From f4c6ff3635ffedc703eee1d3d57e0a7899d4faa0 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 21 Aug 2025 11:39:26 +0200 Subject: [PATCH 1/7] feat: Include the NHANES dataset for exploration and experimentation --- DESCRIPTION | 4 +++- R/helpers.R | 3 ++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7276ef66..c43b72ae 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -64,7 +64,9 @@ Imports: RcppArmadillo, ggcorrplot, shinyjs, - emmeans + emmeans, + readxl, + NHANES Suggests: styler, devtools, diff --git a/R/helpers.R b/R/helpers.R index cb2a1aa4..fe61499d 100644 --- a/R/helpers.R +++ b/R/helpers.R @@ -153,7 +153,8 @@ dummy_Imports <- function() { cardx::all_of(), parameters::ci(), DT::addRow(), - bslib::accordion() + bslib::accordion(), + NHANES::NHANES() ) # https://github.com/hadley/r-pkgs/issues/828 } From 731a09e390997b179ea9407eeafa1134e17ecdf2 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 21 Aug 2025 11:39:39 +0200 Subject: [PATCH 2/7] chore: Updating renv --- renv.lock | 530 ++++++------------------------------------------ renv/activate.R | 2 +- 2 files changed, 64 insertions(+), 468 deletions(-) diff --git a/renv.lock b/renv.lock index 57077d00..a72c6c40 100644 --- a/renv.lock +++ b/renv.lock @@ -4,16 +4,16 @@ "Repositories": [ { "Name": "CRAN", - "URL": "https://cloud.r-project.org" + "URL": "https://mirrors.dotsrc.org/cran" } ] }, "Packages": { "DEoptimR": { "Package": "DEoptimR", - "Version": "1.1-3-1", + "Version": "1.1-4", "Source": "Repository", - "Date": "2024-11-23", + "Date": "2025-07-27", "Title": "Differential Evolution Optimization in Pure R", "Authors@R": "c( person(c(\"Eduardo\", \"L. T.\"), \"Conceicao\", role = c(\"aut\", \"cre\"), email = \"mail@eduardoconceicao.org\"), person(\"Martin\", \"Maechler\", role = \"ctb\", email = \"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) )", "URL": "svn://svn.r-forge.r-project.org/svnroot/robustbase/pkg/DEoptimR", @@ -25,12 +25,12 @@ "robustbase" ], "License": "GPL (>= 2)", - "Author": "Eduardo L. T. Conceicao [aut, cre], Martin Maechler [ctb] ()", + "Author": "Eduardo L. T. Conceicao [aut, cre], Martin Maechler [ctb] (ORCID: )", "Maintainer": "Eduardo L. T. Conceicao ", "Repository": "CRAN", "Repository/R-Forge/Project": "robustbase", - "Repository/R-Forge/Revision": "1008", - "Repository/R-Forge/DateTimeStamp": "2024-11-23 19:13:45", + "Repository/R-Forge/Revision": "1009", + "Repository/R-Forge/DateTimeStamp": "2025-07-27 18:16:52", "NeedsCompilation": "no" }, "DHARMa": { @@ -241,7 +241,7 @@ }, "IDEAFilter": { "Package": "IDEAFilter", - "Version": "0.2.0", + "Version": "0.2.1", "Source": "Repository", "Type": "Package", "Title": "Agnostic, Idiomatic Data Filter Module for Shiny", @@ -251,7 +251,7 @@ "URL": "https://biogen-inc.github.io/IDEAFilter/, https://github.com/Biogen-Inc/IDEAFilter", "BugReports": "https://github.com/Biogen-Inc/IDEAFilter/issues", "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "Imports": [ "crayon", "ggplot2", @@ -276,7 +276,7 @@ "R (>= 2.10)" ], "NeedsCompilation": "no", - "Author": "Aaron Clark [aut, cre] (), Jeff Thompson [aut], Doug Kelkhoff [ctb, cph] (Author of shinyDataFilter), Maya Gans [ctb], SortableJS contributors [ctb] (SortableJS library), Biogen [cph]", + "Author": "Aaron Clark [aut, cre] (ORCID: ), Jeff Thompson [aut], Doug Kelkhoff [ctb, cph] (Author of shinyDataFilter), Maya Gans [ctb], SortableJS contributors [ctb] (SortableJS library), Biogen [cph]", "Maintainer": "Aaron Clark ", "Repository": "CRAN" }, @@ -575,7 +575,7 @@ }, "REDCapR": { "Package": "REDCapR", - "Version": "1.4.0", + "Version": "1.5.0", "Source": "Repository", "Title": "Interaction Between R and REDCap", "Description": "Encapsulates functions to streamline calls from R to the REDCap API. REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.", @@ -583,7 +583,7 @@ "URL": "https://ouhscbbmc.github.io/REDCapR/, https://github.com/OuhscBbmc/REDCapR, https://www.ouhsc.edu/bbmc/, https://projectredcap.org", "BugReports": "https://github.com/OuhscBbmc/REDCapR/issues", "Depends": [ - "R(>= 3.5.0)" + "R (>= 4.1.0)" ], "Imports": [ "checkmate (>= 2.0)", @@ -618,7 +618,7 @@ "Config/testthat/edition": "3", "Language": "en-US", "NeedsCompilation": "no", - "Author": "Will Beasley [aut, cre] (), David Bard [ctb] (), Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb] (), Benjamin Nutter [ctb], Andrew Peters [ctb] (), Hao Zhu [ctb] (), Janosch Linkersdörfer [ctb] (), Jonathan Mang [ctb] (), Felix Torres [ctb], Philip Chase [ctb] (), Victor Castro [ctb] (), Greg Botwin [ctb], Stephan Kadauke [ctb] (), Ezra Porter [ctb] (), Matthew Schuelke [ctb] ()", + "Author": "Will Beasley [aut, cre] (ORCID: ), David Bard [ctb] (ORCID: ), Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb] (ORCID: ), Benjamin Nutter [ctb], Andrew Peters [ctb] (ORCID: ), Hao Zhu [ctb] (ORCID: ), Janosch Linkersdörfer [ctb] (ORCID: ), Jonathan Mang [ctb] (ORCID: ), Felix Torres [ctb], Philip Chase [ctb] (ORCID: ), Victor Castro [ctb] (ORCID: ), Greg Botwin [ctb], Stephan Kadauke [ctb] (ORCID: ), Ezra Porter [ctb] (ORCID: ), Matthew Schuelke [ctb] (ORCID: )", "Maintainer": "Will Beasley ", "Repository": "CRAN" }, @@ -689,80 +689,9 @@ "Maintainer": "Dirk Eddelbuettel ", "Repository": "CRAN" }, - "RcppEigen": { - "Package": "RcppEigen", - "Version": "0.3.4.0.2", - "Source": "Repository", - "Type": "Package", - "Title": "'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library", - "Date": "2024-08-23", - "Authors@R": "c(person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Yixuan\", \"Qiu\", role = \"aut\", comment = c(ORCID = \"0000-0003-0109-6692\")), person(\"Authors of\", \"Eigen\", role = \"cph\", comment = \"Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS\"))", - "Copyright": "See the file COPYRIGHTS for various Eigen copyright details", - "Description": "R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library. Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", - "License": "GPL (>= 2) | file LICENSE", - "LazyLoad": "yes", - "Depends": [ - "R (>= 3.6.0)" - ], - "LinkingTo": [ - "Rcpp" - ], - "Imports": [ - "Rcpp (>= 0.11.0)", - "stats", - "utils" - ], - "Suggests": [ - "Matrix", - "inline", - "tinytest", - "pkgKitten", - "microbenchmark" - ], - "URL": "https://github.com/RcppCore/RcppEigen, https://dirk.eddelbuettel.com/code/rcpp.eigen.html", - "BugReports": "https://github.com/RcppCore/RcppEigen/issues", - "NeedsCompilation": "yes", - "Author": "Doug Bates [aut] (), Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), Yixuan Qiu [aut] (), Authors of Eigen [cph] (Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS)", - "Maintainer": "Dirk Eddelbuettel ", - "Repository": "CRAN" - }, - "Rdpack": { - "Package": "Rdpack", - "Version": "2.6.4", - "Source": "Repository", - "Type": "Package", - "Title": "Update and Manipulate Rd Documentation Objects", - "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), email = \"georgi.boshnakov@manchester.ac.uk\", comment = c(ORCID = \"0000-0003-2839-346X\")), person(given = \"Duncan\", family = \"Murdoch\", role = \"ctb\", email = \"murdoch.duncan@gmail.com\") )", - "Description": "Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.", - "URL": "https://geobosh.github.io/Rdpack/ (doc), https://github.com/GeoBosh/Rdpack (devel)", - "BugReports": "https://github.com/GeoBosh/Rdpack/issues", - "Depends": [ - "R (>= 2.15.0)", - "methods" - ], - "Imports": [ - "tools", - "utils", - "rbibutils (>= 1.3)" - ], - "Suggests": [ - "grDevices", - "testthat", - "rstudioapi", - "rprojroot", - "gbRd" - ], - "License": "GPL (>= 2)", - "LazyLoad": "yes", - "RoxygenNote": "7.1.1", - "NeedsCompilation": "no", - "Author": "Georgi N. Boshnakov [aut, cre] (), Duncan Murdoch [ctb]", - "Maintainer": "Georgi N. Boshnakov ", - "Repository": "CRAN" - }, "V8": { "Package": "V8", - "Version": "6.0.4", + "Version": "6.0.5", "Source": "Repository", "Type": "Package", "Title": "Embedded JavaScript and WebAssembly Engine for R", @@ -1154,33 +1083,6 @@ "Maintainer": "Martin Maechler ", "Repository": "CRAN" }, - "boot": { - "Package": "boot", - "Version": "1.3-31", - "Source": "Repository", - "Priority": "recommended", - "Date": "2024-08-28", - "Authors@R": "c(person(\"Angelo\", \"Canty\", role = \"aut\", email = \"cantya@mcmaster.ca\", comment = \"author of original code for S\"), person(\"Brian\", \"Ripley\", role = c(\"aut\", \"trl\"), email = \"ripley@stats.ox.ac.uk\", comment = \"conversion to R, maintainer 1999--2022, author of parallel support\"), person(\"Alessandra R.\", \"Brazzale\", role = c(\"ctb\", \"cre\"), email = \"brazzale@stat.unipd.it\", comment = \"minor bug fixes\"))", - "Maintainer": "Alessandra R. Brazzale ", - "Note": "Maintainers are not available to give advice on using a package they did not author.", - "Description": "Functions and datasets for bootstrapping from the book \"Bootstrap Methods and Their Application\" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.", - "Title": "Bootstrap Functions (Originally by Angelo Canty for S)", - "Depends": [ - "R (>= 3.0.0)", - "graphics", - "stats" - ], - "Suggests": [ - "MASS", - "survival" - ], - "LazyData": "yes", - "ByteCompile": "yes", - "License": "Unlimited", - "NeedsCompilation": "no", - "Author": "Angelo Canty [aut] (author of original code for S), Brian Ripley [aut, trl] (conversion to R, maintainer 1999--2022, author of parallel support), Alessandra R. Brazzale [ctb, cre] (minor bug fixes)", - "Repository": "CRAN" - }, "brio": { "Package": "brio", "Version": "1.1.5", @@ -1209,17 +1111,17 @@ }, "broom": { "Package": "broom", - "Version": "1.0.8", + "Version": "1.0.9", "Source": "Repository", "Type": "Package", "Title": "Convert Statistical Objects into Tidy Tibbles", - "Authors@R": "c(person(given = \"David\", family = \"Robinson\", role = \"aut\", email = \"admiral.david@gmail.com\"), person(given = \"Alex\", family = \"Hayes\", role = \"aut\", email = \"alexpghayes@gmail.com\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(given = \"Simon\", family = \"Couch\", role = c(\"aut\", \"cre\"), email = \"simon.couch@posit.co\", comment = c(ORCID = \"0000-0001-5676-5107\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"ctb\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Derek\", family 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\"sergioller@gmail.com\"), person(given = \"Luke\", family = \"Sonnet\", role = \"ctb\", email = \"luke.sonnet@gmail.com\"), person(given = \"Jim\", family = \"Hester\", role = \"ctb\", email = \"jim.hester@posit.co\"), person(given = \"Ben\", family = \"Schneider\", role = \"ctb\", email = \"benjamin.julius.schneider@gmail.com\"), person(given = \"Bernie\", family = \"Gray\", role = \"ctb\", email = \"bfgray3@gmail.com\", comment = c(ORCID = \"0000-0001-9190-6032\")), person(given = \"Mara\", family = \"Averick\", role = \"ctb\", email = \"mara@posit.co\"), person(given = \"Aaron\", family = \"Jacobs\", role = \"ctb\", email = \"atheriel@gmail.com\"), person(given = \"Andreas\", family = \"Bender\", role = \"ctb\", email = \"bender.at.R@gmail.com\"), person(given = \"Sven\", family = \"Templer\", role = \"ctb\", email = \"sven.templer@gmail.com\"), person(given = \"Paul-Christian\", family = \"Buerkner\", role = \"ctb\", email = \"paul.buerkner@gmail.com\"), person(given = 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\"ctb\", email = \"Roger.Bivand@nhh.no\"), person(given = \"Riinu\", family = \"Ots\", role = \"ctb\", email = \"riinuots@gmail.com\"), person(given = \"Nicholas\", family = \"Williams\", role = \"ctb\", email = \"ntwilliams.personal@gmail.com\"), person(given = \"Nina\", family = \"Jakobsen\", role = \"ctb\"), person(given = \"Michael\", family = \"Weylandt\", role = \"ctb\", email = \"michael.weylandt@gmail.com\"), person(given = \"Lisa\", family = \"Lendway\", role = \"ctb\", email = \"llendway@macalester.edu\"), person(given = \"Karl\", family = \"Hailperin\", role = \"ctb\", email = \"khailper@gmail.com\"), person(given = \"Josue\", family = \"Rodriguez\", role = \"ctb\", email = \"jerrodriguez@ucdavis.edu\"), person(given = \"Jenny\", family = \"Bryan\", role = \"ctb\", email = \"jenny@posit.co\"), person(given = \"Chris\", family = \"Jarvis\", role = \"ctb\", email = \"Christopher1.jarvis@gmail.com\"), person(given = \"Greg\", family = \"Macfarlane\", role = \"ctb\", email = \"gregmacfarlane@gmail.com\"), person(given = \"Brian\", family = \"Mannakee\", role = \"ctb\", email = \"bmannakee@gmail.com\"), person(given = \"Drew\", family = \"Tyre\", role = \"ctb\", email = \"atyre2@unl.edu\"), person(given = \"Shreyas\", family = \"Singh\", role = \"ctb\", email = \"shreyas.singh.298@gmail.com\"), person(given = \"Laurens\", family = \"Geffert\", role = \"ctb\", email = \"laurensgeffert@gmail.com\"), person(given = \"Hong\", family = \"Ooi\", role = \"ctb\", email = \"hongooi@microsoft.com\"), person(given = \"Henrik\", family = \"Bengtsson\", role = \"ctb\", email = \"henrikb@braju.com\"), person(given = \"Eduard\", family = \"Szocs\", role = \"ctb\", email = \"eduardszoecs@gmail.com\"), person(given = \"David\", family = \"Hugh-Jones\", role = \"ctb\", email = \"davidhughjones@gmail.com\"), person(given = \"Matthieu\", family = \"Stigler\", role = \"ctb\", email = \"Matthieu.Stigler@gmail.com\"), person(given = \"Hugo\", family = \"Tavares\", role = \"ctb\", email = \"hm533@cam.ac.uk\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(given = \"R. Willem\", family = \"Vervoort\", role = \"ctb\", email = \"Willemvervoort@gmail.com\"), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"ctb\", email = \"brenton@wiernik.org\"), person(given = \"Josh\", family = \"Yamamoto\", role = \"ctb\", email = \"joshuayamamoto5@gmail.com\"), person(given = \"Jasme\", family = \"Lee\", role = \"ctb\"), person(given = \"Taren\", family = \"Sanders\", role = \"ctb\", email = \"taren.sanders@acu.edu.au\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(given = \"Ilaria\", family = \"Prosdocimi\", role = \"ctb\", email = \"prosdocimi.ilaria@gmail.com\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(given = \"Daniel D.\", family = \"Sjoberg\", role = \"ctb\", email = \"danield.sjoberg@gmail.com\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(given = \"Alex\", family = \"Reinhart\", role = \"ctb\", email = \"areinhar@stat.cmu.edu\", comment = c(ORCID = \"0000-0002-6658-514X\")))", - "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", + "Authors@R": "c( person(\"David\", \"Robinson\", , \"admiral.david@gmail.com\", role = \"aut\"), person(\"Alex\", \"Hayes\", , \"alexpghayes@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(\"Simon\", \"Couch\", , \"simon.couch@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5676-5107\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(\"Indrajeet\", \"Patil\", , \"patilindrajeet.science@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(\"Derek\", \"Chiu\", , \"dchiu@bccrc.ca\", role = \"ctb\"), person(\"Matthieu\", \"Gomez\", , \"mattg@princeton.edu\", role = \"ctb\"), person(\"Boris\", \"Demeshev\", , \"boris.demeshev@gmail.com\", role = \"ctb\"), person(\"Dieter\", \"Menne\", , \"dieter.menne@menne-biomed.de\", role = \"ctb\"), person(\"Benjamin\", \"Nutter\", , \"nutter@battelle.org\", role = \"ctb\"), person(\"Luke\", \"Johnston\", , \"luke.johnston@mail.utoronto.ca\", role = \"ctb\"), person(\"Ben\", \"Bolker\", , \"bolker@mcmaster.ca\", role = \"ctb\"), person(\"Francois\", \"Briatte\", , \"f.briatte@gmail.com\", role = \"ctb\"), person(\"Jeffrey\", \"Arnold\", , \"jeffrey.arnold@gmail.com\", role = \"ctb\"), person(\"Jonah\", \"Gabry\", , \"jsg2201@columbia.edu\", role = \"ctb\"), person(\"Luciano\", \"Selzer\", , \"luciano.selzer@gmail.com\", role = \"ctb\"), person(\"Gavin\", \"Simpson\", , \"ucfagls@gmail.com\", role = \"ctb\"), person(\"Jens\", \"Preussner\", , \"jens.preussner@mpi-bn.mpg.de\", role = \"ctb\"), person(\"Jay\", \"Hesselberth\", , \"jay.hesselberth@gmail.com\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"ctb\"), person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = \"ctb\"), person(\"Alessandro\", \"Gasparini\", , \"ag475@leicester.ac.uk\", role = \"ctb\"), person(\"Lukasz\", \"Komsta\", , \"lukasz.komsta@umlub.pl\", role = \"ctb\"), person(\"Frederick\", \"Novometsky\", role = \"ctb\"), person(\"Wilson\", \"Freitas\", role = \"ctb\"), person(\"Michelle\", \"Evans\", role = \"ctb\"), person(\"Jason Cory\", \"Brunson\", , \"cornelioid@gmail.com\", role = \"ctb\"), person(\"Simon\", \"Jackson\", , \"drsimonjackson@gmail.com\", role = \"ctb\"), person(\"Ben\", \"Whalley\", , \"ben.whalley@plymouth.ac.uk\", role = \"ctb\"), person(\"Karissa\", \"Whiting\", , \"karissa.whiting@gmail.com\", role = \"ctb\"), person(\"Yves\", \"Rosseel\", , \"yrosseel@gmail.com\", role = \"ctb\"), person(\"Michael\", \"Kuehn\", , \"mkuehn10@gmail.com\", role = \"ctb\"), person(\"Jorge\", \"Cimentada\", , \"cimentadaj@gmail.com\", role = \"ctb\"), person(\"Erle\", \"Holgersen\", , \"erle.holgersen@gmail.com\", role = \"ctb\"), person(\"Karl\", \"Dunkle Werner\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0523-7309\")), person(\"Ethan\", \"Christensen\", , \"christensen.ej@gmail.com\", role = \"ctb\"), person(\"Steven\", \"Pav\", , \"shabbychef@gmail.com\", role = \"ctb\"), person(\"Paul\", \"PJ\", , \"pjpaul.stephens@gmail.com\", role = \"ctb\"), person(\"Ben\", \"Schneider\", , \"benjamin.julius.schneider@gmail.com\", role = \"ctb\"), person(\"Patrick\", \"Kennedy\", , \"pkqstr@protonmail.com\", role = \"ctb\"), person(\"Lily\", \"Medina\", , \"lilymiru@gmail.com\", role = \"ctb\"), person(\"Brian\", \"Fannin\", , \"captain@pirategrunt.com\", role = \"ctb\"), person(\"Jason\", \"Muhlenkamp\", , \"jason.muhlenkamp@gmail.com\", role = \"ctb\"), person(\"Matt\", \"Lehman\", role = \"ctb\"), person(\"Bill\", \"Denney\", , \"wdenney@humanpredictions.