.55937504768372
starttime: 2022-09-24 22:04:23
summary: {"class":["list"],"object":{"errors":[1],"warnings":[0],"notes":[0]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/new/Gifi.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘Gifi/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘Gifi’ version ‘0.3-10’\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘Gifi’ can be installed ... ERROR\nInstallation failed.\nSee ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/new/Gifi.Rcheck/00install.out’ for details.\n* DONE\n\nStatus: 1 ERROR\nSee\n  ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/new/Gifi.Rcheck/00check.log’\nfor details.\n\n\n"],"stderr":[""],"status":[1],"duration":[1.6749],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":["checking whether package ‘Gifi’ can be installed ... ERROR\nInstallation failed.\nSee ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/new/Gifi.Rcheck/00install.out’ for details."],"warnings":[],"notes":[],"description":["Package: Gifi\nType: Package\nTitle: Multivariate Analysis with Optimal Scaling\nVersion: 0.3-10\nDate: 2022-06-09\nAuthors@R: c(person(\"Patrick\", \"Mair\", role = c(\"aut\", \"cre\"), email = \"mair@fas.harvard.edu\"), person(\"Jan\", \"De Leeuw\", role = \"aut\"), person(\"Patrick J. F.\", \"Groenen\", role = \"ctb\"))\nDescription: Implements categorical principal component analysis ('PRINCALS'), multiple correspondence analysis ('HOMALS'), monotone regression analysis ('MORALS'). It replaces the 'homals' package. \nURL: https://r-forge.r-project.org/projects/psychor/\nImports: graphics, stats, colorspace\nDepends: R (>= 3.1.0)\nLicense: GPL-3\nSuggests: knitr, psych, psychTools\nLazyData: yes\nLazyLoad: yes\nByteCompile: yes\nNeedsCompilation: yes\nPackaged: 2022-06-09 15:18:16 UTC; patrick\nAuthor: Patrick Mair [aut, cre],\n  Jan De Leeuw [aut],\n  Patrick J. F. Groenen [ctb]\nMaintainer: Patrick Mair <mair@fas.harvard.edu>\nRepository: CRAN\nDate/Publication: 2022-06-10 16:33:26 UTC"],"package":["Gifi"],"version":["0.3-10"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/new/Gifi.Rcheck"],"test_fail":{},"test_output":{},"install_out":["* installing *source* package ‘Gifi’ ...\n** package ‘Gifi’ successfully unpacked and MD5 sums checked\n** using staged installation\n** libs\nclang -arch arm64 -I\"/Library/Frameworks/R.framework/Resources/include\" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c coding.c -o coding.o\nclang -arch arm64 -I\"/Library/Frameworks/R.framework/Resources/include\" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c gsC.c -o gsC.o\nclang -arch arm64 -I\"/Library/Frameworks/R.framework/Resources/include\" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o\n/opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c pava.f -o pava.o\nmake: /opt/R/arm64/bin/gfortran: No such file or directory\nmake: *** [pava.o] Error 1\nERROR: compilation failed for package ‘Gifi’\n* removing ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/Gifi/new/Gifi.Rcheck/Gifi’\n"],"session_info":{"platform":{"version":["R version 4.2.1 (2022-06-23)"],"os":["macOS Monterey 12.6"],"system":["aarch64, darwin20"],"ui":["X11"],"language":["(EN)"],"collate":["C"],"ctype":["en_US.UTF-8"],"tz":["America/Chicago"],"date":["2022-09-24"],"pandoc":["2.19 @ /usr/local/bin/pandoc"]},"packages":[{"package":"Gifi","attached":false,"is_base":false,"_row":"Gifi"}]}}}


package: conogive
version: 1.0.0
maintainer: Jonas Moss <jonas.gjertsen@gmail.com>
status: NOTE
which: old
duration: 8.75680589675903
starttime: 2022-09-24 22:04:20
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[1]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/conogive/old/conogive.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘conogive/DESCRIPTION’ ... OK\n* this is package ‘conogive’ version ‘1.0.0’\n* package encoding: UTF-8\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘conogive’ can be installed ... OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking LazyData ... NOTE\n  'LazyData' is specified without a 'data' directory\n* checking examples ... OK\n* checking for unstated dependencies in ‘tests’ ... OK\n* checking tests ...\n  Running ‘testthat.R’\n OK\n* DONE\n\nStatus: 1 NOTE\nSee\n  ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/conogive/old/conogive.Rcheck/00check.log’\nfor details.\n\n\n\n"],"stderr":[""],"status":[0],"duration":[8.7572],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":["checking LazyData ... NOTE\n  'LazyData' is specified without a 'data' directory"],"description":["Package: conogive\nTitle: Congeneric Normal-Ogive Model\nVersion: 1.0.0\nAuthors@R: c(\n    person(\"Jonas\", \"Moss\", , \"jonas.gjertsen@gmail.com\", role = c(\"aut\", \"cre\"), \n      comment = c(ORCID = \"0000-0002-6876-6964\")\n    ))\nDescription: The congeneric normal-ogive model is a popular model for \n   psychometric data (McDonald, R. P. (1997) <doi:10.1007/978-1-4757-2691-6_15>).\n   This model estimates the model, calculates theoretical and concrete \n   reliability coefficients, and predicts the latent variable of the model. \n   This is the companion package to Moss (2020) <doi:10.31234/osf.io/nvg5d>.\nLicense: MIT + file LICENSE\nEncoding: UTF-8\nLazyData: true\nURL: https://github.com/JonasMoss/conogive\nBugReports: https://github.com/JonasMoss/conogive/issues\nRoxygenNote: 7.1.0\nImports: psych, mvtnorm, checkmate, assertthat\nSuggests: testthat (>= 2.1.0), psychTools, covr\nNeedsCompilation: no\nPackaged: 2020-06-30 10:02:28 UTC; jonas\nAuthor: Jonas Moss [aut, cre] (<https://orcid.org/0000-0002-6876-6964>)\nMaintainer: Jonas Moss <jonas.gjertsen@gmail.com>\nRepository: CRAN\nDate/Publication: 2020-06-30 10:30:02 UTC"],"package":["conogive"],"version":["1.0.0"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/conogive/old/conogive.Rcheck"],"test_fail":{},"test_output":{"testthat":["> library(testthat)\n> library(conogive)\n> \n> test_check(\"conogive\")\n[ FAIL 0 | WARN 0 | SKIP 0 | PASS 35 ]\n> \n> proc.time()\n   user  system elapsed \n  0.540   0.100   1.101 \n"]},"install_out":["* installing *source* package ‘conogive’ ...\n** package ‘conogive’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n*** copying figures\n** building package indices\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (conogive)\n"],"session_info":{"platform":{"version":["R version 4.2.1 (2022-06-23)"],"os":["macOS Monterey 12.6"],"system":["aarch64, darwin20"],"ui":["X11"],"language":["(EN)"],"collate":["C"],"ctype":["en_US.UTF-8"],"tz":["America/Chicago"],"date":["2022-09-24"],"pandoc":["2.19 @ /usr/local/bin/pandoc"]},"packages":[{"package":"conogive","attached":false,"is_base":false,"_row":"conogive"}]}}}


package: conogive
version: 1.0.0
maintainer: Jonas Moss <jonas.gjertsen@gmail.com>
status: NOTE
which: new
duration: 8.33570098876953
starttime: 2022-09-24 22:04:21
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[1]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/conogive/new/conogive.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘conogive/DESCRIPTION’ ... OK\n* this is package ‘conogive’ version ‘1.0.0’\n* package encoding: UTF-8\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘conogive’ can be installed ... OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking LazyData ... NOTE\n  'LazyData' is specified without a 'data' directory\n* checking examples ... OK\n* checking for unstated dependencies in ‘tests’ ... OK\n* checking tests ...\n  Running ‘testthat.R’\n OK\n* DONE\n\nStatus: 1 NOTE\nSee\n  ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/conogive/new/conogive.Rcheck/00check.log’\nfor details.\n\n\n\n"],"stderr":[""],"status":[0],"duration":[8.5038],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":["checking LazyData ... NOTE\n  'LazyData' is specified without a 'data' directory"],"description":["Package: conogive\nTitle: Congeneric Normal-Ogive Model\nVersion: 1.0.0\nAuthors@R: c(\n    person(\"Jonas\", \"Moss\", , \"jonas.gjertsen@gmail.com\", role = c(\"aut\", \"cre\"), \n      comment = c(ORCID = \"0000-0002-6876-6964\")\n    ))\nDescription: The congeneric normal-ogive model is a popular model for \n   psychometric data (McDonald, R. P. (1997) <doi:10.1007/978-1-4757-2691-6_15>).\n   This model estimates the model, calculates theoretical and concrete \n   reliability coefficients, and predicts the latent variable of the model. \n   This is the companion package to Moss (2020) <doi:10.31234/osf.io/nvg5d>.\nLicense: MIT + file LICENSE\nEncoding: UTF-8\nLazyData: true\nURL: https://github.com/JonasMoss/conogive\nBugReports: https://github.com/JonasMoss/conogive/issues\nRoxygenNote: 7.1.0\nImports: psych, mvtnorm, checkmate, assertthat\nSuggests: testthat (>= 2.1.0), psychTools, covr\nNeedsCompilation: no\nPackaged: 2020-06-30 10:02:28 UTC; jonas\nAuthor: Jonas Moss [aut, cre] (<https://orcid.org/0000-0002-6876-6964>)\nMaintainer: Jonas Moss <jonas.gjertsen@gmail.com>\nRepository: CRAN\nDate/Publication: 2020-06-30 10:30:02 UTC"],"package":["conogive"],"version":["1.0.0"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/conogive/new/conogive.Rcheck"],"test_fail":{},"test_output":{"testthat":["> library(testthat)\n> library(conogive)\n> \n> test_check(\"conogive\")\n[ FAIL 0 | WARN 0 | SKIP 0 | PASS 35 ]\n> \n> proc.time()\n   user  system elapsed \n  0.539   0.097   0.843 \n"]},"install_out":["* installing *source* package ‘conogive’ ...\n** package ‘conogive’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n*** copying figures\n** building package indices\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (conogive)\n"],"session_info":{"platform":{"version":["R version 4.2.1 (2022-06-23)"],"os":["macOS Monterey 12.6"],"system":["aarch64, darwin20"],"ui":["X11"],"language":["(EN)"],"collate":["C"],"ctype":["en_US.UTF-8"],"tz":["America/Chicago"],"date":["2022-09-24"],"pandoc":["2.19 @ /usr/local/bin/pandoc"]},"packages":[{"package":"conogive","attached":false,"is_base":false,"_row":"conogive"}]}}}


package: bootnet
version: 1.5
maintainer: Sacha Epskamp <mail@sachaepskamp.com>
status: OK
which: old
duration: 48.6073019504547
starttime: 2022-09-24 22:04:26
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/bootnet/old/bootnet.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘bootnet/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘bootnet’ version ‘1.5’\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘bootnet’ can be installed ... OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking examples ... OK\n* DONE\n\nStatus: OK\n\n\n"],"stderr":[""],"status":[0],"duration":[48.6076],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":[],"description":["Package: bootnet\nType: Package\nTitle: Bootstrap Methods for Various Network Estimation Routines\nVersion: 1.5\nAuthors@R: c(\n  person(\"Sacha\", \"Epskamp\", email = \"mail@sachaepskamp.com\",role = c(\"aut\", \"cre\")),\n  person(\"Eiko I.\", \"Fried\", role = c(\"ctb\"))\n  )\nMaintainer: Sacha Epskamp <mail@sachaepskamp.com>\nDepends: ggplot2, R (>= 3.0.0)\nImports: methods, igraph, IsingFit, qgraph, dplyr (>= 0.3.0.2), tidyr,\n        gtools, corpcor, IsingSampler, mvtnorm, abind, Matrix, snow,\n        mgm (>= 1.2), NetworkToolbox (>= 1.1.0), pbapply, networktools,\n        rlang, tibble\nSuggests: glasso, GGMncv, BDgraph, graphicalVAR, relaimpo, lavaan,\n        psychTools, huge\nDescription: Bootstrap methods to assess accuracy and stability of estimated network structures\n              and centrality indices <doi:10.3758/s13428-017-0862-1>. Allows for flexible \n              specification of any undirected network estimation procedure in R, and offers \n              default sets for various estimation routines.\nLicense: GPL-2\nNeedsCompilation: no\nPackaged: 2021-10-25 14:38:34 UTC; sacha\nAuthor: Sacha Epskamp [aut, cre],\n  Eiko I. Fried [ctb]\nRepository: CRAN\nDate/Publication: 2021-10-25 16:20:09 UTC"],"package":["bootnet"],"version":["1.5"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/bootnet/old/bootnet.Rcheck"],"test_fail":{},"test_output":{},"install_out":["* installing *source* package ‘bootnet’ ...\n** package ‘bootnet’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n** building package indices\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (bootnet)\n"],"session_info":{"platform":{"version":["R version 4.2.1 (2022-06-23)"],"os":["macOS Monterey 12.6"],"system":["aarch64, darwin20"],"ui":["X11"],"language":["(EN)"],"collate":["C"],"ctype":["en_US.UTF-8"],"tz":["America/Chicago"],"date":["2022-09-24"],"pandoc":["2.19 @ /usr/local/bin/pandoc"]},"packages":[{"package":"bootnet","attached":false,"is_base":false,"_row":"bootnet"}]}}}


package: bootnet
version: 1.5
maintainer: Sacha Epskamp <mail@sachaepskamp.com>
status: OK
which: new
duration: 48.2314689159393
starttime: 2022-09-24 22:04:26
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
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package: modnets
version: 0.9.0
maintainer: Trevor Swanson <trevorswanson222@gmail.com>
status: OK
which: new
duration: 1.01061106920242
starttime: 2022-09-24 22:04:28
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
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OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking LazyData ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking examples ... OK\n* DONE\n\nStatus: OK\n\n\n"],"stderr":[""],"status":[0],"duration":[60.6371],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":[],"description":["Package: modnets\nTitle: Modeling Moderated Networks\nVersion: 0.9.0\nAuthors@R: \n    person(given = \"Trevor\",\n           family = \"Swanson\",\n           role = c(\"aut\", \"cre\"),\n           email = \"trevorswanson222@gmail.com\")\nMaintainer: Trevor Swanson <trevorswanson222@gmail.com>\nDescription: Methods for modeling moderator variables in cross-sectional, temporal, and multi-level networks. Includes model selection techniques and a variety of plotting functions. 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package: modnets
version: 0.9.0
maintainer: Trevor Swanson <trevorswanson222@gmail.com>
status: OK
which: old
duration: 1.02693154811859
starttime: 2022-09-24 22:04:27
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
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OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking LazyData ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking examples ... 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package: psych
version: 2.2.5
maintainer: William Revelle <revelle@northwestern.edu>
status: OK
which: old
duration: 1.12856640021006
starttime: 2022-09-24 22:04:29