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\")), person(\"Nic\", \"Crane\", role = \"ctb\"), person(\"Andrew\", \"Bates\", role = \"ctb\"), person(\"Vincent\", \"Arel-Bundock\", , \"vincent.arel-bundock@umontreal.ca\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2042-7063\")), person(\"Hideaki\", \"Hayashi\", role = \"ctb\"), person(\"Luis\", \"Tobalina\", role = \"ctb\"), person(\"Annie\", \"Wang\", , \"anniewang.uc@gmail.com\", role = \"ctb\"), person(\"Wei Yang\", \"Tham\", , \"weiyang.tham@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", , \"clara.wang.94@gmail.com\", role = \"ctb\"), person(\"Abby\", \"Smith\", , \"als1@u.northwestern.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3207-0375\")), person(\"Jasper\", \"Cooper\", , \"jaspercooper@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8639-3188\")), person(\"E Auden\", \"Krauska\", , \"krauskae@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1466-5850\")), person(\"Alex\", \"Wang\", , \"x249wang@uwaterloo.ca\", role = \"ctb\"), person(\"Malcolm\", \"Barrett\", , \"malcolmbarrett@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(\"Charles\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9978-011X\")), person(\"Jared\", \"Wilber\", role = \"ctb\"), person(\"Vilmantas\", \"Gegzna\", , \"GegznaV@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9500-5167\")), person(\"Eduard\", \"Szoecs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"Frederik\", \"Aust\", , \"frederik.aust@uni-koeln.de\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4900-788X\")), person(\"Angus\", \"Moore\", , \"angusmoore9@gmail.com\", role = \"ctb\"), person(\"Nick\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Marius\", \"Barth\", , \"marius.barth.uni.koeln@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3421-6665\")), person(\"Bruna\", \"Wundervald\", , \"brunadaviesw@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8163-220X\")), person(\"Joyce\", \"Cahoon\", , \"joyceyu48@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7217-4702\")), person(\"Grant\", \"McDermott\", , \"grantmcd@uoregon.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7883-8573\")), person(\"Kevin\", \"Zarca\", , \"kevin.zarca@gmail.com\", role = \"ctb\"), person(\"Shiro\", \"Kuriwaki\", , \"shirokuriwaki@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5687-2647\")), person(\"Lukas\", \"Wallrich\", , \"lukas.wallrich@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2121-5177\")), person(\"James\", \"Martherus\", , \"james@martherus.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8285-3300\")), person(\"Chuliang\", \"Xiao\", , \"cxiao@umich.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8466-9398\")), person(\"Joseph\", \"Larmarange\", , \"joseph@larmarange.net\", role = \"ctb\"), person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", , \"michal2992@gmail.com\", role = \"ctb\"), person(\"Hakon\", \"Malmedal\", , \"hmalmedal@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", role = \"ctb\"), person(\"Sergio\", \"Oller\", , \"sergioller@gmail.com\", role = \"ctb\"), person(\"Luke\", \"Sonnet\", , \"luke.sonnet@gmail.com\", role = \"ctb\"), person(\"Jim\", \"Hester\", , \"jim.hester@posit.co\", role = \"ctb\"), person(\"Ben\", \"Schneider\", , \"benjamin.julius.schneider@gmail.com\", role = \"ctb\"), person(\"Bernie\", \"Gray\", , \"bfgray3@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9190-6032\")), person(\"Mara\", \"Averick\", , \"mara@posit.co\", role = \"ctb\"), person(\"Aaron\", \"Jacobs\", , \"atheriel@gmail.com\", role = \"ctb\"), person(\"Andreas\", \"Bender\", , \"bender.at.R@gmail.com\", role = \"ctb\"), person(\"Sven\", \"Templer\", , \"sven.templer@gmail.com\", role = \"ctb\"), person(\"Paul-Christian\", \"Buerkner\", , \"paul.buerkner@gmail.com\", role = \"ctb\"), person(\"Matthew\", \"Kay\", , \"mjskay@umich.edu\", role = \"ctb\"), person(\"Erwan\", \"Le Pennec\", , \"lepennec@gmail.com\", role = \"ctb\"), person(\"Johan\", \"Junkka\", , \"johan.junkka@umu.se\", role = \"ctb\"), person(\"Hao\", \"Zhu\", , \"haozhu233@gmail.com\", role = \"ctb\"), person(\"Benjamin\", \"Soltoff\", , \"soltoffbc@uchicago.edu\", role = \"ctb\"), person(\"Zoe\", \"Wilkinson Saldana\", , \"zoewsaldana@gmail.com\", role = \"ctb\"), person(\"Tyler\", \"Littlefield\", , \"tylurp1@gmail.com\", role = \"ctb\"), person(\"Charles T.\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\"), person(\"Shabbh E.\", \"Banks\", role = \"ctb\"), person(\"Serina\", \"Robinson\", , \"robi0916@umn.edu\", role = \"ctb\"), person(\"Roger\", \"Bivand\", , \"Roger.Bivand@nhh.no\", role = \"ctb\"), person(\"Riinu\", \"Ots\", , \"riinuots@gmail.com\", role = \"ctb\"), person(\"Nicholas\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Nina\", \"Jakobsen\", role = \"ctb\"), person(\"Michael\", \"Weylandt\", , \"michael.weylandt@gmail.com\", role = \"ctb\"), person(\"Lisa\", \"Lendway\", , \"llendway@macalester.edu\", role = \"ctb\"), person(\"Karl\", \"Hailperin\", , \"khailper@gmail.com\", role = \"ctb\"), person(\"Josue\", \"Rodriguez\", , \"jerrodriguez@ucdavis.edu\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", , \"jenny@posit.co\", role = \"ctb\"), person(\"Chris\", \"Jarvis\", , \"Christopher1.jarvis@gmail.com\", role = \"ctb\"), person(\"Greg\", \"Macfarlane\", , \"gregmacfarlane@gmail.com\", role = \"ctb\"), person(\"Brian\", \"Mannakee\", , \"bmannakee@gmail.com\", role = \"ctb\"), person(\"Drew\", \"Tyre\", , \"atyre2@unl.edu\", role = \"ctb\"), person(\"Shreyas\", \"Singh\", , \"shreyas.singh.298@gmail.com\", role = \"ctb\"), person(\"Laurens\", \"Geffert\", , \"laurensgeffert@gmail.com\", role = \"ctb\"), person(\"Hong\", \"Ooi\", , \"hongooi@microsoft.com\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", , \"henrikb@braju.com\", role = \"ctb\"), person(\"Eduard\", \"Szocs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", , \"davidhughjones@gmail.com\", role = \"ctb\"), person(\"Matthieu\", \"Stigler\", , \"Matthieu.Stigler@gmail.com\", role = \"ctb\"), person(\"Hugo\", \"Tavares\", , \"hm533@cam.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(\"R. Willem\", \"Vervoort\", , \"Willemvervoort@gmail.com\", role = \"ctb\"), person(\"Brenton M.\", \"Wiernik\", , \"brenton@wiernik.org\", role = \"ctb\"), person(\"Josh\", \"Yamamoto\", , \"joshuayamamoto5@gmail.com\", role = \"ctb\"), person(\"Jasme\", \"Lee\", role = \"ctb\"), person(\"Taren\", \"Sanders\", , \"taren.sanders@acu.edu.au\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(\"Ilaria\", \"Prosdocimi\", , \"prosdocimi.ilaria@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(\"Alex\", \"Reinhart\", , \"areinhar@stat.cmu.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-6658-514X\")) )", + "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", "License": "MIT + file LICENSE", "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", "BugReports": "https://github.com/tidymodels/broom/issues", "Depends": [ - "R (>= 3.5)" + "R (>= 4.1)" ], "Imports": [ "backports", @@ -1253,7 +1155,7 @@ "drc", "e1071", "emmeans", - "epiR", + "epiR (>= 2.0.85)", "ergm (>= 3.10.4)", "fixest (>= 0.9.0)", "gam (>= 1.15)", @@ -1264,8 +1166,8 @@ "glmnetUtils", "gmm", "Hmisc", - "irlba", "interp", + "irlba", "joineRML", "Kendall", "knitr", @@ -1304,8 +1206,8 @@ "robustbase", "rsample", "sandwich", - "spdep (>= 1.1)", "spatialreg", + "spdep (>= 1.1)", "speedglm", "spelling", "survey", @@ -1318,13 +1220,14 @@ ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", - 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"Author": "David Robinson [aut], Alex Hayes [aut] (), Simon Couch [aut, cre] (), Posit Software, PBC [cph, fnd], Indrajeet Patil [ctb] (), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (), Jasper Cooper [ctb] (), E Auden Krauska [ctb] (), Alex Wang [ctb], Malcolm Barrett [ctb] (), Charles Gray [ctb] (), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (), Eduard Szoecs [ctb], Frederik Aust [ctb] (), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (), Bruna Wundervald [ctb] (), Joyce Cahoon [ctb] (), Grant McDermott [ctb] (), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (), Lukas Wallrich [ctb] (), James Martherus [ctb] (), Chuliang Xiao [ctb] (), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (), Ilaria Prosdocimi [ctb] (), Daniel D. Sjoberg [ctb] (), Alex Reinhart [ctb] ()", + "Author": "David Robinson [aut], Alex Hayes [aut] (ORCID: ), Simon Couch [aut, cre] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: ), Indrajeet Patil [ctb] (ORCID: ), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (ORCID: ), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (ORCID: ), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (ORCID: ), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (ORCID: ), Jasper Cooper [ctb] (ORCID: ), E Auden Krauska [ctb] (ORCID: ), Alex Wang [ctb], Malcolm Barrett [ctb] (ORCID: ), Charles Gray [ctb] (ORCID: ), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (ORCID: ), Eduard Szoecs [ctb], Frederik Aust [ctb] (ORCID: ), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (ORCID: ), Bruna Wundervald [ctb] (ORCID: ), Joyce Cahoon [ctb] (ORCID: ), Grant McDermott [ctb] (ORCID: ), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (ORCID: ), Lukas Wallrich [ctb] (ORCID: ), James Martherus [ctb] (ORCID: ), Chuliang Xiao [ctb] (ORCID: ), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (ORCID: ), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (ORCID: ), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (ORCID: ), Ilaria Prosdocimi [ctb] (ORCID: ), Daniel D. Sjoberg [ctb] (ORCID: ), Alex Reinhart [ctb] (ORCID: )", "Maintainer": "Simon Couch ", "Repository": "CRAN" }, @@ -1911,23 +1814,6 @@ "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", "Repository": "CRAN" }, - "codetools": { - "Package": "codetools", - "Version": "0.2-20", - "Source": "Repository", - "Priority": "recommended", - "Author": "Luke Tierney ", - "Description": "Code analysis tools for R.", - "Title": "Code Analysis Tools for R", - "Depends": [ - "R (>= 2.1)" - ], - "Maintainer": "Luke Tierney ", - "URL": "https://gitlab.com/luke-tierney/codetools", - "License": "GPL", - "NeedsCompilation": "no", - "Repository": "CRAN" - }, "colorspace": { "Package": "colorspace", "Version": "2.1-1", @@ -3051,7 +2937,7 @@ "NeedsCompilation": "yes", "Author": "Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd]", "Maintainer": "Gábor Csárdi ", - "Repository": "RSPM" + "Repository": "CRAN" }, "flextable": { "Package": "flextable", @@ -3260,41 +3146,6 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "foreach": { - "Package": "foreach", - "Version": "1.5.2", - "Source": "Repository", - "Type": "Package", - "Title": "Provides Foreach Looping Construct", - "Authors@R": "c(person(\"Folashade\", \"Daniel\", role=\"cre\", email=\"fdaniel@microsoft.com\"), person(\"Hong\", \"Ooi\", role=\"ctb\"), person(\"Rich\", \"Calaway\", role=\"ctb\"), person(\"Microsoft\", role=c(\"aut\", \"cph\")), person(\"Steve\", \"Weston\", role=\"aut\"))", - "Description": "Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.", - "License": "Apache License (== 2.0)", - "URL": "https://github.com/RevolutionAnalytics/foreach", - "BugReports": "https://github.com/RevolutionAnalytics/foreach/issues", - "Depends": [ - "R (>= 2.5.0)" - ], - "Imports": [ - "codetools", - "utils", - "iterators" - ], - "Suggests": [ - "randomForest", - "doMC", - "doParallel", - "testthat", - "knitr", - "rmarkdown" - ], - "VignetteBuilder": "knitr", - "RoxygenNote": "7.1.1", - "Collate": "'callCombine.R' 'foreach.R' 'do.R' 'foreach-ext.R' 'foreach-pkg.R' 'getDoPar.R' 'getDoSeq.R' 'getsyms.R' 'iter.R' 'nextElem.R' 'onLoad.R' 'setDoPar.R' 'setDoSeq.R' 'times.R' 'utils.R'", - "NeedsCompilation": "no", - "Author": "Folashade Daniel [cre], Hong Ooi [ctb], Rich Calaway [ctb], Microsoft [aut, cph], Steve Weston [aut]", - "Maintainer": "Folashade Daniel ", - "Repository": "CRAN" - }, "foreign": { "Package": "foreign", "Version": "0.8-90", @@ -4445,7 +4296,7 @@ }, "insight": { "Package": "insight", - "Version": "1.3.1", + "Version": "1.4.0", "Source": "Repository", "Type": "Package", "Title": "Easy Access to Model Information for Various Model Objects", @@ -4491,7 +4342,7 @@ "cplm", "crch", "curl", - "datawizard", + "datawizard (>= 1.2.0)", "dbarts", "effectsize", "emmeans", @@ -4547,6 +4398,7 @@ "modelbased (>= 0.9.0)", "multgee", "MuMIn", + "mvtnorm", "nestedLogit", "nlme", "nnet", @@ -4559,7 +4411,6 @@ "performance", "phylolm", "plm", - "poorman", "PROreg (>= 1.3.0)", "pscl", "psych", @@ -4577,6 +4428,7 @@ "RWiener", "sandwich", "sdmTMB", + "sampleSelection", "serp", "speedglm", "splines", @@ -4642,29 +4494,6 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "iterators": { - "Package": "iterators", - "Version": "1.0.14", - "Source": "Repository", - "Type": "Package", - "Title": "Provides Iterator Construct", - "Authors@R": "c(person(\"Folashade\", \"Daniel\", role=\"cre\", email=\"fdaniel@microsoft.com\"), person(\"Revolution\", \"Analytics\", role=c(\"aut\", \"cph\")), person(\"Steve\", \"Weston\", role=\"aut\"))", - "Description": "Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.", - "URL": "https://github.com/RevolutionAnalytics/iterators", - "Depends": [ - "R (>= 2.5.0)", - "utils" - ], - "Suggests": [ - "RUnit", - "foreach" - ], - "License": "Apache License (== 2.0)", - "NeedsCompilation": "no", - "Author": "Folashade Daniel [cre], Revolution Analytics [aut, cph], Steve Weston [aut]", - "Maintainer": "Folashade Daniel ", - "Repository": "CRAN" - }, "jquerylib": { "Package": "jquerylib", "Version": "0.1.4", @@ -5082,70 +4911,6 @@ "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, - "lme4": { - "Package": "lme4", - "Version": "1.1-37", - "Source": "Repository", - "Title": "Linear Mixed-Effects Models using 'Eigen' and S4", - "Authors@R": "c( person(\"Douglas\",\"Bates\", role=\"aut\", comment=c(ORCID=\"0000-0001-8316-9503\")), person(\"Martin\",\"Maechler\", role=\"aut\", comment=c(ORCID=\"0000-0002-8685-9910\")), person(\"Ben\",\"Bolker\",email=\"bbolker+lme4@gmail.com\", role=c(\"aut\",\"cre\"), comment=c(ORCID=\"0000-0002-2127-0443\")), person(\"Steven\",\"Walker\",role=\"aut\", comment=c(ORCID=\"0000-0002-4394-9078\")), person(\"Rune Haubo Bojesen\",\"Christensen\", role=\"ctb\", comment=c(ORCID=\"0000-0002-4494-3399\")), person(\"Henrik\",\"Singmann\", role=\"ctb\", comment=c(ORCID=\"0000-0002-4842-3657\")), person(\"Bin\", \"Dai\", role=\"ctb\"), person(\"Fabian\", \"Scheipl\", role=\"ctb\", comment=c(ORCID=\"0000-0001-8172-3603\")), person(\"Gabor\", \"Grothendieck\", role=\"ctb\"), person(\"Peter\", \"Green\", role=\"ctb\", comment=c(ORCID=\"0000-0002-0238-9852\")), person(\"John\", \"Fox\", role=\"ctb\"), person(\"Alexander\", \"Bauer\", role=\"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role=c(\"ctb\",\"cph\"), comment=c(ORCID=\"0000-0002-9101-3362\", \"shared copyright on simulate.formula\")), person(\"Emi\", \"Tanaka\", role = \"ctb\", comment = c(ORCID=\"0000-0002-1455-259X\")), person(\"Mikael\", \"Jagan\", role = \"ctb\", comment = c(ORCID=\"0000-0002-3542-2938\")), person(\"Ross D.\", \"Boylan\", email=\"ross.boylan@ucsf.edu\", role=(\"ctb\"), comment = c(ORCID=\"0009-0003-4123-8090\")) )", - "Description": "Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' \"glue\".", - "Depends": [ - "R (>= 3.6.0)", - "Matrix", - "methods", - "stats" - ], - "LinkingTo": [ - "Rcpp (>= 0.10.5)", - "RcppEigen (>= 0.3.3.9.4)", - "Matrix (>= 1.2-3)" - ], - "Imports": [ - "graphics", - "grid", - "splines", - "utils", - "parallel", - "MASS", - "lattice", - "boot", - "nlme (>= 3.1-123)", - "minqa (>= 1.1.15)", - "nloptr (>= 1.0.4)", - "reformulas (>= 0.3.0)" - ], - "Suggests": [ - "knitr", - "rmarkdown", - "MEMSS", - "testthat (>= 0.8.1)", - "ggplot2", - "mlmRev", - "optimx (>= 2013.8.6)", - "gamm4", - "pbkrtest", - "HSAUR3", - "numDeriv", - "car", - "dfoptim", - "mgcv", - "statmod", - "rr2", - "semEff", - "tibble", - "merDeriv" - ], - "VignetteBuilder": "knitr", - "LazyData": "yes", - "License": "GPL (>= 2)", - "URL": "https://github.com/lme4/lme4/", - "BugReports": "https://github.com/lme4/lme4/issues", - "Encoding": "UTF-8", - "NeedsCompilation": "yes", - "Author": "Douglas Bates [aut] (), Martin Maechler [aut] (), Ben Bolker [aut, cre] (), Steven Walker [aut] (), Rune Haubo Bojesen Christensen [ctb] (), Henrik Singmann [ctb] (), Bin Dai [ctb], Fabian Scheipl [ctb] (), Gabor Grothendieck [ctb], Peter Green [ctb] (), John Fox [ctb], Alexander Bauer [ctb], Pavel N. Krivitsky [ctb, cph] (, shared copyright on simulate.formula), Emi Tanaka [ctb] (), Mikael Jagan [ctb] (), Ross D. Boylan [ctb] ()", - "Maintainer": "Ben Bolker ", - "Repository": "CRAN" - }, "lmtest": { "Package": "lmtest", "Version": "0.9-40", @@ -5371,28 +5136,6 @@ "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, - "minqa": { - "Package": "minqa", - "Version": "1.2.8", - "Source": "Repository", - "Type": "Package", - "Title": "Derivative-Free Optimization Algorithms by Quadratic Approximation", - "Authors@R": "c(person(given = \"Douglas\", family = \"Bates\", role = \"aut\"), person(given = c(\"Katharine\", \"M.\"), family = \"Mullen\", role = c(\"aut\", \"cre\"), email = \"katharine.mullen@stat.ucla.edu\"), person(given = c(\"John\", \"C.