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
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OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking LazyData ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking sizes of PDF files under ‘inst/doc’ ... OK\n* checking installed files from ‘inst/doc’ ... OK\n* checking files in ‘vignettes’ ... OK\n* checking examples ... OK\n* checking for unstated dependencies in vignettes ... OK\n* checking package vignettes in ‘inst/doc’ ... OK\n* checking running R code from vignettes ...\n  ‘scoring.Rnw’ using ‘UTF-8’... OK\n  ‘intro.Rnw’ using ‘UTF-8’... OK\n OK\n* checking re-building of vignette outputs ... 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package: psych
version: 2.2.5
maintainer: William Revelle <revelle@northwestern.edu>
status: OK
which: new
duration: 1.12240521510442
starttime: 2022-09-24 22:04:30
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
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SKIPPED\n* DONE\n\nStatus: OK\n\n\n"],"stderr":[""],"status":[0],"duration":[68.2279],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":[],"description":["Package: psych\nVersion: 2.2.5\nDate: 2022-05-01\nTitle: Procedures for Psychological, Psychometric, and Personality\n        Research\nAuthors@R: person(\"William\", \"Revelle\", role =c(\"aut\",\"cre\"), email=\"revelle@northwestern.edu\", comment=c(ORCID  = \"0000-0003-4880-9610\") )\nDescription: A general purpose toolbox for personality, psychometric theory and experimental psychology.   Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using  factor analysis of tetrachoric and polychoric correlations. 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For more information, see the <https://personality-project.org/r/> web page.\nLicense: GPL (>= 2)\nImports: mnormt,parallel,stats,graphics,grDevices,methods,lattice,nlme\nSuggests: psychTools, GPArotation, lavaan, lme4, Rcsdp, graph, knitr,\n        Rgraphviz\nLazyData: yes\nByteCompile: true\nVignetteBuilder: knitr\nURL: https://personality-project.org/r/psych/\n        https://personality-project.org/r/psych-manual.pdf\nNeedsCompilation: no\nPackaged: 2022-05-10 15:33:14 UTC; WR\nAuthor: William Revelle [aut, cre] (<https://orcid.org/0000-0003-4880-9610>)\nMaintainer: William Revelle <revelle@northwestern.edu>\nRepository: CRAN\nDate/Publication: 2022-05-10 17:00:08 UTC"],"package":["psych"],"version":["2.2.5"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/psych/new/psych.Rcheck"],"test_fail":{},"test_output":{},"install_out":["* installing *source* package ‘psych’ ...\n** package ‘psych’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** data\n*** moving datasets to lazyload DB\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (psych)\n"],"session_info":{"platform":{"version":["R version 4.2.1 (2022-06-23)"],"os":["macOS Monterey 12.6"],"system":["aarch64, darwin20"],"ui":["X11"],"language":["(EN)"],"collate":["C"],"ctype":["en_US.UTF-8"],"tz":["America/Chicago"],"date":["2022-09-24"],"pandoc":["2.19 @ /usr/local/bin/pandoc"]},"packages":[{"package":"lattice","ondiskversion":"0.20-45","path":"/Users/WR/Dropbox/psychTools/revdep/library.noindex/psych/lattice","attached":false,"is_base":false,"date":"2021-09-22","source":"CRAN (R 4.2.0)","library":"/Users/WR/Dropbox/psychTools/revdep/library.noindex/psych","_row":"lattice"},{"package":"mnormt","ondiskversion":"2.1.0","path":"/Users/WR/Dropbox/psychTools/revdep/library.noindex/psychTools/new/mnormt","attached":false,"is_base":false,"date":"2022-06-07","source":"CRAN (R 4.2.0)","library":"/Users/WR/Dropbox/psychTools/revdep/library.noindex/psychTools/new","_row":"mnormt"},{"package":"nlme","ondiskversion":"3.1-159","path":"/Users/WR/Dropbox/psychTools/revdep/library.noindex/psych/nlme","attached":false,"is_base":false,"date":"2022-08-09","source":"CRAN (R 4.2.0)","library":"/Users/WR/Dropbox/psychTools/revdep/library.noindex/psych","_row":"nlme"},{"package":"psych","ondiskversion":"2.2.9","path":"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/psych","attached":false,"is_base":false,"date":"2022-09-24","source":"local","library":"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library","_row":"psych"},{"package":"tmvnsim","ondiskversion":"1.0-2","path":"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/tmvnsim","attached":false,"is_base":false,"date":"2016-12-15","source":"CRAN (R 4.2.0)","library":"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library","_row":"tmvnsim"}]}}}


package: afex
version: 1.1-1
maintainer: Henrik Singmann <singmann@gmail.com>
status: OK
which: old
duration: 1.10728147029877
starttime: 2022-09-24 22:04:31
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/afex/old/afex.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘afex/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘afex’ version ‘1.1-1’\n* package encoding: UTF-8\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘afex’ can be installed ... OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking ‘build’ directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking LazyData ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking sizes of PDF files under ‘inst/doc’ ... OK\n* checking installed files from ‘inst/doc’ ... OK\n* checking files in ‘vignettes’ ... OK\n* checking examples ... OK\n* checking for unstated dependencies in ‘tests’ ... OK\n* checking tests ...\n  Running ‘testthat.R’\n OK\n* checking for unstated dependencies in vignettes ... OK\n* checking package vignettes in ‘inst/doc’ ... OK\n* checking running R code from vignettes ...\n  ‘afex_analysing_accuracy_data.Rmd’ using ‘UTF-8’... OK\n  ‘afex_anova_example.Rmd’ using ‘UTF-8’... OK\n  ‘afex_mixed_example.Rmd’ using ‘UTF-8’... OK\n  ‘afex_plot_introduction.Rmd’ using ‘UTF-8’... OK\n  ‘afex_plot_supported_models.Rmd’ using ‘UTF-8’... OK\n  ‘assumptions_of_ANOVAs.Rmd’ using ‘UTF-8’... OK\n  ‘introduction-mixed-models.pdf.asis’ using ‘UTF-8’... OK\n NONE\n* checking re-building of vignette outputs ... SKIPPED\n* DONE\n\nStatus: OK\n\n\n"],"stderr":[""],"status":[0],"duration":[66.4373],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":[],"description":["Package: afex\nType: Package\nTitle: Analysis of Factorial Experiments\nDepends: R (>= 3.5.0), lme4 (>= 1.1-8)\nSuggests: emmeans (>= 1.4), coin, xtable, parallel, plyr, optimx,\n        nloptr, knitr, rmarkdown, R.rsp, lattice, latticeExtra,\n        multcomp, testthat, mlmRev, dplyr, tidyr, dfoptim, Matrix,\n        psychTools, ggplot2, MEMSS, effects, carData, ggbeeswarm, nlme,\n        cowplot, jtools, ggpubr, ggpol, MASS, glmmTMB, brms, rstanarm,\n        statmod, performance (>= 0.7.2), see (>= 0.6.4), ez,\n        ggResidpanel\nImports: pbkrtest (>= 0.4-1), lmerTest (>= 3.0-0), car, reshape2,\n        stats, methods, utils\nDescription: Convenience functions for analyzing factorial experiments using ANOVA or\n         mixed models. aov_ez(), aov_car(), and aov_4() allow specification of\n         between, within (i.e., repeated-measures), or mixed (i.e., split-plot) \n         ANOVAs for data in long format (i.e., one observation per row),\n         automatically aggregating multiple observations per individual and cell \n         of the design. mixed() fits mixed models using lme4::lmer() and computes \n         p-values for all fixed effects using either Kenward-Roger or Satterthwaite \n         approximation for degrees of freedom (LMM only), parametric bootstrap \n         (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). \n         afex_plot() provides a high-level interface for interaction or one-way \n         plots using ggplot2, combining raw data and model estimates. afex uses \n         type 3 sums of squares as default (imitating commercial statistical software).\nURL: https://afex.singmann.science/, https://github.com/singmann/afex\nBugReports: https://github.com/singmann/afex/issues\nLicense: GPL (>= 2)\nEncoding: UTF-8\nVignetteBuilder: knitr, R.rsp\nAuthors@R: c(person(given=\"Henrik\", family=\"Singmann\", role=c(\"aut\", \"cre\"),\n          email=\"singmann@gmail.com\", comment=c(ORCID=\"0000-0002-4842-3657\")),\n         person(given=\"Ben\", family=\"Bolker\", role=c(\"aut\")), \n         person(given=\"Jake\",family=\"Westfall\", role=c(\"aut\")), \n         person(given=\"Frederik\", family=\"Aust\", role=c(\"aut\"), \n          comment = c(ORCID = \"0000-0003-4900-788X\")),\n         person(given=\"Mattan S.\",family=\"Ben-Shachar\", role=c(\"aut\")), \n         person(given=\"Søren\", family=\"Højsgaard\", role=c(\"ctb\")),\n         person(given=\"John\", family=\"Fox\", role=c(\"ctb\")), \n         person(given=\"Michael A.\", family=\"Lawrence\", role=c(\"ctb\")), \n         person(given=\"Ulf\", family=\"Mertens\", role=c(\"ctb\")), \n         person(given=\"Jonathon\", family=\"Love\", role=c(\"ctb\")), \n         person(given=\"Russell\", family=\"Lenth\", role=c(\"ctb\")), \n         person(given=\"Rune\", family=\"Haubo Bojesen Christensen\", role=c(\"ctb\")))\nVersion: 1.1-1\nRoxygenNote: 7.1.2\nLazyData: true\nNeedsCompilation: no\nPackaged: 2022-04-28 19:06:12 UTC; singm\nAuthor: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>),\n  Ben Bolker [aut],\n  Jake Westfall [aut],\n  Frederik Aust [aut] (<https://orcid.org/0000-0003-4900-788X>),\n  Mattan S. Ben-Shachar [aut],\n  Søren Højsgaard [ctb],\n  John Fox [ctb],\n  Michael A. Lawrence [ctb],\n  Ulf Mertens [ctb],\n  Jonathon Love [ctb],\n  Russell Lenth [ctb],\n  Rune Haubo Bojesen Christensen [ctb]\nMaintainer: Henrik Singmann <singmann@gmail.com>\nRepository: CRAN\nDate/Publication: 2022-04-29 23:30:07 UTC"],"package":["afex"],"version":["1.1-1"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/afex/old/afex.Rcheck"],"test_fail":{},"test_output":{"testthat":["> library(testthat)\n> library(afex)\nLoading required package: lme4\nLoading required package: Matrix\n************\nWelcome to afex. For support visit: http://afex.singmann.science/\n- Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()\n- Methods for calculating p-values with mixed(): 'S', 'KR', 'LRT', and 'PB'\n- 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests\n- NEWS: emmeans() for ANOVA models now uses model = 'multivariate' as default.\n- Get and set global package options with: afex_options()\n- Set orthogonal sum-to-zero contrasts globally: set_sum_contrasts()\n- For example analyses see: browseVignettes(\"afex\")\n************\n\nAttaching package: 'afex'\n\nThe following object is masked from 'package:lme4':\n\n    lmer\n\n> \n> test_check(\"afex\")\nMixed Model Anova Table (Type 3 tests, S-method)\n\nModel: value ~ treatment + (1 | id)\nData: obk.long\n     Effect       df      F p.value\n1 treatment 2, 13.00 2.91 +    .090\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\nMixed Model Anova Table (Type 3 tests, S-method)\n\nModel: value ~ treatment + phase + (1 | id)\nData: obk.long\n     Effect        df         F p.value\n1 treatment  2, 13.00    2.91 +    .090\n2     phase 2, 222.00 38.48 ***   <.001\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\nMixed Model Anova Table (Type 3 tests, LRT-method)\n\nModel: value ~ treatment + (1 | id)\nData: obk.long\nDf full model: 5\n     Effect df  Chisq p.value\n1 treatment  2 5.93 +    .052\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\nMixed Model Anova Table (Type 3 tests, LRT-method)\n\nModel: value ~ treatment + phase + (1 | id)\nData: obk.long\nDf full model: 7\n     Effect df     Chisq p.value\n1 treatment  2    5.93 +    .052\n2     phase  2 66.67 ***   <.001\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\nMixed Model Anova Table (Type 3 tests, PB-method)\n\nModel: use ~ urban + (1 | district)\nData: Contraception\n  Effect df Chisq p.value\n1  urban  1 31.28    .333\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\nMixed Model Anova Table (Type 3 tests, PB-method)\n\nModel: use ~ urban + livch + (1 | district)\nData: Contraception\n  Effect df Chisq p.value\n1  urban  1 36.33    .333\n2  livch  3 77.91    .333\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\n[ FAIL 0 | WARN 0 | SKIP 18 | PASS 381 ]\n\n══ Skipped tests ═══════════════════════════════════════════════════════════════\n• On CRAN (17)\n• empty test (1)\n\n[ FAIL 0 | WARN 0 | SKIP 18 | PASS 381 ]\n> \n> proc.time()\n   user  system elapsed \n 18.842   0.356  20.245 \n"]},"install_out":["* installing *source* package ‘afex’ ...\n** package ‘afex’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** data\n*** moving datasets to lazyload DB\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n*** copying figures\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded from 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package: afex
version: 1.1-1
maintainer: Henrik Singmann <singmann@gmail.com>
status: OK
which: new
duration: 1.10043004751205
starttime: 2022-09-24 22:04:32