\"), family = \"Nash\", role = \"aut\"), person(given = \"Ravi\", family = \"Varadhan\", role = \"aut\"))", - "Maintainer": "Katharine M. Mullen ", - "Description": "Derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.", - "License": "GPL-2", - "URL": "http://optimizer.r-forge.r-project.org", - "Imports": [ - "Rcpp (>= 0.9.10)" - ], - "LinkingTo": [ - "Rcpp" - ], - "SystemRequirements": "GNU make", - "NeedsCompilation": "yes", - "Repository": "CRAN", - "Author": "Douglas Bates [aut], Katharine M. Mullen [aut, cre], John C. Nash [aut], Ravi Varadhan [aut]" - }, "minty": { "Package": "minty", "Version": "0.0.5", @@ -5524,31 +5267,6 @@ "Author": "Dominique Makowski [aut, cre] (ORCID: ), Daniel Lüdecke [aut] (ORCID: ), Mattan S. Ben-Shachar [aut] (ORCID: ), Indrajeet Patil [aut] (ORCID: ), Rémi Thériault [aut] (ORCID: )", "Repository": "CRAN" }, - "mvtnorm": { - "Package": "mvtnorm", - "Version": "1.3-3", - "Source": "Repository", - "Title": "Multivariate Normal and t Distributions", - "Date": "2025-01-09", - "Authors@R": "c(person(\"Alan\", \"Genz\", role = \"aut\"), person(\"Frank\", \"Bretz\", role = \"aut\"), person(\"Tetsuhisa\", \"Miwa\", role = \"aut\"), person(\"Xuefei\", \"Mi\", role = \"aut\"), person(\"Friedrich\", \"Leisch\", role = \"ctb\"), person(\"Fabian\", \"Scheipl\", role = \"ctb\"), person(\"Bjoern\", \"Bornkamp\", role = \"ctb\", comment = c(ORCID = \"0000-0002-6294-8185\")), person(\"Martin\", \"Maechler\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Torsten\", \"Hothorn\", role = c(\"aut\", \"cre\"), email = \"Torsten.Hothorn@R-project.org\", comment = c(ORCID = \"0000-0001-8301-0471\")))", - "Description": "Computes multivariate normal and t probabilities, quantiles, random deviates, and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae parameterised by Cholesky factors of covariance or precision matrices are implemented for interval-censored and exact data, or a mix thereof. Score functions for these log-likelihoods are available. A class representing multiple lower triangular matrices and corresponding methods are part of this package.", - "Imports": [ - "stats" - ], - "Depends": [ - "R(>= 3.5.0)" - ], - "Suggests": [ - "qrng", - "numDeriv" - ], - "License": "GPL-2", - "URL": "http://mvtnorm.R-forge.R-project.org", - "NeedsCompilation": "yes", - "Author": "Alan Genz [aut], Frank Bretz [aut], Tetsuhisa Miwa [aut], Xuefei Mi [aut], Friedrich Leisch [ctb], Fabian Scheipl [ctb], Bjoern Bornkamp [ctb] (), Martin Maechler [ctb] (), Torsten Hothorn [aut, cre] ()", - "Maintainer": "Torsten Hothorn ", - "Repository": "CRAN" - }, "nlme": { "Package": "nlme", "Version": "3.1-168", @@ -5583,33 +5301,6 @@ "Maintainer": "R Core Team ", "Repository": "CRAN" }, - "nloptr": { - "Package": "nloptr", - "Version": "2.2.1", - "Source": "Repository", - "Type": "Package", - "Title": "R Interface to NLopt", - "Authors@R": "c(person(\"Jelmer\", \"Ypma\", role = \"aut\", email = \"uctpjyy@ucl.ac.uk\"), person(c(\"Steven\", \"G.\"), \"Johnson\", role = \"aut\", comment = \"author of the NLopt C library\"), person(\"Aymeric\", \"Stamm\", role = c(\"ctb\", \"cre\"), email = \"aymeric.stamm@cnrs.fr\", comment = c(ORCID = \"0000-0002-8725-3654\")), person(c(\"Hans\", \"W.\"), \"Borchers\", role = \"ctb\", email = \"hwborchers@googlemail.com\"), person(\"Dirk\", \"Eddelbuettel\", role = \"ctb\", email = \"edd@debian.org\"), person(\"Brian\", \"Ripley\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Kurt\", \"Hornik\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Julien\", \"Chiquet\", role = \"ctb\"), person(\"Avraham\", \"Adler\", role = \"ctb\", email = \"Avraham.Adler@gmail.com\", comment = c(ORCID = \"0000-0002-3039-0703\")), person(\"Xiongtao\", \"Dai\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\", email = \"jeroen@berkeley.edu\"), person(\"Tomas\", \"Kalibera\", role = \"ctb\"), person(\"Mikael\", \"Jagan\", role = \"ctb\"))", - "Description": "Solve optimization problems using an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See for more information on the available algorithms. Building from included sources requires 'CMake'. On Linux and 'macOS', if a suitable system build of NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from included sources via 'CMake'. On Windows, NLopt is obtained through 'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for 'R >= 4.2.0'.", - "License": "LGPL (>= 3)", - "SystemRequirements": "cmake (>= 3.2.0) which is used only on Linux or macOS systems when no system build of nlopt (>= 2.7.0) can be found.", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "Suggests": [ - "knitr", - "rmarkdown", - "covr", - "tinytest" - ], - "VignetteBuilder": "knitr", - "URL": "https://github.com/astamm/nloptr, https://astamm.github.io/nloptr/", - "BugReports": "https://github.com/astamm/nloptr/issues", - "NeedsCompilation": "yes", - "UseLTO": "yes", - "Author": "Jelmer Ypma [aut], Steven G. Johnson [aut] (author of the NLopt C library), Aymeric Stamm [ctb, cre] (), Hans W. Borchers [ctb], Dirk Eddelbuettel [ctb], Brian Ripley [ctb] (build process on multiple OS), Kurt Hornik [ctb] (build process on multiple OS), Julien Chiquet [ctb], Avraham Adler [ctb] (), Xiongtao Dai [ctb], Jeroen Ooms [ctb], Tomas Kalibera [ctb], Mikael Jagan [ctb]", - "Maintainer": "Aymeric Stamm ", - "Repository": "CRAN" - }, "nnet": { "Package": "nnet", "Version": "7.3-20", @@ -5635,26 +5326,6 @@ "Maintainer": "Brian Ripley ", "Repository": "CRAN" }, - "numDeriv": { - "Package": "numDeriv", - "Version": "2016.8-1.1", - "Source": "Repository", - "Title": "Accurate Numerical Derivatives", - "Description": "Methods for calculating (usually) accurate numerical first and second order derivatives. Accurate calculations are done using 'Richardson''s' extrapolation or, when applicable, a complex step derivative is available. A simple difference method is also provided. Simple difference is (usually) less accurate but is much quicker than 'Richardson''s' extrapolation and provides a useful cross-check. Methods are provided for real scalar and vector valued functions.", - "Depends": [ - "R (>= 2.11.1)" - ], - "LazyLoad": "yes", - "ByteCompile": "yes", - "License": "GPL-2", - "Copyright": "2006-2011, Bank of Canada. 