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/afex/new/afex.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘afex/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘afex’ version ‘1.1-1’\n* package encoding: UTF-8\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘afex’ can be installed ... OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking ‘build’ directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking LazyData ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking sizes of PDF files under ‘inst/doc’ ... OK\n* checking installed files from ‘inst/doc’ ... OK\n* checking files in ‘vignettes’ ... OK\n* checking examples ... OK\n* checking for unstated dependencies in ‘tests’ ... OK\n* checking tests ...\n  Running ‘testthat.R’\n OK\n* checking for unstated dependencies in vignettes ... OK\n* checking package vignettes in ‘inst/doc’ ... OK\n* checking running R code from vignettes ...\n  ‘afex_analysing_accuracy_data.Rmd’ using ‘UTF-8’... OK\n  ‘afex_anova_example.Rmd’ using ‘UTF-8’... OK\n  ‘afex_mixed_example.Rmd’ using ‘UTF-8’... OK\n  ‘afex_plot_introduction.Rmd’ using ‘UTF-8’... OK\n  ‘afex_plot_supported_models.Rmd’ using ‘UTF-8’... OK\n  ‘assumptions_of_ANOVAs.Rmd’ using ‘UTF-8’... OK\n  ‘introduction-mixed-models.pdf.asis’ using ‘UTF-8’... OK\n NONE\n* checking re-building of vignette outputs ... SKIPPED\n* DONE\n\nStatus: OK\n\n\n"],"stderr":[""],"status":[0],"duration":[68.1456],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":[],"description":["Package: afex\nType: Package\nTitle: Analysis of Factorial Experiments\nDepends: R (>= 3.5.0), lme4 (>= 1.1-8)\nSuggests: emmeans (>= 1.4), coin, xtable, parallel, plyr, optimx,\n        nloptr, knitr, rmarkdown, R.rsp, lattice, latticeExtra,\n        multcomp, testthat, mlmRev, dplyr, tidyr, dfoptim, Matrix,\n        psychTools, ggplot2, MEMSS, effects, carData, ggbeeswarm, nlme,\n        cowplot, jtools, ggpubr, ggpol, MASS, glmmTMB, brms, rstanarm,\n        statmod, performance (>= 0.7.2), see (>= 0.6.4), ez,\n        ggResidpanel\nImports: pbkrtest (>= 0.4-1), lmerTest (>= 3.0-0), car, reshape2,\n        stats, methods, utils\nDescription: Convenience functions for analyzing factorial experiments using ANOVA or\n         mixed models. aov_ez(), aov_car(), and aov_4() allow specification of\n         between, within (i.e., repeated-measures), or mixed (i.e., split-plot) \n         ANOVAs for data in long format (i.e., one observation per row),\n         automatically aggregating multiple observations per individual and cell \n         of the design. mixed() fits mixed models using lme4::lmer() and computes \n         p-values for all fixed effects using either Kenward-Roger or Satterthwaite \n         approximation for degrees of freedom (LMM only), parametric bootstrap \n         (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). \n         afex_plot() provides a high-level interface for interaction or one-way \n         plots using ggplot2, combining raw data and model estimates. afex uses \n         type 3 sums of squares as default (imitating commercial statistical software).\nURL: https://afex.singmann.science/, https://github.com/singmann/afex\nBugReports: https://github.com/singmann/afex/issues\nLicense: GPL (>= 2)\nEncoding: UTF-8\nVignetteBuilder: knitr, R.rsp\nAuthors@R: c(person(given=\"Henrik\", family=\"Singmann\", role=c(\"aut\", \"cre\"),\n          email=\"singmann@gmail.com\", comment=c(ORCID=\"0000-0002-4842-3657\")),\n         person(given=\"Ben\", family=\"Bolker\", role=c(\"aut\")), \n         person(given=\"Jake\",family=\"Westfall\", role=c(\"aut\")), \n         person(given=\"Frederik\", family=\"Aust\", role=c(\"aut\"), \n          comment = c(ORCID = \"0000-0003-4900-788X\")),\n         person(given=\"Mattan S.\",family=\"Ben-Shachar\", role=c(\"aut\")), \n         person(given=\"Søren\", family=\"Højsgaard\", role=c(\"ctb\")),\n         person(given=\"John\", family=\"Fox\", role=c(\"ctb\")), \n         person(given=\"Michael A.\", family=\"Lawrence\", role=c(\"ctb\")), \n         person(given=\"Ulf\", family=\"Mertens\", role=c(\"ctb\")), \n         person(given=\"Jonathon\", family=\"Love\", role=c(\"ctb\")), \n         person(given=\"Russell\", family=\"Lenth\", role=c(\"ctb\")), \n         person(given=\"Rune\", family=\"Haubo Bojesen Christensen\", role=c(\"ctb\")))\nVersion: 1.1-1\nRoxygenNote: 7.1.2\nLazyData: true\nNeedsCompilation: no\nPackaged: 2022-04-28 19:06:12 UTC; singm\nAuthor: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>),\n  Ben Bolker [aut],\n  Jake Westfall [aut],\n  Frederik Aust [aut] (<https://orcid.org/0000-0003-4900-788X>),\n  Mattan S. Ben-Shachar [aut],\n  Søren Højsgaard [ctb],\n  John Fox [ctb],\n  Michael A. Lawrence [ctb],\n  Ulf Mertens [ctb],\n  Jonathon Love [ctb],\n  Russell Lenth [ctb],\n  Rune Haubo Bojesen Christensen [ctb]\nMaintainer: Henrik Singmann <singmann@gmail.com>\nRepository: CRAN\nDate/Publication: 2022-04-29 23:30:07 UTC"],"package":["afex"],"version":["1.1-1"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/afex/new/afex.Rcheck"],"test_fail":{},"test_output":{"testthat":["> library(testthat)\n> library(afex)\nLoading required package: lme4\nLoading required package: Matrix\n************\nWelcome to afex. For support visit: http://afex.singmann.science/\n- Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()\n- Methods for calculating p-values with mixed(): 'S', 'KR', 'LRT', and 'PB'\n- 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests\n- NEWS: emmeans() for ANOVA models now uses model = 'multivariate' as default.\n- Get and set global package options with: afex_options()\n- Set orthogonal sum-to-zero contrasts globally: set_sum_contrasts()\n- For example analyses see: browseVignettes(\"afex\")\n************\n\nAttaching package: 'afex'\n\nThe following object is masked from 'package:lme4':\n\n    lmer\n\n> \n> test_check(\"afex\")\nMixed Model Anova Table (Type 3 tests, S-method)\n\nModel: value ~ treatment + (1 | id)\nData: obk.long\n     Effect       df      F p.value\n1 treatment 2, 13.00 2.91 +    .090\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\nMixed Model Anova Table (Type 3 tests, S-method)\n\nModel: value ~ treatment + phase + (1 | id)\nData: obk.long\n     Effect        df         F p.value\n1 treatment  2, 13.00    2.91 +    .090\n2     phase 2, 222.00 38.48 ***   <.001\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\nMixed Model Anova Table (Type 3 tests, LRT-method)\n\nModel: value ~ treatment + (1 | id)\nData: obk.long\nDf full model: 5\n     Effect df  Chisq p.value\n1 treatment  2 5.93 +    .052\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\nMixed Model Anova Table (Type 3 tests, LRT-method)\n\nModel: value ~ treatment + phase + (1 | id)\nData: obk.long\nDf full model: 7\n     Effect df     Chisq p.value\n1 treatment  2    5.93 +    .052\n2     phase  2 66.67 ***   <.001\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\nMixed Model Anova Table (Type 3 tests, PB-method)\n\nModel: use ~ urban + (1 | district)\nData: Contraception\n  Effect df Chisq p.value\n1  urban  1 31.28    .333\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\nMixed Model Anova Table (Type 3 tests, PB-method)\n\nModel: use ~ urban + livch + (1 | district)\nData: Contraception\n  Effect df Chisq p.value\n1  urban  1 36.33    .333\n2  livch  3 77.91    .333\n---\nSignif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1\n[ FAIL 0 | WARN 0 | SKIP 18 | PASS 381 ]\n\n══ Skipped tests ═══════════════════════════════════════════════════════════════\n• On CRAN (17)\n• empty test (1)\n\n[ FAIL 0 | WARN 0 | SKIP 18 | PASS 381 ]\n> \n> proc.time()\n   user  system elapsed \n 18.857   0.354  20.025 \n"]},"install_out":["* installing *source* package ‘afex’ ...\n** package ‘afex’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** data\n*** moving datasets to lazyload DB\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n*** copying figures\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (afex)\n"],"session_info":{"platform":{"version":["R version 4.2.1 (2022-06-23)"],"os":["macOS Monterey 12.6"],"system":["aarch64, darwin20"],"ui":["X11"],"language":["(EN)"],"collate":["C"],"ctype":["en_US.UTF-8"],"tz":["America/Chicago"],"date":["2022-09-24"],"pandoc":["2.19 @ /usr/local/bin/pandoc"]},"packages":[{"package":"abind","ondiskversion":"1.4-5","path":"/Users/WR/Dropbox/psychTools/revdep/library.noindex/afex/abind","attached":false,"is_base":false,"date":"2016-07-21","source":"CRAN (R 4.2.0)","library":"/Users/WR/Dropbox/psychTools/revdep/library.noindex/afex","_row":"abind"},{"package":"afex","ondiskversion":"1.1-1","path":"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/afex","attached":false,"is_base":false,"date":"2022-04-29","source":"CRAN (R 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package: EGAnet
version: 1.2.3
maintainer: Hudson Golino <hfg9s@virginia.edu>
status: OK
which: new
duration: 29.566654920578
starttime: 2022-09-24 22:05:16
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
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OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking LazyData ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking installed files from ‘inst/doc’ ... OK\n* checking files in ‘vignettes’ ... OK\n* checking examples ... OK\n* checking for unstated dependencies in vignettes ... OK\n* checking package vignettes in ‘inst/doc’ ... OK\n* checking running R code from vignettes ...\n  ‘Exploratory_Graph_Analysis.Rmd’ using ‘UTF-8’... OK\n NONE\n* checking re-building of vignette outputs ... SKIPPED\n* DONE\n\nStatus: OK\n\n\n"],"stderr":[""],"status":[0],"duration":[29.5671],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":[],"description":["Package: EGAnet\nTitle: Exploratory Graph Analysis – a Framework for Estimating the\n        Number of Dimensions in Multivariate Data using Network\n        Psychometrics\nVersion: 1.2.3\nDate: 2022-09-05\nAuthors@R: c(person(\"Hudson\", \"Golino\", email = \"hfg9s@virginia.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1601-1447\")),\n\t     person(\"Alexander\", \"Christensen\", email = \"alexpaulchristensen@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-9798-7037\")),\n\t     person(\"Robert\", \"Moulder\", email = \"rgm4fd@virginia.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7504-9560\")),\n\t     person(\"Luis\", \"E. Garrido\", email = \"garrido.luiseduardo@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8932-6063\")),\n\t     person(\"Laura\", \"Jamison\", email = \"lj5yn@virginia.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4656-8684\")))\nMaintainer: Hudson Golino <hfg9s@virginia.edu>\nDescription: Implements the Exploratory Graph Analysis (EGA) framework for dimensionality and psychometric assessment. EGA is part of a new area called network psychometrics that uses undirected network models for the assessment of psychometric properties. EGA estimates the number of dimensions (or factors) using graphical lasso or Triangulated Maximally Filtered Graph (TMFG) and a weighted network community detection algorithm. A bootstrap method for verifying the stability of the dimensions and items in those dimensions is available. The fit of the structure suggested by EGA can be verified using Entropy Fit Indices. A novel approach called Unique Variable Analysis (UVA) can be used to identify and reduce redundant variables in multivariate data. Network loadings, which are roughly equivalent to factor loadings when the data generating model is a factor model, are available. Network scores can also be computed using the network loadings. Dynamic EGA (dynEGA) will estimate dimensions from time series data for individual, group, and sample levels. Golino, H., & Epskamp, S. (2017) <doi:10.1371/journal.pone.0174035>. Golino, H., Shi, D., Christensen, A. P., Garrido, L. E., Nieto, M. D., Sadana, R., & Thiyagarajan, J. A. (2020) <doi:10.31234/osf.io/gzcre>. Christensen, A. P., & Golino, H. (under review) <doi:10.31234/osf.io/hz89e>. Golino, H., Moulder, R. G., Shi, D., Christensen, A. P., Garrido, L. E., Nieto, M. D., Nesselroade, J., Sadana, R., Thiyagarajan, J. A., & Boker, S. M. (2020) <doi:10.31234/osf.io/mtka2>. Christensen, A. P. & Golino, H. (2021)  <doi:10.3390/psych3030032>. Christensen, A. P., Garrido, L. E., & Golino, H. (under review) <doi:10.31234/osf.io/4kra2>. Golino, H., Christensen, A. P., Moulder, R. G., Kim, S., & Boker, S. M. (under review) <doi:10.31234/osf.io/tfs7c>.\nDepends: R (>= 3.5.0)\nLicense: GPL (>= 3.0)\nEncoding: UTF-8\nLazyData: true\nImports: glasso, GGally, ggdendro, ggplot2, ggpubr, igraph (>= 1.3.0),\n        lavaan, Matrix, matrixcalc, methods, network, OpenMx, pbapply,\n        qgraph, semPlot, stats\nSuggests: GPArotation, gridExtra, knitr, markdown, psych, psychTools,\n        pwr, RColorBrewer, rmarkdown, rstudioapi, sna\nVignetteBuilder: knitr\nRoxygenNote: 7.2.1\nNeedsCompilation: no\nPackaged: 2022-09-05 15:25:57 UTC; Hudson\nAuthor: Hudson Golino [aut, cre] (<https://orcid.org/0000-0002-1601-1447>),\n  Alexander Christensen [aut] (<https://orcid.org/0000-0002-9798-7037>),\n  Robert Moulder [ctb] (<https://orcid.org/0000-0001-7504-9560>),\n  Luis E. Garrido [ctb] (<https://orcid.org/0000-0001-8932-6063>),\n  Laura Jamison [ctb] (<https://orcid.org/0000-0002-4656-8684>)\nRepository: CRAN\nDate/Publication: 2022-09-05 15:50:02 UTC"],"package":["EGAnet"],"version":["1.2.3"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/EGAnet/new/EGAnet.Rcheck"],"test_fail":{},"test_output":{},"install_out":["* installing *source* package ‘EGAnet’ ...\n** package ‘EGAnet’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** data\n*** moving datasets to lazyload DB\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE 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package: EGAnet
version: 1.2.3
maintainer: Hudson Golino <hfg9s@virginia.edu>
status: OK
which: old
duration: 30.7524528503418
starttime: 2022-09-24 22:05:15
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
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OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking LazyData ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking installed files from ‘inst/doc’ ... OK\n* checking files in ‘vignettes’ ... OK\n* checking examples ... OK\n* checking for unstated dependencies in vignettes ... OK\n* checking package vignettes in ‘inst/doc’ ... OK\n* checking running R code from vignettes ...\n  ‘Exploratory_Graph_Analysis.Rmd’ using ‘UTF-8’... OK\n NONE\n* checking re-building of vignette outputs ... SKIPPED\n* DONE\n\nStatus: OK\n\n\n"],"stderr":[""],"status":[0],"duration":[33.5592],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":[],"description":["Package: EGAnet\nTitle: Exploratory Graph Analysis – a Framework for Estimating the\n        Number of Dimensions in Multivariate Data using Network\n        Psychometrics\nVersion: 1.2.3\nDate: 2022-09-05\nAuthors@R: c(person(\"Hudson\", \"Golino\", email = \"hfg9s@virginia.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1601-1447\")),\n\t     person(\"Alexander\", \"Christensen\", email = \"alexpaulchristensen@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-9798-7037\")),\n\t     person(\"Robert\", \"Moulder\", email = \"rgm4fd@virginia.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7504-9560\")),\n\t     person(\"Luis\", \"E. Garrido\", email = \"garrido.luiseduardo@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8932-6063\")),\n\t     person(\"Laura\", \"Jamison\", email = \"lj5yn@virginia.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4656-8684\")))\nMaintainer: Hudson Golino <hfg9s@virginia.edu>\nDescription: Implements the Exploratory Graph Analysis (EGA) framework for dimensionality and psychometric assessment. EGA is part of a new area called network psychometrics that uses undirected network models for the assessment of psychometric properties. EGA estimates the number of dimensions (or factors) using graphical lasso or Triangulated Maximally Filtered Graph (TMFG) and a weighted network community detection algorithm. A bootstrap method for verifying the stability of the dimensions and items in those dimensions is available. The fit of the structure suggested by EGA can be verified using Entropy Fit Indices. A novel approach called Unique Variable Analysis (UVA) can be used to identify and reduce redundant variables in multivariate data. Network loadings, which are roughly equivalent to factor loadings when the data generating model is a factor model, are available. Network scores can also be computed using the network loadings. Dynamic EGA (dynEGA) will estimate dimensions from time series data for individual, group, and sample levels. Golino, H., & Epskamp, S. (2017) <doi:10.1371/journal.pone.0174035>. Golino, H., Shi, D., Christensen, A. P., Garrido, L. E., Nieto, M. D., Sadana, R., & Thiyagarajan, J. A. (2020) <doi:10.31234/osf.io/gzcre>. Christensen, A. P., & Golino, H. (under review) <doi:10.31234/osf.io/hz89e>. Golino, H., Moulder, R. G., Shi, D., Christensen, A. P., Garrido, L. E., Nieto, M. D., Nesselroade, J., Sadana, R., Thiyagarajan, J. A., & Boker, S. M. (2020) <doi:10.31234/osf.io/mtka2>. Christensen, A. P. & Golino, H. (2021)  <doi:10.3390/psych3030032>. Christensen, A. P., Garrido, L. E., & Golino, H. (under review) <doi:10.31234/osf.io/4kra2>. Golino, H., Christensen, A. P., Moulder, R. G., Kim, S., & Boker, S. M. (under review) <doi:10.31234/osf.io/tfs7c>.\nDepends: R (>= 3.5.0)\nLicense: GPL (>= 3.0)\nEncoding: UTF-8\nLazyData: true\nImports: glasso, GGally, ggdendro, ggplot2, ggpubr, igraph (>= 1.3.0),\n        lavaan, Matrix, matrixcalc, methods, network, OpenMx, pbapply,\n        qgraph, semPlot, stats\nSuggests: GPArotation, gridExtra, knitr, markdown, psych, psychTools,\n        pwr, RColorBrewer, rmarkdown, rstudioapi, sna\nVignetteBuilder: knitr\nRoxygenNote: 7.2.1\nNeedsCompilation: no\nPackaged: 2022-09-05 15:25:57 UTC; Hudson\nAuthor: Hudson Golino [aut, cre] (<https://orcid.org/0000-0002-1601-1447>),\n  Alexander Christensen [aut] (<https://orcid.org/0000-0002-9798-7037>),\n  Robert Moulder [ctb] (<https://orcid.org/0000-0001-7504-9560>),\n  Luis E. Garrido [ctb] (<https://orcid.org/0000-0001-8932-6063>),\n  Laura Jamison [ctb] (<https://orcid.org/0000-0002-4656-8684>)\nRepository: CRAN\nDate/Publication: 2022-09-05 15:50:02 UTC"],"package":["EGAnet"],"version":["1.2.3"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/EGAnet/old/EGAnet.Rcheck"],"test_fail":{},"test_output":{},"install_out":["* installing *source* package ‘EGAnet’ ...\n** package ‘EGAnet’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** data\n*** moving datasets to lazyload DB\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE 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package: quest
version: 0.1.0
maintainer: David Disabato <ddisab01@gmail.com>
status: NOTE
which: new
duration: 12.7418210506439
starttime: 2022-09-24 22:05:42
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[1]}}
result:
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OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... NOTE\nNamespaces in Imports field not imported from:\n  ‘psych’ ‘psychTools’\n  All declared Imports should be used.\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... 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package: quest
version: 0.1.0
maintainer: David Disabato <ddisab01@gmail.com>
status: NOTE
which: old
duration: 13.2998559474945
starttime: 2022-09-24 22:05:42
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[1]}}
result:
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package: XICOR
version: 0.3.3
maintainer: Susan Holmes <sp.holmes@gmail.com>
status: NOTE
which: old
duration: 7.95700407028198
starttime: 2022-09-24 22:05:53
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[2]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/XICOR/old/XICOR.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘XICOR/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘XICOR’ version ‘0.3.3’\n* package encoding: UTF-8\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘XICOR’ can be installed ... OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... NOTE\nNamespace in Imports field not imported from: ‘psychTools’\n  All declared Imports should be used.\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking LazyData ... NOTE\n  'LazyData' is specified without a 'data' directory\n* checking examples ... OK\n* DONE\n\nStatus: 2 NOTEs\nSee\n  ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/XICOR/old/XICOR.Rcheck/00check.log’\nfor details.\n\n\n\n"],"stderr":[""],"status":[0],"duration":[7.9574],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":["checking dependencies in R code ... NOTE\nNamespace in Imports field not imported from: ‘psychTools’\n  All declared Imports should be used.","checking LazyData ... NOTE\n  'LazyData' is specified without a 'data' directory"],"description":["Package: XICOR\nType: Package\nTitle: Association Measurement Through Cross Rank Increments\nVersion: 0.3.3\nAuthor: Susan Holmes [aut,cre], Sourav Chatterjee [aut] \nMaintainer: Susan Holmes <sp.holmes@gmail.com>\nDescription: Computes robust association measures that do not \n    presuppose linearity. The xi correlation (xicor) is based\n    on cross correlation between ranked increments.\n    The reference for the methods implemented here is \n    Chatterjee, Sourav (2020) <arXiv:1909.10140>\n    This package includes the Galton peas example.\nDepends: R (>= 3.5.0)\nLicense: GPL-3\nDate: 2020-05-25\nEncoding: UTF-8\nLazyData: true\nImports: psychTools, stats\nSuggests: testthat (>= 2.1.0), ggplot2\nRoxygenNote: 7.1.0\nNeedsCompilation: no\nPackaged: 2020-05-25 09:40:57 UTC; Susan\nRepository: CRAN\nDate/Publication: 2020-05-26 09:10:02 UTC"],"package":["XICOR"],"version":["0.3.3"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/XICOR/old/XICOR.Rcheck"],"test_fail":{},"test_output":{},"install_out":["* installing *source* package ‘XICOR’ ...\n** package ‘XICOR’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n** building package indices\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (XICOR)\n"],"session_info":{"platform":{"version":["R version 4.2.1 (2022-06-23)"],"os":["macOS Monterey 12.6"],"system":["aarch64, darwin20"],"ui":["X11"],"language":["(EN)"],"collate":["C"],"ctype":["en_US.UTF-8"],"tz":["America/Chicago"],"date":["2022-09-24"],"pandoc":["2.19 @ /usr/local/bin/pandoc"]},"packages":[{"package":"XICOR","attached":false,"is_base":false,"_row":"XICOR"}]}}}


package: XICOR
version: 0.3.3
maintainer: Susan Holmes <sp.holmes@gmail.com>
status: NOTE
which: new
duration: 7.47704815864563
starttime: 2022-09-24 22:05:54
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[2]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/XICOR/new/XICOR.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘XICOR/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘XICOR’ version ‘0.3.3’\n* package encoding: UTF-8\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘XICOR’ can be installed ... OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... NOTE\nNamespace in Imports field not imported from: ‘psychTools’\n  All declared Imports should be used.\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking LazyData ... NOTE\n  'LazyData' is specified without a 'data' directory\n* checking examples ... OK\n* DONE\n\nStatus: 2 NOTEs\nSee\n  ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/XICOR/new/XICOR.Rcheck/00check.log’\nfor details.\n\n\n\n"],"stderr":[""],"status":[0],"duration":[7.6324],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":["checking dependencies in R code ... NOTE\nNamespace in Imports field not imported from: ‘psychTools’\n  All declared Imports should be used.","checking LazyData ... NOTE\n  'LazyData' is specified without a 'data' directory"],"description":["Package: XICOR\nType: Package\nTitle: Association Measurement Through Cross Rank Increments\nVersion: 0.3.3\nAuthor: Susan Holmes [aut,cre], Sourav Chatterjee [aut] \nMaintainer: Susan Holmes <sp.holmes@gmail.com>\nDescription: Computes robust association measures that do not \n    presuppose linearity. The xi correlation (xicor) is based\n    on cross correlation between ranked increments.\n    The reference for the methods implemented here is \n    Chatterjee, Sourav (2020) <arXiv:1909.10140>\n    This package includes the Galton peas example.\nDepends: R (>= 3.5.0)\nLicense: GPL-3\nDate: 2020-05-25\nEncoding: UTF-8\nLazyData: true\nImports: psychTools, stats\nSuggests: testthat (>= 2.1.0), ggplot2\nRoxygenNote: 7.1.0\nNeedsCompilation: no\nPackaged: 2020-05-25 09:40:57 UTC; Susan\nRepository: CRAN\nDate/Publication: 2020-05-26 09:10:02 UTC"],"package":["XICOR"],"version":["0.3.3"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/XICOR/new/XICOR.Rcheck"],"test_fail":{},"test_output":{},"install_out":["* installing *source* package ‘XICOR’ ...\n** package ‘XICOR’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n** building package indices\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (XICOR)\n"],"session_info":{"platform":{"version":["R version 4.2.1 (2022-06-23)"],"os":["macOS Monterey 12.6"],"system":["aarch64, darwin20"],"ui":["X11"],"language":["(EN)"],"collate":["C"],"ctype":["en_US.UTF-8"],"tz":["America/Chicago"],"date":["2022-09-24"],"pandoc":["2.19 @ /usr/local/bin/pandoc"]},"packages":[{"package":"XICOR","attached":false,"is_base":false,"_row":"XICOR"}]}}}


package: semtree
version: 0.9.18
maintainer: Andreas M. Brandmaier <andy@brandmaier.de>
status: OK
which: new
duration: 51.2013518810272
starttime: 2022-09-24 22:05:55
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/semtree/new/semtree.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘semtree/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘semtree’ version ‘0.9.18’\n* package encoding: UTF-8\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘semtree’ can be installed ... OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking ‘build’ directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking installed files from ‘inst/doc’ ... OK\n* checking files in ‘vignettes’ ... OK\n* checking examples ... OK\n* checking for unstated dependencies in ‘tests’ ... OK\n* checking tests ...\n  Running ‘invariance.R’\n  Running ‘lavaan.R’\n  Running ‘tree.R’\n  Running ‘vim.R’\n OK\n* checking for unstated dependencies in vignettes ... OK\n* checking package vignettes in ‘inst/doc’ ... OK\n* checking running R code from vignettes ...\n  ‘constraints.Rmd’ using ‘UTF-8’... OK\n  ‘forests.Rmd’ using ‘UTF-8’... OK\n  ‘getting-started.Rmd’ using ‘UTF-8’... OK\n  ‘score-based-tests.Rmd’ using ‘UTF-8’... OK\n  ‘semforest-focus.Rmd’ using ‘UTF-8’... OK\n NONE\n* checking re-building of vignette outputs ... SKIPPED\n* DONE\n\nStatus: OK\n\n\n"],"stderr":[""],"status":[0],"duration":[51.2018],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":[],"description":["Package: semtree\nType: Package\nTitle: Recursive Partitioning for Structural Equation Models\nAuthors@R: c(person(\"Andreas M. Brandmaier\", email=\"andy@brandmaier.de\", role=c(\"aut\",\"cre\")), person(\"John J. Prindle\", email=\"jprindle@usc.edu\",role=c(\"aut\")),person(\"Manuel Arnold\", email=\"arnoldmz@hu-berlin.de\",role=c(\"aut\")),person(\"Caspar J. Van Lissa\", email=\"C.J.vanLissa@uu.nl\",role=c(\"aut\")))\nAuthor: Andreas M. Brandmaier [aut, cre],\n  John J. Prindle [aut],\n  Manuel Arnold [aut],\n  Caspar J. Van Lissa [aut]\nMaintainer: Andreas M. Brandmaier <andy@brandmaier.de>\nDepends: R (>= 2.10), OpenMx (>= 2.6.9),\nImports: bitops, sets, digest, rpart, rpart.plot (>= 3.0.6), plotrix,\n        cluster, stringr, lavaan, ggplot2, tidyr, methods, strucchange,\n        sandwich, zoo, crayon, clisymbols, future.apply, data.table\nSuggests: knitr, rmarkdown, viridis, MASS, psychTools, testthat\nDescription: SEM Trees and SEM Forests -- an extension of model-based decision\n    trees and forests to Structural Equation Models (SEM). SEM trees hierarchically\n    split empirical data into homogeneous groups each sharing similar data patterns\n    with respect to a SEM by recursively selecting optimal predictors of these\n    differences. SEM forests are an extension of SEM trees. They are ensembles of\n    SEM trees each built on a random sample of the original data. By aggregating\n    over a forest, we obtain measures of variable importance that are more robust\n    than measures from single trees. A description of the method was published by\n    Brandmaier, von Oertzen, McArdle, & Lindenberger (2013) <doi:10.1037/a0030001> \n    and Arnold, Voelkle, & Brandmaier (2020) <doi:10.3389/fpsyg.2020.564403>.\nLicense: GPL-3\nEncoding: UTF-8\nLazyLoad: yes\nVersion: 0.9.18\nDate: 2022-05-13\nRoxygenNote: 7.1.2\nVignetteBuilder: knitr\nNeedsCompilation: no\nPackaged: 2022-05-13 09:17:23 UTC; andreas.brandmaier\nRepository: CRAN\nDate/Publication: 2022-05-13 20:20:02 UTC"],"package":["semtree"],"version":["0.9.18"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/semtree/new/semtree.Rcheck"],"test_fail":{},"test_output":{"invariance":["> #\n> # testing invariance \n> #\n> \n> # simulation:\n> # factor structure holds over SES but not over age\n> # both SES and age predict a mean difference in cognitive outcome\n> \n> set.seed(123)\n> \n> require(\"semtree\")\nLoading required package: semtree\nLoading required package: OpenMx\nOpenMx may run faster if it is compiled to take advantage of multiple cores.\n> require(\"lavaan\")\nLoading required package: lavaan\nThis is lavaan 0.6-12\nlavaan is FREE software! Please report any bugs.\n> #\n> lambda <- list()\n> age <- c(0,0,1,1) # 0=young, 1 =old\n> ses <- c(0,1,0,1) # 0=low, 1=high\n> lambda[[1]] <- c(1,0.9,0.8,0.8)\n> lambda[[2]] <- c(1,0.9,0.8,0.8)\n> lambda[[3]] <- c(1,0.4,0.2,0.9)\n> lambda[[4]] <- c(1,0.4,0.2,0.9)\n> cogmean <- 80-age*30 + ses*20\n> cogsd <- 1\n> errsd <- 1\n> \n> Nsub <- 200 # persons per agexSES group\n> \n> cbind(age,ses,cogmean)\n     age ses cogmean\n[1,]   0   0      80\n[2,]   0   1     100\n[3,]   1   0      50\n[4,]   1   1      70\n> \n> # simulate data from 4 groups\n> data <- c()\n> for (i in 1:4) {\n+   cogsim <- rnorm(n = Nsub,mean = cogmean[i],cogsd)\n+   scores <- as.matrix(t(outer(lambda[[i]],cogsim))) + rnorm(Nsub*4,0,errsd)\n+   data <- rbind(data,scores)\n+ }\n> \n> # rescale data\n> data <- scale(data)\n> \n> # put data into dataframe and label observed variables\n> data <- data.frame(data)\n> names(data) <- paste0(\"x\",1:4)\n> \n> # add predictors to create full data set\n> fulldata <- cbind(data, age=factor(rep(age,each=Nsub)),ses=factor(rep(ses,each=Nsub)))\n> \n> # specify model\n> model<-\"\n+ ! regressions \n+ F=~1.0*x1\n+ F=~l2*x2\n+ F=~l3*x3\n+ F=~l4*x4\n+ ! residuals, variances and covariances\n+ x1 ~~ VAR_x1*x1\n+ x2 ~~ VAR_x2*x2\n+ x3 ~~ VAR_x3*x3\n+ x4 ~~ VAR_x4*x4\n+ F ~~ 1.0*F\n+ ! means\n+ F~1\n+ x1~0*1;\n+ x2~0*1;\n+ x3~0*1;\n+ x4~0*1;\n+ \";\n> result<-lavaan(model, data=data, fixed.x=FALSE, missing=\"FIML\");\nWarning message:\nIn lav_object_post_check(object) :\n  lavaan WARNING: some estimated ov variances are negative\n> \n> manifests<-c(\"x1\",\"x2\",\"x3\",\"x4\")\n> latents<-c(\"F\")\n> model <- mxModel(\"Unnamed_Model\", \n+                  type=\"RAM\",\n+                  manifestVars = manifests,\n+                  latentVars = latents,\n+                  mxPath(from=\"F\",to=c(\"x1\",\"x2\",\"x3\",\"x4\"), free=c(FALSE,TRUE,TRUE,TRUE),\n+                         value=c(1.0,1.0,1.0,1.0) , arrows=1, label=c(\"F__x1\",\"l2\",\"l3\",\"l4\") ),\n+                  mxPath(from=\"one\",to=c(\"F\"), free=c(TRUE), value=c(1.0) , arrows=1, label=c(\"const__F\") ),\n+                  mxPath(from=\"one\",to=c(\"x2\",\"x3\",\"x4\"), free=c(TRUE,TRUE,TRUE), value=c(1.0,1.0,1.0) , arrows=1, label=c(\"const__x2\",\"const__x3\",\"const__x4\") ),\n+                  mxPath(from=\"x1\",to=c(\"x1\"), free=c(TRUE), value=c(1.0) , arrows=2, label=c(\"VAR_x1\") ),\n+                  mxPath(from=\"x2\",to=c(\"x2\"), free=c(TRUE), value=c(1.0) , arrows=2, label=c(\"VAR_x2\") ),\n+                  mxPath(from=\"x3\",to=c(\"x3\"), free=c(TRUE), value=c(1.0) , arrows=2, label=c(\"VAR_x3\") ),\n+                  mxPath(from=\"x4\",to=c(\"x4\"), free=c(TRUE), value=c(1.0) , arrows=2, label=c(\"VAR_x4\") ),\n+                  mxPath(from=\"F\",to=c(\"F\"), free=c(FALSE), value=c(1.0) , arrows=2, label=c(\"VAR_F\") ),\n+                  mxPath(from=\"one\",to=c(\"x1\"), free=F, value=0, arrows=1),\n+                  mxData(data[1:50,], type = \"raw\")\n+ );\n> \n> result <- mxRun(model)\nRunning Unnamed_Model with 11 parameters\nWarning message:\nIn model 'Unnamed_Model' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) \n> summary(result)\nSummary of Unnamed_Model \n \nThe model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) \n \nfree parameters:\n        name matrix row col     Estimate    Std.Error A\n1         l2      A  x2   F  0.110678568 0.0700805290  \n2         l3      A  x3   F  0.258544075 0.0784025322  \n3         l4      A  x4   F  0.577941732 0.1992714893  \n4     VAR_x1      S  x1  x1  0.004467946 0.0035870198  \n5     VAR_x2      S  x2  x2  0.001213062 0.0002540564  \n6     VAR_x3      S  x3  x3  0.001042327 0.0003111298  \n7     VAR_x4      S  x4  x4  0.006968770 0.0018057182  \n8  const__x2      M   1  x2  0.629669122 0.0201836183  \n9  const__x3      M   1  x3  0.641787994 0.0224712984  \n10 const__x4      M   1  x4 -0.081925673 0.0570787646  \n11  const__F      M   1   F  0.278899274 0.1417368576  \n\nModel Statistics: \n               |  Parameters  |  Degrees of Freedom  |  Fit (-2lnL units)\n       Model:             11                    189             -387.4425\n   Saturated:             14                    186                    NA\nIndependence:              8                    192                    NA\nNumber of observations/statistics: 50/200\n\nInformation Criteria: \n      |  df Penalty  |  Parameters Penalty  |  Sample-Size Adjusted\nAIC:      -765.4425              -365.4425                -358.4951\nBIC:     -1126.8149              -344.4103                -378.9374\nTo get additional fit indices, see help(mxRefModels)\ntimestamp: 2022-09-24 17:06:28 \nWall clock time: 0.1147821 secs \noptimizer:  SLSQP \nOpenMx version number: 2.20.6 \nNeed help?  See help(mxSummary) \n\n> \n> subset <- data[1:50, ]\n> \n> \n> ctr <- semtree.control(verbose=TRUE)\n> ctr$exclude.heywood <- FALSE\n> # naive tree should find both effects, age & ses, with age having the stronger effect \n> tree <- semtree(model = result, data=fulldata, control=ctr)\nDetected OpenMx model.\nOpenMx model estimation selected!\n❯ Growing level 0 n = 800\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n✔ Best split is  age with statistic = 7071.74\n❯ Growing level 1 n = 400\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n✔ Best split is  ses with statistic = 3345.91\n❯ Growing level 2 n = 200\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n❯ Best Likelihood Ratio was NULL. Stop splitting\n❯ Growing level 2 n = 200\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n❯ Best Likelihood Ratio was NULL. Stop splitting\n❯ Growing level 1 n = 400\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n✔ Best split is  ses with statistic = 969.14\n❯ Growing level 2 n = 200\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n❯ Best Likelihood Ratio was NULL. Stop splitting\n❯ Growing level 2 n = 200\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n❯ Best Likelihood Ratio was NULL. Stop splitting\n✔ Tree construction finished [took less than a second].\n> #plot(tree)\n> \n> # invariance tree should exclude splits wrt age and only splir wrt to ses\n> ctr$report.level <- 99\n> ctr$alpha.invariance <- 0.01\n> \n> cnst <- semtree.constraints(local.invariance = c(\"l2\",\"l3\",\"l4\"))\n> #cnst <- semtree.constraints(local.invariance=)\n> tree2 <- semtree(model = result, data=fulldata, control=ctr, constraints = cnst )\nDetected OpenMx model.\nOpenMx model estimation selected!\n❯ Growing level 0 n = 800\nGrowing tree level 0\n  |--Estimating baseline likelihood:  2843.02725567512\n❯ Testing Predictor: age\n  |--Estimating baseline likelihood:  2843.02725567512\n❯ Testing Predictor: ses\n❯ Filtering possible splits by invariance\nLL.within: 7071.73687619766,6670.01382647738 \nLL.max:  NA \nwithin.split:  1,1 \nsplit max NA \n❯ Best Likelihood Ratio was NULL. Stop splitting\n✔ Tree construction finished [took less than a second].\nWarning messages:\n1: In model 'sharedModel' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) \n2: In model 'sharedModel' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) \n> \n> #plot(tree2)\n> \n> proc.time()\n   user  system elapsed \n  2.526   0.090   2.615 \n"],"lavaan":["> # DEMO FOR SEMTREE\n> \n> \n> require(\"semtree\")\nLoading required package: semtree\nLoading required package: OpenMx\nOpenMx may run faster if it is compiled to take advantage of multiple cores.\n> require(\"lavaan\")\nLoading required package: lavaan\nThis is lavaan 0.6-12\nlavaan is FREE software! Please report any bugs.\n> \n> # ORGANIZE DATA BY TYPE FOR COVARIATES.\n> # SOME COVARIATES ARE ORGANIZED IN THE DATA. MODEL VARIABLES AND \n> # COVARIATES DO NOT NEED TO BE ORDERED IN THE DATASET. ONLY VARIABLE\n> # TYPE NEEDS TO BE DEFINED FOR THE COVARIATES (FACTOR/ORDERED/NUMERIC)\n> # BE AWARE OF THE EXPONENTIAL GROWTH OF MODEL COMPARISON WITH INCREASES\n> # IN NUMBER OF FACTORS PER A COVARIATE.\n> \n> data(lgcm)\n> \n> lgcm$agegroup <- as.ordered(lgcm$agegroup)\n> lgcm$training <- as.factor(lgcm$training)\n> lgcm$noise <- as.numeric(lgcm$noise)\n> \n> # LOAD IN LAVAAN MODEL.\n> # A SIMPLE LINEAR GROWTH MODEL WITH 5 TIME POINTS FROM SIMULATED DATA\n> \n> lgcModelstr <- '\n+ g0 =~ 1*o1 + 1*o2 + 1*o3 + 1*o4 + 1*o5;\n+ g1 =~ 0*o1 + 1*o2 + 2*o3 + 3*o4 + 4*o5;\n+ g0 ~~ g0; g0 ~ mui*1;\n+ g1 ~~ g1; g1 ~ sli*1;\n+ g0 ~~ g1;\n+ o1 ~~ o1; o1 ~ 0*1;\n+ o2 ~~ o2; o2 ~ 0*1;\n+ o3 ~~ o3; o3 ~ 0*1;\n+ o4 ~~ o4; o4 ~ 0*1;\n+ o5 ~~ o5; o5 ~ 0*1;\n+ '\n> lgcModel <- lavaan(lgcModelstr, lgcm, do.fit=TRUE)\n> \n> # TREE CONTROL OPTIONS.\n> # TO OBTAIN BASIC/DEFAULT SMETREE OPTIONS, SIMPLY TPYE THE FOLLOWING:\n> \n> controlOptions <- semtree.control()\n> \n> # THE CONTENTS OF THE DEFAULT CONTROLS CAN THEN BE VIEWED.\n> \n> controlOptions\n SEM-Tree control:\n ▔▔▔▔▔▔▔▔▔▔ \n● Splitting Method: naive\n● Alpha Level: 0.05\n● Bonferroni Correction:FALSE\n● Minimum Number of Cases: 20\n● Maximum Tree Depth: NA\n● Number of CV Folds: 5\n● Exclude Heywood Cases: TRUE\n● Test Invariance Alpha Level: NA\n● Use all Cases: FALSE\n● Verbosity: FALSE\n● Progress Bar: TRUE\n● Seed: NA\n> \n> # AND MODEL OPTIONS CAN BE CHANGED BY REDEFINING ELEMENTS OF THE \n> # CONTROL OBJECT.\n> \n> controlOptions$alpha <- 0.01\n> \n> # RUN TREE.\n> \n> tree <- semtree(model=lgcModel, data=lgcm, control = controlOptions)\n✖ Variable noise is numeric but has only few unique values. Consider recoding as ordered factor.\n✔ Tree construction finished [took 1s].\n> \n> # SEE PLOT.\n> # THE PLOT FUNCTION WILL SHOW ALL FREE PARAMETERS AT EACH TERMINAL NODE.\n> # THIS CAN CREATE UNREADABLE FIGURES FOR MODELS WITH MANY FREE PARAMETERS.\n> \n> plot(tree)\n> \n> # SEE SUMMARY.\n> # OVERALL MODEL FACTS ARE GIVEN WITH THE SUMMARY FUNCTION.\n> \n> summary(tree)\nSEMtree Summary\nTemplate model:  \nTotal Sample Size:  400 \nNumber of nodes:  5 \nNumber of leaf nodes:  3 \nFree Parameters:  10  ( g0~~g0 mui g1~~g1 sli g0~~g1 o1~~o1 o2~~o2 o3~~o3 o4~~o4 o5~~o5 )\n> \n> # summary(treeConstrained)\n> \n> # USING THE PRINT FUNCTION WILL PROVIDE AN OVERVIEW OF THE MODEL\n> # SPLITS, LR TESTS WITH DF, AND SUBGROUP SIZES (N).\n> \n> print(tree)\nSEMtree with numbered nodes\n |-[1] agegroup > 0 [N=400 LR=1258.08, df=10]\n |   |-[2] TERMINAL [N=200]\n |   |-[3] training  in [ 0  ] [N=200 LR=40.85, df=10]\n |   |   |-[4] TERMINAL [N=100]\n |   |   |-[5] TERMINAL [N=100]\n> \n> # GET NODE PARAMETERS (leafs only as default).\n> # THE DEFAULT IS ONLY DISPLAYING LEAF NODE PARAMETER ESTIMATES.\n> \n> parameters(tree)\n            2      4      5\ng0~~g0  0.082  0.104  0.085\nmui     5.017  1.941  2.005\ng1~~g1  0.499  0.674  1.629\nsli    -0.142 -0.494 -1.084\ng0~~g1 -0.011  0.028 -0.044\no1~~o1  0.068  0.048  0.042\no2~~o2  0.049  0.069  0.049\no3~~o3  0.043  0.053  0.053\no4~~o4  0.055  0.039  0.063\no5~~o5  0.037  0.048  0.011\n> \n> # TO GET ALL PARAMETER ESTIMATES FOR EVERY NODE CHANGE THE DEFAULT TO.\n> \n> parameters(tree, leafs.only=FALSE)\n            1      2      3      4      5\ng0~~g0  2.410  0.082  0.095  0.104  0.085\nmui     3.496  5.017  1.973  1.941  2.005\ng1~~g1  0.973  0.499  1.239  0.674  1.629\nsli    -0.466 -0.142 -0.789 -0.494 -1.084\ng0~~g1  0.477 -0.011 -0.017  0.028 -0.044\no1~~o1  0.052  0.068  0.045  0.048  0.042\no2~~o2  0.058  0.049  0.059  0.069  0.049\no3~~o3  0.047  0.043  0.053  0.053  0.053\no4~~o4  0.052  0.055  0.051  0.039  0.063\no5~~o5  0.036  0.037  0.030  0.048  0.011\n> \n> # SUBTREE FUNCTION.\n> # IF ONLY A SUBSET OF THE TREE IS TO BE EXAMINED, THEN THE TREE CAN \n> # BE PARED. THIS IS DONE WITH A SUBSET FUNCTION WHICH STORES THE TREE\n> # FROM A GIVEN NODE ON. IF THE TREE FROM NODE 2 ON IS DESIRED, THEN:\n> \n> treeSub <- subtree(tree, startNode=3)\n> \n> \n> # ALTERNATIVE SPLIT RULE\n> \n> controlOptions$method <- \"fair\"\n> tree2 <- semtree(model=lgcModel, data=lgcm, control = controlOptions)\n✖ Variable noise is numeric but has only few unique values. Consider recoding as ordered factor.\n✔ Tree construction finished [took 2s].\n> \n> # disabled for time restrictions on CRAN\n> #controlOptions$method <- \"cv\"\n> #tree3 <- semtree(model=lgcModel, data=lgcm, control = controlOptions)\n> \n> proc.time()\n   user  system elapsed \n  3.272   0.402   3.780 \n"],"tree":["> set.seed(789)\n> require(\"semtree\")\nLoading required package: semtree\nLoading required package: OpenMx\nOpenMx may run faster if it is compiled to take advantage of multiple cores.\n> data(lgcm)\n> \n> lgcm$agegroup <- ordered(lgcm$agegroup, labels=c(\"young\",\"old\") )\n> lgcm$training <- as.factor(lgcm$training)\n> lgcm$noise <- as.factor(lgcm$noise)\n> \n> # LOAD IN OPENMX MODEL.\n> # A SIMPLE LINEAR GROWTH MODEL WITH 5 TIME POINTS FROM SIMULATED DATA\n> \n> manifests <- names(lgcm)[1:5]\n> lgcModel <- mxModel(\"Linear Growth Curve Model Path Specification\",\n+                             type=\"RAM\",\n+                             manifestVars=manifests,\n+                             latentVars=c(\"intercept\",\"slope\"),\n+                             # residual variances\n+                             mxPath(\n+                               from=manifests,\n+                               arrows=2,\n+                               free=TRUE,\n+                               values = c(1, 1, 1, 1, 1),\n+                               labels=c(\"residual1\",\"residual2\",\"residual3\",\"residual4\",\"residual5\")\n+                             ),\n+                             # latent variances and covariance\n+                             mxPath(\n+                               from=c(\"intercept\",\"slope\"),\n+                               connect=\"unique.pairs\",\n+                               arrows=2,\n+                               free=TRUE,\n+                               values=c(1, 1, 1),\n+                               labels=c(\"vari\", \"cov\", \"vars\")\n+                             ),\n+                             # intercept loadings\n+                             mxPath(\n+                               from=\"intercept\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(1, 1, 1, 1, 1)\n+                             ),\n+                             # slope loadings\n+                             mxPath(\n+                               from=\"slope\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(0, 1, 2, 3, 4)\n+                             ),\n+                             # manifest means\n+                             mxPath(\n+                               from=\"one\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(0, 0, 0, 0, 0)\n+                             ),\n+                             # latent means\n+                             mxPath(\n+                               from=\"one\",\n+                               to=c(\"intercept\", \"slope\"),\n+                               arrows=1,\n+                               free=TRUE,\n+                               values=c(1, 1),\n+                               labels=c(\"meani\", \"means\")\n+                             ),\n+                     mxData(lgcm,type=\"raw\")\n+                     )\n> \n> \n> # TREE CONTROL OPTIONS.\n> # TO OBTAIN BASIC/DEFAULT SMETREE OPTIONS, SIMPLY TPYE THE FOLLOWING:\n> \n> controlOptions <- semtree.control(method = \"naive\")\n> controlOptions$alpha <- 0.05\n> \n> # RUN TREE.\n> \n> tree <- semtree(model=lgcModel, data=lgcm, control = controlOptions)\n✔ Tree construction finished [took less than a second].\n> \n> # RERUN TREE WITH MODEL CONSTRAINTS.\n> # MODEL CONSTRAINTS CAN BE ADDED BY IDENTIFYING THE PARAMETERS TO BE\n> # CONSTRAINED IN EVERY NODE. ONLY UNCONSTRAINED PARAMETERS ARE THEN\n> # TESTED AT EACH NODE FOR GROUP DIFFERENCES. IN THIS EXAMPLE THE MODEL \n> # RESIDUALS ARE CONSTRAINED OVER THE NODES.\n> \n> constraints <- semtree.constraints(global.invariance = names(omxGetParameters(lgcModel))[1:5])\n> \n> treeConstrained <- semtree(model=lgcModel, data=lgcm, control = controlOptions,\n+                            constraints=constraints)\n❯ Global Constraints:\nresidual1 residual2 residual3 residual4 residual5\n❯ Freely Estimated Parameters:\nvari cov vars meani means\n✔ Tree construction finished [took less than a second].\n> \n> # SEE PLOT.\n> # THE PLOT FUNCTION WILL SHOW ALL FREE PARAMETERS AT EACH TERMINAL NODE.\n> # THIS CAN CREATE UNREADABLE FIGURES FOR MODELS WITH MANY FREE PARAMETERS.\n> \n> plot(tree)\n> \n> summary(tree)\nSEMtree Summary\nTemplate model:  \nTotal Sample Size:  400 \nNumber of nodes:  5 \nNumber of leaf nodes:  3 \nFree Parameters:  10  ( residual1 residual2 residual3 residual4 residual5 vari cov vars meani means )\n> \n> summary(treeConstrained)\nSEMtree Summary\nTemplate model:  \nTotal Sample Size:  400 \nNumber of nodes:  5 \nNumber of leaf nodes:  3 \nFree Parameters:  5  ( vari cov vars meani means )\n> \n> print(tree)\nSEMtree with numbered nodes\n |-[1] agegroup > young [N=400 LR=1258.08, df=10]\n |   |-[2] TERMINAL [N=200]\n |   |-[3] training  in [ 0  ] [N=200 LR=40.85, df=10]\n |   |   |-[4] TERMINAL [N=100]\n |   |   |-[5] TERMINAL [N=100]\n> \n> parameters(tree)\n               2      4      5\nresidual1  0.068  0.048  0.042\nresidual2  0.049  0.069  0.049\nresidual3  0.043  0.053  0.053\nresidual4  0.055  0.039  0.063\nresidual5  0.037  0.048  0.011\nvari       0.082  0.104  0.085\ncov       -0.011  0.028 -0.044\nvars       0.499  0.674  1.629\nmeani      5.017  1.941  2.005\nmeans     -0.142 -0.494 -1.084\n> \n> parameters(tree, leafs.only=FALSE)\n               1      2      3      4      5\nresidual1  0.052  0.068  0.045  0.048  0.042\nresidual2  0.058  0.049  0.059  0.069  0.049\nresidual3  0.047  0.043  0.053  0.053  0.053\nresidual4  0.052  0.055  0.051  0.039  0.063\nresidual5  0.036  0.037  0.030  0.048  0.011\nvari       2.410  0.082  0.095  0.104  0.085\ncov        0.477 -0.011 -0.017  0.028 -0.044\nvars       0.973  0.499  1.239  0.674  1.629\nmeani      3.496  5.017  1.973  1.941  2.005\nmeans     -0.466 -0.142 -0.789 -0.494 -1.084\n> \n> treeSub <- subtree(tree, startNode=3)\n> \n> if (!is.null(treeSub))\n+ \tplot(treeSub)\n> \n> toTable(tree)\n     agegroup  training\n[1,] \"UNKNOWN\" \"\"      \n[2,] \"UNKNOWN\" \"not 0\" \n[3,] \"UNKNOWN\" \"0\"     \n> \n> \n> controlOptions <- semtree.control(method = \"fair\")\n> \n> tree2 <- semtree(lgcModel, lgcm, control=controlOptions)\n✔ Tree construction finished [took less than a second].\n> \n> \n> controlOptions <- semtree.control(method = \"score\")\n> tree3 <- semtree(lgcModel, lgcm, control=controlOptions)\n❯ Model was not run. Estimating parameters now.\nRunning Linear Growth Curve Model Path Specification with 10 parameters\n\nBeginning initial fit attempt\nRunning Linear Growth Curve Model Path Specification with 10 parameters\n\n Lowest minimum so far:  3946.79931515404\n\nSolution found\n\n\r\n Solution found!  Final fit=3946.7993 (started at 12364.579)  (1 attempt(s): 1 valid, 0 errors)\n\n Start values from best fit:\n0.0517425500974165,0.057996464842973,0.0467583755756157,0.0520836958577161,0.0361130739855864,2.41004053260765,0.477157340565657,0.973042383133384,3.49639424449095,-0.465977315382569\n✔ Tree construction finished [took less than a second].\n> \n> proc.time()\n   user  system elapsed \n  4.179   0.104   4.327 \n"],"vim":["> set.seed(789)\n> require(\"semtree\")\nLoading required package: semtree\nLoading required package: OpenMx\nOpenMx may run faster if it is compiled to take advantage of multiple cores.\n> data(lgcm)\n> \n> lgcm$agegroup <- ordered(lgcm$agegroup)\n> lgcm$training <- factor(lgcm$training)\n> lgcm$noise <- as.numeric(lgcm$noise)\n> \n> # LOAD IN OPENMX MODEL.\n> # A SIMPLE LINEAR GROWTH MODEL WITH 5 TIME POINTS FROM SIMULATED DATA\n> \n> manifests <- names(lgcm)[1:5]\n> lgcModel <- mxModel(\"Linear Growth Curve Model Path Specification\",\n+                             type=\"RAM\",\n+                             manifestVars=manifests,\n+                             latentVars=c(\"intercept\",\"slope\"),\n+                             # residual variances\n+                             mxPath(\n+                               from=manifests,\n+                               arrows=2,\n+                               free=TRUE,\n+                               values = c(1, 1, 1, 1, 1),\n+                               labels=c(\"residual1\",\"residual2\",\"residual3\",\"residual4\",\"residual5\")\n+                             ),\n+                             # latent variances and covariance\n+                             mxPath(\n+                               from=c(\"intercept\",\"slope\"),\n+                               connect=\"unique.pairs\",\n+                               arrows=2,\n+                               free=TRUE,\n+                               values=c(1, 1, 1),\n+                               labels=c(\"vari\", \"cov\", \"vars\")\n+                             ),\n+                             # intercept loadings\n+                             mxPath(\n+                               from=\"intercept\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(1, 1, 1, 1, 1)\n+                             ),\n+                             # slope loadings\n+                             mxPath(\n+                               from=\"slope\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(0, 1, 2, 3, 4)\n+                             ),\n+                             # manifest means\n+                             mxPath(\n+                               from=\"one\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(0, 0, 0, 0, 0)\n+                             ),\n+                             # latent means\n+                             mxPath(\n+                               from=\"one\",\n+                               to=c(\"intercept\", \"slope\"),\n+                               arrows=1,\n+                               free=TRUE,\n+                               values=c(1, 1),\n+                               labels=c(\"meani\", \"means\")\n+                             ),\n+                     mxData(lgcm,type=\"raw\")\n+                     )\n> \n> \n> fr <- semforest(lgcModel, lgcm,control = semforest.control(num.trees = 3))\n❯ Model was not run. Estimating parameters now before running the forest.\nRunning Linear Growth Curve Model Path Specification with 10 parameters\n\nBeginning initial fit attempt\nRunning Linear Growth Curve Model Path Specification with 10 parameters\n\n Lowest minimum so far:  3946.79931515404\n\nSolution found\n\n\r\n Solution found!  Final fit=3946.7993 (started at 12364.579)  (1 attempt(s): 1 valid, 0 errors)\n\n Start values from best fit:\n0.0517425500974165,0.057996464842973,0.0467583755756157,0.0520836958577161,0.0361130739855864,2.41004053260765,0.477157340565657,0.973042383133384,3.49639424449095,-0.465977315382569\n✖ Variable noise is numeric but has only few unique values. Consider recoding as ordered factor.\n✔ Tree construction finished [took 2s].\n✖ Variable noise is numeric but has only few unique values. Consider recoding as ordered factor.\n✔ Tree construction finished [took 1s].\n✖ Variable noise is numeric but has only few unique values. Consider recoding as ordered factor.\n✔ Tree construction finished [took 2s].\n✔ Forest completed [took 5s]\n> \n>   \n> vimp <- varimp(fr)\n> \n> print(vimp)\nVariable Importance\n   agegroup    training       noise \n6750.526689   34.849484   -4.840505 \n> print(vimp, na.omit=TRUE)\nVariable Importance\n   agegroup    training       noise \n6750.526689   34.849484   -4.840505 \n> \n> \n> proc.time()\n   user  system elapsed \n  7.403   0.104   7.515 \n"]},"install_out":["* installing *source* package ‘semtree’ ...\n** package ‘semtree’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** data\n** demo\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (semtree)\n"],"session_info":{"platform":{"version":["R version 4.2.1 (2022-06-23)"],"os":["macOS Monterey 12.6"],"system":["aarch64, darwin20"],"ui":["X11"],"language":["(EN)"],"collate":["C"],"ctype":["en_US.UTF-8"],"tz":["America/Chicago"],"date":["2022-09-24"],"pandoc":["2.19 @ /usr/local/bin/pandoc"]},"packages":[{"package":"semtree","attached":false,"is_base":false,"_row":"semtree"}]}}}


package: semtree
version: 0.9.18
maintainer: Andreas M. Brandmaier <andy@brandmaier.de>
status: OK
which: old
duration: 51.8948130607605
starttime: 2022-09-24 22:05:54
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[0]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/semtree/old/semtree.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘semtree/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘semtree’ version ‘0.9.18’\n* package encoding: UTF-8\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘semtree’ can be installed ... OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking ‘build’ directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking installed files from ‘inst/doc’ ... OK\n* checking files in ‘vignettes’ ... OK\n* checking examples ... OK\n* checking for unstated dependencies in ‘tests’ ... OK\n* checking tests ...\n  Running ‘invariance.R’\n  Running ‘lavaan.R’\n  Running ‘tree.R’\n  Running ‘vim.R’\n OK\n* checking for unstated dependencies in vignettes ... OK\n* checking package vignettes in ‘inst/doc’ ... OK\n* checking running R code from vignettes ...\n  ‘constraints.Rmd’ using ‘UTF-8’... OK\n  ‘forests.Rmd’ using ‘UTF-8’... OK\n  ‘getting-started.Rmd’ using ‘UTF-8’... OK\n  ‘score-based-tests.Rmd’ using ‘UTF-8’... OK\n  ‘semforest-focus.Rmd’ using ‘UTF-8’... OK\n NONE\n* checking re-building of vignette outputs ... SKIPPED\n* DONE\n\nStatus: OK\n\n\n"],"stderr":[""],"status":[0],"duration":[53.271],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":[],"description":["Package: semtree\nType: Package\nTitle: Recursive Partitioning for Structural Equation Models\nAuthors@R: c(person(\"Andreas M. Brandmaier\", email=\"andy@brandmaier.de\", role=c(\"aut\",\"cre\")), person(\"John J. Prindle\", email=\"jprindle@usc.edu\",role=c(\"aut\")),person(\"Manuel Arnold\", email=\"arnoldmz@hu-berlin.de\",role=c(\"aut\")),person(\"Caspar J. Van Lissa\", email=\"C.J.vanLissa@uu.nl\",role=c(\"aut\")))\nAuthor: Andreas M. Brandmaier [aut, cre],\n  John J. Prindle [aut],\n  Manuel Arnold [aut],\n  Caspar J. Van Lissa [aut]\nMaintainer: Andreas M. Brandmaier <andy@brandmaier.de>\nDepends: R (>= 2.10), OpenMx (>= 2.6.9),\nImports: bitops, sets, digest, rpart, rpart.plot (>= 3.0.6), plotrix,\n        cluster, stringr, lavaan, ggplot2, tidyr, methods, strucchange,\n        sandwich, zoo, crayon, clisymbols, future.apply, data.table\nSuggests: knitr, rmarkdown, viridis, MASS, psychTools, testthat\nDescription: SEM Trees and SEM Forests -- an extension of model-based decision\n    trees and forests to Structural Equation Models (SEM). SEM trees hierarchically\n    split empirical data into homogeneous groups each sharing similar data patterns\n    with respect to a SEM by recursively selecting optimal predictors of these\n    differences. SEM forests are an extension of SEM trees. They are ensembles of\n    SEM trees each built on a random sample of the original data. By aggregating\n    over a forest, we obtain measures of variable importance that are more robust\n    than measures from single trees. A description of the method was published by\n    Brandmaier, von Oertzen, McArdle, & Lindenberger (2013) <doi:10.1037/a0030001> \n    and Arnold, Voelkle, & Brandmaier (2020) <doi:10.3389/fpsyg.2020.564403>.\nLicense: GPL-3\nEncoding: UTF-8\nLazyLoad: yes\nVersion: 0.9.18\nDate: 2022-05-13\nRoxygenNote: 7.1.2\nVignetteBuilder: knitr\nNeedsCompilation: no\nPackaged: 2022-05-13 09:17:23 UTC; andreas.brandmaier\nRepository: CRAN\nDate/Publication: 2022-05-13 20:20:02 UTC"],"package":["semtree"],"version":["0.9.18"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/semtree/old/semtree.Rcheck"],"test_fail":{},"test_output":{"invariance":["> #\n> # testing invariance \n> #\n> \n> # simulation:\n> # factor structure holds over SES but not over age\n> # both SES and age predict a mean difference in cognitive outcome\n> \n> set.seed(123)\n> \n> require(\"semtree\")\nLoading required package: semtree\nLoading required package: OpenMx\nOpenMx may run faster if it is compiled to take advantage of multiple cores.\n> require(\"lavaan\")\nLoading required package: lavaan\nThis is lavaan 0.6-12\nlavaan is FREE software! Please report any bugs.\n> #\n> lambda <- list()\n> age <- c(0,0,1,1) # 0=young, 1 =old\n> ses <- c(0,1,0,1) # 0=low, 1=high\n> lambda[[1]] <- c(1,0.9,0.8,0.8)\n> lambda[[2]] <- c(1,0.9,0.8,0.8)\n> lambda[[3]] <- c(1,0.4,0.2,0.9)\n> lambda[[4]] <- c(1,0.4,0.2,0.9)\n> cogmean <- 80-age*30 + ses*20\n> cogsd <- 1\n> errsd <- 1\n> \n> Nsub <- 200 # persons per agexSES group\n> \n> cbind(age,ses,cogmean)\n     age ses cogmean\n[1,]   0   0      80\n[2,]   0   1     100\n[3,]   1   0      50\n[4,]   1   1      70\n> \n> # simulate data from 4 groups\n> data <- c()\n> for (i in 1:4) {\n+   cogsim <- rnorm(n = Nsub,mean = cogmean[i],cogsd)\n+   scores <- as.matrix(t(outer(lambda[[i]],cogsim))) + rnorm(Nsub*4,0,errsd)\n+   data <- rbind(data,scores)\n+ }\n> \n> # rescale data\n> data <- scale(data)\n> \n> # put data into dataframe and label observed variables\n> data <- data.frame(data)\n> names(data) <- paste0(\"x\",1:4)\n> \n> # add predictors to create full data set\n> fulldata <- cbind(data, age=factor(rep(age,each=Nsub)),ses=factor(rep(ses,each=Nsub)))\n> \n> # specify model\n> model<-\"\n+ ! regressions \n+ F=~1.0*x1\n+ F=~l2*x2\n+ F=~l3*x3\n+ F=~l4*x4\n+ ! residuals, variances and covariances\n+ x1 ~~ VAR_x1*x1\n+ x2 ~~ VAR_x2*x2\n+ x3 ~~ VAR_x3*x3\n+ x4 ~~ VAR_x4*x4\n+ F ~~ 1.0*F\n+ ! means\n+ F~1\n+ x1~0*1;\n+ x2~0*1;\n+ x3~0*1;\n+ x4~0*1;\n+ \";\n> result<-lavaan(model, data=data, fixed.x=FALSE, missing=\"FIML\");\nWarning message:\nIn lav_object_post_check(object) :\n  lavaan WARNING: some estimated ov variances are negative\n> \n> manifests<-c(\"x1\",\"x2\",\"x3\",\"x4\")\n> latents<-c(\"F\")\n> model <- mxModel(\"Unnamed_Model\", \n+                  type=\"RAM\",\n+                  manifestVars = manifests,\n+                  latentVars = latents,\n+                  mxPath(from=\"F\",to=c(\"x1\",\"x2\",\"x3\",\"x4\"), free=c(FALSE,TRUE,TRUE,TRUE),\n+                         value=c(1.0,1.0,1.0,1.0) , arrows=1, label=c(\"F__x1\",\"l2\",\"l3\",\"l4\") ),\n+                  mxPath(from=\"one\",to=c(\"F\"), free=c(TRUE), value=c(1.0) , arrows=1, label=c(\"const__F\") ),\n+                  mxPath(from=\"one\",to=c(\"x2\",\"x3\",\"x4\"), free=c(TRUE,TRUE,TRUE), value=c(1.0,1.0,1.0) , arrows=1, label=c(\"const__x2\",\"const__x3\",\"const__x4\") ),\n+                  mxPath(from=\"x1\",to=c(\"x1\"), free=c(TRUE), value=c(1.0) , arrows=2, label=c(\"VAR_x1\") ),\n+                  mxPath(from=\"x2\",to=c(\"x2\"), free=c(TRUE), value=c(1.0) , arrows=2, label=c(\"VAR_x2\") ),\n+                  mxPath(from=\"x3\",to=c(\"x3\"), free=c(TRUE), value=c(1.0) , arrows=2, label=c(\"VAR_x3\") ),\n+                  mxPath(from=\"x4\",to=c(\"x4\"), free=c(TRUE), value=c(1.0) , arrows=2, label=c(\"VAR_x4\") ),\n+                  mxPath(from=\"F\",to=c(\"F\"), free=c(FALSE), value=c(1.0) , arrows=2, label=c(\"VAR_F\") ),\n+                  mxPath(from=\"one\",to=c(\"x1\"), free=F, value=0, arrows=1),\n+                  mxData(data[1:50,], type = \"raw\")\n+ );\n> \n> result <- mxRun(model)\nRunning Unnamed_Model with 11 parameters\nWarning message:\nIn model 'Unnamed_Model' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) \n> summary(result)\nSummary of Unnamed_Model \n \nThe model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) \n \nfree parameters:\n        name matrix row col     Estimate    Std.Error A\n1         l2      A  x2   F  0.110678568 0.0700805290  \n2         l3      A  x3   F  0.258544075 0.0784025322  \n3         l4      A  x4   F  0.577941732 0.1992714893  \n4     VAR_x1      S  x1  x1  0.004467946 0.0035870198  \n5     VAR_x2      S  x2  x2  0.001213062 0.0002540564  \n6     VAR_x3      S  x3  x3  0.001042327 0.0003111298  \n7     VAR_x4      S  x4  x4  0.006968770 0.0018057182  \n8  const__x2      M   1  x2  0.629669122 0.0201836183  \n9  const__x3      M   1  x3  0.641787994 0.0224712984  \n10 const__x4      M   1  x4 -0.081925673 0.0570787646  \n11  const__F      M   1   F  0.278899274 0.1417368576  \n\nModel Statistics: \n               |  Parameters  |  Degrees of Freedom  |  Fit (-2lnL units)\n       Model:             11                    189             -387.4425\n   Saturated:             14                    186                    NA\nIndependence:              8                    192                    NA\nNumber of observations/statistics: 50/200\n\nInformation Criteria: \n      |  df Penalty  |  Parameters Penalty  |  Sample-Size Adjusted\nAIC:      -765.4425              -365.4425                -358.4951\nBIC:     -1126.8149              -344.4103                -378.9374\nTo get additional fit indices, see help(mxRefModels)\ntimestamp: 2022-09-24 17:06:28 \nWall clock time: 0.1159739 secs \noptimizer:  SLSQP \nOpenMx version number: 2.20.6 \nNeed help?  See help(mxSummary) \n\n> \n> subset <- data[1:50, ]\n> \n> \n> ctr <- semtree.control(verbose=TRUE)\n> ctr$exclude.heywood <- FALSE\n> # naive tree should find both effects, age & ses, with age having the stronger effect \n> tree <- semtree(model = result, data=fulldata, control=ctr)\nDetected OpenMx model.\nOpenMx model estimation selected!\n❯ Growing level 0 n = 800\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n✔ Best split is  age with statistic = 7071.74\n❯ Growing level 1 n = 400\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n✔ Best split is  ses with statistic = 3345.91\n❯ Growing level 2 n = 200\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n❯ Best Likelihood Ratio was NULL. Stop splitting\n❯ Growing level 2 n = 200\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n❯ Best Likelihood Ratio was NULL. Stop splitting\n❯ Growing level 1 n = 400\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n✔ Best split is  ses with statistic = 969.14\n❯ Growing level 2 n = 200\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n❯ Best Likelihood Ratio was NULL. Stop splitting\n❯ Growing level 2 n = 200\n❯ Testing Predictor: age\n❯ Testing Predictor: ses\n❯ Best Likelihood Ratio was NULL. Stop splitting\n✔ Tree construction finished [took less than a second].\n> #plot(tree)\n> \n> # invariance tree should exclude splits wrt age and only splir wrt to ses\n> ctr$report.level <- 99\n> ctr$alpha.invariance <- 0.01\n> \n> cnst <- semtree.constraints(local.invariance = c(\"l2\",\"l3\",\"l4\"))\n> #cnst <- semtree.constraints(local.invariance=)\n> tree2 <- semtree(model = result, data=fulldata, control=ctr, constraints = cnst )\nDetected OpenMx model.\nOpenMx model estimation selected!\n❯ Growing level 0 n = 800\nGrowing tree level 0\n  |--Estimating baseline likelihood:  2843.02725567512\n❯ Testing Predictor: age\n  |--Estimating baseline likelihood:  2843.02725567512\n❯ Testing Predictor: ses\n❯ Filtering possible splits by invariance\nLL.within: 7071.73687619766,6670.01382647738 \nLL.max:  NA \nwithin.split:  1,1 \nsplit max NA \n❯ Best Likelihood Ratio was NULL. Stop splitting\n✔ Tree construction finished [took less than a second].\nWarning messages:\n1: In model 'sharedModel' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) \n2: In model 'sharedModel' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) \n> \n> #plot(tree2)\n> \n> proc.time()\n   user  system elapsed \n  2.526   0.091   2.626 \n"],"lavaan":["> # DEMO FOR SEMTREE\n> \n> \n> require(\"semtree\")\nLoading required package: semtree\nLoading required package: OpenMx\nOpenMx may run faster if it is compiled to take advantage of multiple cores.\n> require(\"lavaan\")\nLoading required package: lavaan\nThis is lavaan 0.6-12\nlavaan is FREE software! Please report any bugs.\n> \n> # ORGANIZE DATA BY TYPE FOR COVARIATES.\n> # SOME COVARIATES ARE ORGANIZED IN THE DATA. MODEL VARIABLES AND \n> # COVARIATES DO NOT NEED TO BE ORDERED IN THE DATASET. ONLY VARIABLE\n> # TYPE NEEDS TO BE DEFINED FOR THE COVARIATES (FACTOR/ORDERED/NUMERIC)\n> # BE AWARE OF THE EXPONENTIAL GROWTH OF MODEL COMPARISON WITH INCREASES\n> # IN NUMBER OF FACTORS PER A COVARIATE.\n> \n> data(lgcm)\n> \n> lgcm$agegroup <- as.ordered(lgcm$agegroup)\n> lgcm$training <- as.factor(lgcm$training)\n> lgcm$noise <- as.numeric(lgcm$noise)\n> \n> # LOAD IN LAVAAN MODEL.\n> # A SIMPLE LINEAR GROWTH MODEL WITH 5 TIME POINTS FROM SIMULATED DATA\n> \n> lgcModelstr <- '\n+ g0 =~ 1*o1 + 1*o2 + 1*o3 + 1*o4 + 1*o5;\n+ g1 =~ 0*o1 + 1*o2 + 2*o3 + 3*o4 + 4*o5;\n+ g0 ~~ g0; g0 ~ mui*1;\n+ g1 ~~ g1; g1 ~ sli*1;\n+ g0 ~~ g1;\n+ o1 ~~ o1; o1 ~ 0*1;\n+ o2 ~~ o2; o2 ~ 0*1;\n+ o3 ~~ o3; o3 ~ 0*1;\n+ o4 ~~ o4; o4 ~ 0*1;\n+ o5 ~~ o5; o5 ~ 0*1;\n+ '\n> lgcModel <- lavaan(lgcModelstr, lgcm, do.fit=TRUE)\n> \n> # TREE CONTROL OPTIONS.\n> # TO OBTAIN BASIC/DEFAULT SMETREE OPTIONS, SIMPLY TPYE THE FOLLOWING:\n> \n> controlOptions <- semtree.control()\n> \n> # THE CONTENTS OF THE DEFAULT CONTROLS CAN THEN BE VIEWED.\n> \n> controlOptions\n SEM-Tree control:\n ▔▔▔▔▔▔▔▔▔▔ \n● Splitting Method: naive\n● Alpha Level: 0.05\n● Bonferroni Correction:FALSE\n● Minimum Number of Cases: 20\n● Maximum Tree Depth: NA\n● Number of CV Folds: 5\n● Exclude Heywood Cases: TRUE\n● Test Invariance Alpha Level: NA\n● Use all Cases: FALSE\n● Verbosity: FALSE\n● Progress Bar: TRUE\n● Seed: NA\n> \n> # AND MODEL OPTIONS CAN BE CHANGED BY REDEFINING ELEMENTS OF THE \n> # CONTROL OBJECT.\n> \n> controlOptions$alpha <- 0.01\n> \n> # RUN TREE.\n> \n> tree <- semtree(model=lgcModel, data=lgcm, control = controlOptions)\n✖ Variable noise is numeric but has only few unique values. Consider recoding as ordered factor.\n✔ Tree construction finished [took 1s].\n> \n> # SEE PLOT.\n> # THE PLOT FUNCTION WILL SHOW ALL FREE PARAMETERS AT EACH TERMINAL NODE.\n> # THIS CAN CREATE UNREADABLE FIGURES FOR MODELS WITH MANY FREE PARAMETERS.\n> \n> plot(tree)\n> \n> # SEE SUMMARY.\n> # OVERALL MODEL FACTS ARE GIVEN WITH THE SUMMARY FUNCTION.\n> \n> summary(tree)\nSEMtree Summary\nTemplate model:  \nTotal Sample Size:  400 \nNumber of nodes:  5 \nNumber of leaf nodes:  3 \nFree Parameters:  10  ( g0~~g0 mui g1~~g1 sli g0~~g1 o1~~o1 o2~~o2 o3~~o3 o4~~o4 o5~~o5 )\n> \n> # summary(treeConstrained)\n> \n> # USING THE PRINT FUNCTION WILL PROVIDE AN OVERVIEW OF THE MODEL\n> # SPLITS, LR TESTS WITH DF, AND SUBGROUP SIZES (N).\n> \n> print(tree)\nSEMtree with numbered nodes\n |-[1] agegroup > 0 [N=400 LR=1258.08, df=10]\n |   |-[2] TERMINAL [N=200]\n |   |-[3] training  in [ 0  ] [N=200 LR=40.85, df=10]\n |   |   |-[4] TERMINAL [N=100]\n |   |   |-[5] TERMINAL [N=100]\n> \n> # GET NODE PARAMETERS (leafs only as default).\n> # THE DEFAULT IS ONLY DISPLAYING LEAF NODE PARAMETER ESTIMATES.\n> \n> parameters(tree)\n            2      4      5\ng0~~g0  0.082  0.104  0.085\nmui     5.017  1.941  2.005\ng1~~g1  0.499  0.674  1.629\nsli    -0.142 -0.494 -1.084\ng0~~g1 -0.011  0.028 -0.044\no1~~o1  0.068  0.048  0.042\no2~~o2  0.049  0.069  0.049\no3~~o3  0.043  0.053  0.053\no4~~o4  0.055  0.039  0.063\no5~~o5  0.037  0.048  0.011\n> \n> # TO GET ALL PARAMETER ESTIMATES FOR EVERY NODE CHANGE THE DEFAULT TO.\n> \n> parameters(tree, leafs.only=FALSE)\n            1      2      3      4      5\ng0~~g0  2.410  0.082  0.095  0.104  0.085\nmui     3.496  5.017  1.973  1.941  2.005\ng1~~g1  0.973  0.499  1.239  0.674  1.629\nsli    -0.466 -0.142 -0.789 -0.494 -1.084\ng0~~g1  0.477 -0.011 -0.017  0.028 -0.044\no1~~o1  0.052  0.068  0.045  0.048  0.042\no2~~o2  0.058  0.049  0.059  0.069  0.049\no3~~o3  0.047  0.043  0.053  0.053  0.053\no4~~o4  0.052  0.055  0.051  0.039  0.063\no5~~o5  0.036  0.037  0.030  0.048  0.011\n> \n> # SUBTREE FUNCTION.\n> # IF ONLY A SUBSET OF THE TREE IS TO BE EXAMINED, THEN THE TREE CAN \n> # BE PARED. THIS IS DONE WITH A SUBSET FUNCTION WHICH STORES THE TREE\n> # FROM A GIVEN NODE ON. IF THE TREE FROM NODE 2 ON IS DESIRED, THEN:\n> \n> treeSub <- subtree(tree, startNode=3)\n> \n> \n> # ALTERNATIVE SPLIT RULE\n> \n> controlOptions$method <- \"fair\"\n> tree2 <- semtree(model=lgcModel, data=lgcm, control = controlOptions)\n✖ Variable noise is numeric but has only few unique values. Consider recoding as ordered factor.\n✔ Tree construction finished [took 2s].\n> \n> # disabled for time restrictions on CRAN\n> #controlOptions$method <- \"cv\"\n> #tree3 <- semtree(model=lgcModel, data=lgcm, control = controlOptions)\n> \n> proc.time()\n   user  system elapsed \n  3.271   0.398   3.778 \n"],"tree":["> set.seed(789)\n> require(\"semtree\")\nLoading required package: semtree\nLoading required package: OpenMx\nOpenMx may run faster if it is compiled to take advantage of multiple cores.\n> data(lgcm)\n> \n> lgcm$agegroup <- ordered(lgcm$agegroup, labels=c(\"young\",\"old\") )\n> lgcm$training <- as.factor(lgcm$training)\n> lgcm$noise <- as.factor(lgcm$noise)\n> \n> # LOAD IN OPENMX MODEL.\n> # A SIMPLE LINEAR GROWTH MODEL WITH 5 TIME POINTS FROM SIMULATED DATA\n> \n> manifests <- names(lgcm)[1:5]\n> lgcModel <- mxModel(\"Linear Growth Curve Model Path Specification\",\n+                             type=\"RAM\",\n+                             manifestVars=manifests,\n+                             latentVars=c(\"intercept\",\"slope\"),\n+                             # residual variances\n+                             mxPath(\n+                               from=manifests,\n+                               arrows=2,\n+                               free=TRUE,\n+                               values = c(1, 1, 1, 1, 1),\n+                               labels=c(\"residual1\",\"residual2\",\"residual3\",\"residual4\",\"residual5\")\n+                             ),\n+                             # latent variances and covariance\n+                             mxPath(\n+                               from=c(\"intercept\",\"slope\"),\n+                               connect=\"unique.pairs\",\n+                               arrows=2,\n+                               free=TRUE,\n+                               values=c(1, 1, 1),\n+                               labels=c(\"vari\", \"cov\", \"vars\")\n+                             ),\n+                             # intercept loadings\n+                             mxPath(\n+                               from=\"intercept\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(1, 1, 1, 1, 1)\n+                             ),\n+                             # slope loadings\n+                             mxPath(\n+                               from=\"slope\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(0, 1, 2, 3, 4)\n+                             ),\n+                             # manifest means\n+                             mxPath(\n+                               from=\"one\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(0, 0, 0, 0, 0)\n+                             ),\n+                             # latent means\n+                             mxPath(\n+                               from=\"one\",\n+                               to=c(\"intercept\", \"slope\"),\n+                               arrows=1,\n+                               free=TRUE,\n+                               values=c(1, 1),\n+                               labels=c(\"meani\", \"means\")\n+                             ),\n+                     mxData(lgcm,type=\"raw\")\n+                     )\n> \n> \n> # TREE CONTROL OPTIONS.\n> # TO OBTAIN BASIC/DEFAULT SMETREE OPTIONS, SIMPLY TPYE THE FOLLOWING:\n> \n> controlOptions <- semtree.control(method = \"naive\")\n> controlOptions$alpha <- 0.05\n> \n> # RUN TREE.\n> \n> tree <- semtree(model=lgcModel, data=lgcm, control = controlOptions)\n✔ Tree construction finished [took less than a second].\n> \n> # RERUN TREE WITH MODEL CONSTRAINTS.\n> # MODEL CONSTRAINTS CAN BE ADDED BY IDENTIFYING THE PARAMETERS TO BE\n> # CONSTRAINED IN EVERY NODE. ONLY UNCONSTRAINED PARAMETERS ARE THEN\n> # TESTED AT EACH NODE FOR GROUP DIFFERENCES. IN THIS EXAMPLE THE MODEL \n> # RESIDUALS ARE CONSTRAINED OVER THE NODES.\n> \n> constraints <- semtree.constraints(global.invariance = names(omxGetParameters(lgcModel))[1:5])\n> \n> treeConstrained <- semtree(model=lgcModel, data=lgcm, control = controlOptions,\n+                            constraints=constraints)\n❯ Global Constraints:\nresidual1 residual2 residual3 residual4 residual5\n❯ Freely Estimated Parameters:\nvari cov vars meani means\n✔ Tree construction finished [took less than a second].\n> \n> # SEE PLOT.\n> # THE PLOT FUNCTION WILL SHOW ALL FREE PARAMETERS AT EACH TERMINAL NODE.\n> # THIS CAN CREATE UNREADABLE FIGURES FOR MODELS WITH MANY FREE PARAMETERS.\n> \n> plot(tree)\n> \n> summary(tree)\nSEMtree Summary\nTemplate model:  \nTotal Sample Size:  400 \nNumber of nodes:  5 \nNumber of leaf nodes:  3 \nFree Parameters:  10  ( residual1 residual2 residual3 residual4 residual5 vari cov vars meani means )\n> \n> summary(treeConstrained)\nSEMtree Summary\nTemplate model:  \nTotal Sample Size:  400 \nNumber of nodes:  5 \nNumber of leaf nodes:  3 \nFree Parameters:  5  ( vari cov vars meani means )\n> \n> print(tree)\nSEMtree with numbered nodes\n |-[1] agegroup > young [N=400 LR=1258.08, df=10]\n |   |-[2] TERMINAL [N=200]\n |   |-[3] training  in [ 0  ] [N=200 LR=40.85, df=10]\n |   |   |-[4] TERMINAL [N=100]\n |   |   |-[5] TERMINAL [N=100]\n> \n> parameters(tree)\n               2      4      5\nresidual1  0.068  0.048  0.042\nresidual2  0.049  0.069  0.049\nresidual3  0.043  0.053  0.053\nresidual4  0.055  0.039  0.063\nresidual5  0.037  0.048  0.011\nvari       0.082  0.104  0.085\ncov       -0.011  0.028 -0.044\nvars       0.499  0.674  1.629\nmeani      5.017  1.941  2.005\nmeans     -0.142 -0.494 -1.084\n> \n> parameters(tree, leafs.only=FALSE)\n               1      2      3      4      5\nresidual1  0.052  0.068  0.045  0.048  0.042\nresidual2  0.058  0.049  0.059  0.069  0.049\nresidual3  0.047  0.043  0.053  0.053  0.053\nresidual4  0.052  0.055  0.051  0.039  0.063\nresidual5  0.036  0.037  0.030  0.048  0.011\nvari       2.410  0.082  0.095  0.104  0.085\ncov        0.477 -0.011 -0.017  0.028 -0.044\nvars       0.973  0.499  1.239  0.674  1.629\nmeani      3.496  5.017  1.973  1.941  2.005\nmeans     -0.466 -0.142 -0.789 -0.494 -1.084\n> \n> treeSub <- subtree(tree, startNode=3)\n> \n> if (!is.null(treeSub))\n+ \tplot(treeSub)\n> \n> toTable(tree)\n     agegroup  training\n[1,] \"UNKNOWN\" \"\"      \n[2,] \"UNKNOWN\" \"not 0\" \n[3,] \"UNKNOWN\" \"0\"     \n> \n> \n> controlOptions <- semtree.control(method = \"fair\")\n> \n> tree2 <- semtree(lgcModel, lgcm, control=controlOptions)\n✔ Tree construction finished [took less than a second].\n> \n> \n> controlOptions <- semtree.control(method = \"score\")\n> tree3 <- semtree(lgcModel, lgcm, control=controlOptions)\n❯ Model was not run. Estimating parameters now.\nRunning Linear Growth Curve Model Path Specification with 10 parameters\n\nBeginning initial fit attempt\nRunning Linear Growth Curve Model Path Specification with 10 parameters\n\n Lowest minimum so far:  3946.79931515404\n\nSolution found\n\n\r\n Solution found!  Final fit=3946.7993 (started at 12364.579)  (1 attempt(s): 1 valid, 0 errors)\n\n Start values from best fit:\n0.0517425500974165,0.057996464842973,0.0467583755756157,0.0520836958577161,0.0361130739855864,2.41004053260765,0.477157340565657,0.973042383133384,3.49639424449095,-0.465977315382569\n✔ Tree construction finished [took less than a second].\n> \n> proc.time()\n   user  system elapsed \n  4.182   0.105   4.330 \n"],"vim":["> set.seed(789)\n> require(\"semtree\")\nLoading required package: semtree\nLoading required package: OpenMx\nOpenMx may run faster if it is compiled to take advantage of multiple cores.\n> data(lgcm)\n> \n> lgcm$agegroup <- ordered(lgcm$agegroup)\n> lgcm$training <- factor(lgcm$training)\n> lgcm$noise <- as.numeric(lgcm$noise)\n> \n> # LOAD IN OPENMX MODEL.\n> # A SIMPLE LINEAR GROWTH MODEL WITH 5 TIME POINTS FROM SIMULATED DATA\n> \n> manifests <- names(lgcm)[1:5]\n> lgcModel <- mxModel(\"Linear Growth Curve Model Path Specification\",\n+                             type=\"RAM\",\n+                             manifestVars=manifests,\n+                             latentVars=c(\"intercept\",\"slope\"),\n+                             # residual variances\n+                             mxPath(\n+                               from=manifests,\n+                               arrows=2,\n+                               free=TRUE,\n+                               values = c(1, 1, 1, 1, 1),\n+                               labels=c(\"residual1\",\"residual2\",\"residual3\",\"residual4\",\"residual5\")\n+                             ),\n+                             # latent variances and covariance\n+                             mxPath(\n+                               from=c(\"intercept\",\"slope\"),\n+                               connect=\"unique.pairs\",\n+                               arrows=2,\n+                               free=TRUE,\n+                               values=c(1, 1, 1),\n+                               labels=c(\"vari\", \"cov\", \"vars\")\n+                             ),\n+                             # intercept loadings\n+                             mxPath(\n+                               from=\"intercept\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(1, 1, 1, 1, 1)\n+                             ),\n+                             # slope loadings\n+                             mxPath(\n+                               from=\"slope\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(0, 1, 2, 3, 4)\n+                             ),\n+                             # manifest means\n+                             mxPath(\n+                               from=\"one\",\n+                               to=manifests,\n+                               arrows=1,\n+                               free=FALSE,\n+                               values=c(0, 0, 0, 0, 0)\n+                             ),\n+                             # latent means\n+                             mxPath(\n+                               from=\"one\",\n+                               to=c(\"intercept\", \"slope\"),\n+                               arrows=1,\n+                               free=TRUE,\n+                               values=c(1, 1),\n+                               labels=c(\"meani\", \"means\")\n+                             ),\n+                     mxData(lgcm,type=\"raw\")\n+                     )\n> \n> \n> fr <- semforest(lgcModel, lgcm,control = semforest.control(num.trees = 3))\n❯ Model was not run. Estimating parameters now before running the forest.\nRunning Linear Growth Curve Model Path Specification with 10 parameters\n\nBeginning initial fit attempt\nRunning Linear Growth Curve Model Path Specification with 10 parameters\n\n Lowest minimum so far:  3946.79931515404\n\nSolution found\n\n\r\n Solution found!  Final fit=3946.7993 (started at 12364.579)  (1 attempt(s): 1 valid, 0 errors)\n\n Start values from best fit:\n0.0517425500974165,0.057996464842973,0.0467583755756157,0.0520836958577161,0.0361130739855864,2.41004053260765,0.477157340565657,0.973042383133384,3.49639424449095,-0.465977315382569\n✖ Variable noise is numeric but has only few unique values. Consider recoding as ordered factor.\n✔ Tree construction finished [took 2s].\n✖ Variable noise is numeric but has only few unique values. Consider recoding as ordered factor.\n✔ Tree construction finished [took 1s].\n✖ Variable noise is numeric but has only few unique values. Consider recoding as ordered factor.\n✔ Tree construction finished [took 2s].\n✔ Forest completed [took 5s]\n> \n>   \n> vimp <- varimp(fr)\n> \n> print(vimp)\nVariable Importance\n   agegroup    training       noise \n6750.526689   34.849484   -4.840505 \n> print(vimp, na.omit=TRUE)\nVariable Importance\n   agegroup    training       noise \n6750.526689   34.849484   -4.840505 \n> \n> \n> proc.time()\n   user  system elapsed \n  7.438   0.102   7.566 \n"]},"install_out":["* installing *source* package ‘semtree’ ...\n** package ‘semtree’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** data\n** demo\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (semtree)\n"],"session_info":{"platform":{"version":["R version 4.2.1 (2022-06-23)"],"os":["macOS Monterey 12.6"],"system":["aarch64, darwin20"],"ui":["X11"],"language":["(EN)"],"collate":["C"],"ctype":["en_US.UTF-8"],"tz":["America/Chicago"],"date":["2022-09-24"],"pandoc":["2.19 @ /usr/local/bin/pandoc"]},"packages":[{"package":"semtree","attached":false,"is_base":false,"_row":"semtree"}]}}}


package: umx
version: 4.15.1
maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
status: NOTE
which: old
duration: 59.279788017273
starttime: 2022-09-24 22:05:57
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[1]}}
result:
{"class":["rcmdcheck"],"object":{"stdout":["* using log directory ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/umx/old/umx.Rcheck’\n* using R version 4.2.1 (2022-06-23)\n* using platform: aarch64-apple-darwin20 (64-bit)\n* using session charset: UTF-8\n* using options ‘--no-manual --no-build-vignettes’\n* checking for file ‘umx/DESCRIPTION’ ... OK\n* this is package ‘umx’ version ‘4.15.1’\n* package encoding: UTF-8\n* checking package namespace information ... OK\n* checking package dependencies ... OK\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘umx’ can be installed ... OK\n* checking installed package size ... NOTE\n  installed size is  5.8Mb\n  sub-directories of 1Mb or more:\n    help   4.3Mb\n* checking package directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking LazyData ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking examples ... OK\n* DONE\n\nStatus: 1 NOTE\nSee\n  ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/umx/old/umx.Rcheck/00check.log’\nfor details.\n\n\n\n"],"stderr":[""],"status":[0],"duration":[59.2802],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":["checking installed package size ... NOTE\n  installed size is  5.8Mb\n  sub-directories of 1Mb or more:\n    help   4.3Mb"],"description":["Package: umx\nVersion: 4.15.1\nDate: 2022-09-15\nTitle: Structural Equation Modeling and Twin Modeling in R\nAuthors@R: c(\n\tperson(c(\"Timothy\", \"C.\"), \"Bates\"   , role = c(\"aut\", \"cre\"), email = \"timothy.c.bates@gmail.com\", comment = c(ORCID = \"0000-0002-1153-9007\")),\n\tperson(\"Nathan\"          , \"Gillespie\", role = c(\"wit\"), email = \"nathan.gillespie@vcuhealth.org\"),\n\tperson(\"Hermine\"         , \"Maes\"    , role = c(\"ctb\"), email = \"hmeaes@vcu.edu\"),\n\tperson(c(\"Michael\", \"C.\"), \"Neale\"   , role = c(\"ctb\"), email = \"neale@vcu.edu\"),\n\tperson(c(\"Joshua\", \"N.\") , \"Pritikin\", role = c(\"ctb\"), email = \"jpritikin@pobox.com\"),\n\tperson(\"Luis\"            , \"De Araujo\", role = c(\"ctb\"), email = \"ldearaujo@unimelb.edu.au\"),\n\tperson(\"Brenton\"         , \"Wiernik\" , role = c(\"ctb\"), email = \"wiernik@umn.edu\"),\n\tperson(\"Michael\"         , \"Zakharin\", role = c(\"wit\"), email = \"s1775682@sms.ed.ac.uk\")\n\t)\nMaintainer: Timothy C. Bates <timothy.c.bates@gmail.com>\nLicense: GPL-3\nLanguage: en-US\nEncoding: UTF-8\nURL: https://github.com/tbates/umx#readme\nDescription: Quickly create, run, and report structural equation models, and twin models.\n    See '?umx' for help, and umx_open_CRAN_page(\"umx\") for NEWS.\n    Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R.\n    Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.\nDepends: R (>= 4.1.0), OpenMx (>= 2.19.0)\nImports: ggplot2, cowplot, DiagrammeR, DiagrammeRsvg, rsvg, lavaan,\n        MASS, Matrix, methods, MuMIn, mvtnorm, nlme, polycor, R2HTML,\n        RCurl, scales, utils, xtable, kableExtra, knitr\nSuggests: cocor, devtools, gdata, gert, hrbrthemes, spelling, testthat,\n        rmarkdown, paran, psych, psychTools, rhub, pwr\nBugReports: https://github.com/tbates/umx/issues\nLazyData: true\nRoxygenNote: 7.2.1\nNeedsCompilation: no\nPackaged: 2022-09-20 19:55:57 UTC; tim\nAuthor: Timothy C. Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>),\n  Nathan Gillespie [wit],\n  Hermine Maes [ctb],\n  Michael C. Neale [ctb],\n  Joshua N. Pritikin [ctb],\n  Luis De Araujo [ctb],\n  Brenton Wiernik [ctb],\n  Michael Zakharin [wit]\nRepository: CRAN\nDate/Publication: 2022-09-20 20:20:02 UTC"],"package":["umx"],"version":["4.15.1"],"cran":[true],"bioc":[false],"checkdir":["/Users/WR/Dropbox/psychTools/revdep/checks.noindex/umx/old/umx.Rcheck"],"test_fail":{},"test_output":{},"install_out":["* installing *source* package ‘umx’ ...\n** package ‘umx’ successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** data\n*** moving datasets to lazyload DB\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n*** copying figures\n** building package indices\n** testing if installed package can be loaded from temporary location\n** testing if installed package can be loaded from final location\n** testing if installed package keeps a record of temporary installation path\n* DONE (umx)\n"],"session_info":{"platform":{"version":["R version 4.2.1 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package: umx
version: 4.15.1
maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
status: NOTE
which: new
duration: 58.7850940227509
starttime: 2022-09-24 22:05:57
summary: {"class":["list"],"object":{"errors":[0],"warnings":[0],"notes":[1]}}
result:
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NOTE\n  installed size is  5.8Mb\n  sub-directories of 1Mb or more:\n    help   4.3Mb\n* checking package directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies ... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies ... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... OK\n* checking for code/documentation mismatches ... OK\n* checking Rd \\usage sections ... OK\n* checking Rd contents ... OK\n* checking for unstated dependencies in examples ... OK\n* checking contents of ‘data’ directory ... OK\n* checking data for non-ASCII characters ... OK\n* checking LazyData ... OK\n* checking data for ASCII and uncompressed saves ... OK\n* checking examples ... OK\n* DONE\n\nStatus: 1 NOTE\nSee\n  ‘/Users/WR/Dropbox/psychTools/revdep/checks.noindex/umx/new/umx.Rcheck/00check.log’\nfor details.\n\n\n\n"],"stderr":[""],"status":[0],"duration":[60.635],"timeout":[false],"rversion":["4.2.1"],"platform":["aarch64-apple-darwin20"],"errors":[],"warnings":[],"notes":["checking installed package size ... NOTE\n  installed size is  5.8Mb\n  sub-directories of 1Mb or more:\n    help   4.3Mb"],"description":["Package: umx\nVersion: 4.15.1\nDate: 2022-09-15\nTitle: Structural Equation Modeling and Twin Modeling in R\nAuthors@R: c(\n\tperson(c(\"Timothy\", \"C.\"), \"Bates\"   , role = c(\"aut\", \"cre\"), email = \"timothy.c.bates@gmail.com\", comment = c(ORCID = \"0000-0002-1153-9007\")),\n\tperson(\"Nathan\"          , \"Gillespie\", role = c(\"wit\"), email = \"nathan.gillespie@vcuhealth.org\"),\n\tperson(\"Hermine\"         , \"Maes\"    , role = c(\"ctb\"), email = \"hmeaes@vcu.edu\"),\n\tperson(c(\"Michael\", \"C.\"), \"Neale\"   , role = c(\"ctb\"), email = \"neale@vcu.edu\"),\n\tperson(c(\"Joshua\", \"N.\") , \"Pritikin\", role = c(\"ctb\"), email = \"jpritikin@pobox.com\"),\n\tperson(\"Luis\"            , \"De Araujo\", role = c(\"ctb\"), email = \"ldearaujo@unimelb.edu.au\"),\n\tperson(\"Brenton\"         , \"Wiernik\" , role = c(\"ctb\"), email = \"wiernik@umn.edu\"),\n\tperson(\"Michael\"         , \"Zakharin\", role = c(\"wit\"), email = \"s1775682@sms.ed.ac.uk\")\n\t)\nMaintainer: Timothy C. Bates <timothy.c.bates@gmail.com>\nLicense: GPL-3\nLanguage: en-US\nEncoding: UTF-8\nURL: https://github.com/tbates/umx#readme\nDescription: Quickly create, run, and report structural equation models, and twin models.\n    See '?umx' for help, and umx_open_CRAN_page(\"umx\") for NEWS.\n    Timothy C. Bates, Michael C. Neale, Hermine H. 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