2012-2016, Paul Gilbert", - "Author": "Paul Gilbert and Ravi Varadhan", - "Maintainer": "Paul Gilbert ", - "URL": "http://optimizer.r-forge.r-project.org/", - "NeedsCompilation": "no", - "Repository": "RSPM", - "Encoding": "UTF-8" - }, "officer": { "Package": "officer", "Version": "0.6.10", @@ -5768,7 +5439,7 @@ }, "openxlsx2": { "Package": "openxlsx2", - "Version": "1.17", + "Version": "1.18", "Source": "Repository", "Type": "Package", "Title": "Read, Write and Edit 'xlsx' Files", @@ -6841,36 +6512,56 @@ }, "quarto": { "Package": "quarto", - "Version": "1.4.4", + "Version": "1.5.0", "Source": "Repository", "Title": "R Interface to 'Quarto' Markdown Publishing System", - "Authors@R": "c( person(\"JJ\", \"Allaire\", , \"jj@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"JJ\", \"Allaire\", , \"jj@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Gordon\", \"Woodhull\", role = \"ctb\") )", "Description": "Convert R Markdown documents and 'Jupyter' notebooks to a variety of output formats using 'Quarto'.", - "License": "GPL (>= 2)", + "License": "MIT + file LICENSE", "URL": "https://github.com/quarto-dev/quarto-r, https://quarto-dev.github.io/quarto-r/", "BugReports": "https://github.com/quarto-dev/quarto-r/issues", "Depends": [ - "R (>= 3.6)" + "R (>= 4.1.0)" ], "Imports": [ "cli", + "fs", + "htmltools", "jsonlite", "later", + "lifecycle", "processx", "rlang", "rmarkdown", "rstudioapi", "tools", "utils", - "yaml" + "xfun", + "yaml (>= 2.3.10)" ], "Suggests": [ + "bslib", + "callr", "curl", + "dplyr", + "flextable", + "ggiraph", + "ggplot2", + "gt", + "heatmaply", + "kableExtra", "knitr", + "palmerpenguins", + "patchwork", + "pkgload", + "plotly", "rsconnect (>= 0.8.26)", "testthat (>= 3.1.7)", - "withr", - "xfun" + "thematic", + "tidyverse", + "tinytable", + "whoami", + "withr" ], "VignetteBuilder": "quarto", "Config/testthat/edition": "3", @@ -6878,7 +6569,7 @@ "RoxygenNote": "7.3.2", "SystemRequirements": "Quarto command line tool ().", "NeedsCompilation": "no", - "Author": "JJ Allaire [aut] (), Christophe Dervieux [cre, aut] (), Posit Software, PBC [cph, fnd]", + "Author": "JJ Allaire [aut] (ORCID: ), Christophe Dervieux [cre, aut] (ORCID: ), Posit Software, PBC [cph, fnd], Gordon Woodhull [ctb]", "Maintainer": "Christophe Dervieux ", "Repository": "CRAN" }, @@ -6974,34 +6665,6 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "rbibutils": { - "Package": "rbibutils", - "Version": "2.3", - "Source": "Repository", - "Type": "Package", - "Title": "Read 'Bibtex' Files and Convert Between Bibliography Formats", - "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), \t email = \"georgi.boshnakov@manchester.ac.uk\", comment = \"R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)\" ), person(given = \"Chris\", family = \"Putman\", role = \"aut\", comment = \"src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/\"), person(given = \"Richard\", family = \"Mathar\", role = \"ctb\", comment = \"src/addsout.c\"), person(given = \"Johannes\", family = \"Wilm\", role = \"ctb\", comment = \"src/biblatexin.c, src/bltypes.c\"), person(\"R Core Team\", role = \"ctb\", comment = \"base R's bibentry and bibstyle implementation\") )", - "Description": "Read and write 'Bibtex' files. Convert between bibliography formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam . Supports all bibliography formats and character encodings implemented in 'bibutils'.", - "License": "GPL-2", - "URL": "https://geobosh.github.io/rbibutils/ (doc), https://github.com/GeoBosh/rbibutils (devel)", - "BugReports": "https://github.com/GeoBosh/rbibutils/issues", - "Depends": [ - "R (>= 2.10)" - ], - "Imports": [ - "utils", - "tools" - ], - "Suggests": [ - "testthat" - ], - "Encoding": "UTF-8", - "NeedsCompilation": "yes", - "Config/Needs/memcheck": "devtools, rcmdcheck", - "Author": "Georgi N. Boshnakov [aut, cre] (R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)), Chris Putman [aut] (src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/), Richard Mathar [ctb] (src/addsout.c), Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c), R Core Team [ctb] (base R's bibentry and bibstyle implementation)", - "Maintainer": "Georgi N. Boshnakov ", - "Repository": "CRAN" - }, "reactR": { "Package": "reactR", "Version": "0.6.1", @@ -7179,74 +6842,6 @@ "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, - "readxl": { - "Package": "readxl", - "Version": "1.4.5", - "Source": "Repository", - "Title": "Read Excel Files", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = \"Copyright holder of all R code and all C/C++ code without explicit copyright attribution\"), person(\"Marcin\", \"Kalicinski\", role = c(\"ctb\", \"cph\"), comment = \"Author of included RapidXML code\"), person(\"Komarov Valery\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Christophe Leitienne\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Bob Colbert\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"David Hoerl\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Evan Miller\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\") )", - "Description": "Import excel files into R. Supports '.xls' via the embedded 'libxls' C library and '.xlsx' via the embedded 'RapidXML' C++ library . Works on Windows, Mac and Linux without external dependencies.", - "License": "MIT + file LICENSE", - "URL": "https://readxl.tidyverse.org, https://github.com/tidyverse/readxl", - "BugReports": "https://github.com/tidyverse/readxl/issues", - "Depends": [ - "R (>= 3.6)" - ], - "Imports": [ - "cellranger", - "tibble (>= 2.0.1)", - "utils" - ], - "Suggests": [ - "covr", - "knitr", - "rmarkdown", - "testthat (>= 3.1.6)", - "withr" - ], - "LinkingTo": [ - "cpp11 (>= 0.4.0)", - "progress" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate, tidyverse", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "Note": "libxls v1.6.3 c199d13", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "yes", - "Author": "Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Posit, PBC [cph, fnd] (Copyright holder of all R code and all C/C++ code without explicit copyright attribution), Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Komarov Valery [ctb, cph] (Author of included libxls code), Christophe Leitienne [ctb, cph] (Author of included libxls code), Bob Colbert [ctb, cph] (Author of included libxls code), David Hoerl [ctb, cph] (Author of included libxls code), Evan Miller [ctb, cph] (Author of included libxls code)", - "Maintainer": "Jennifer Bryan ", - "Repository": "CRAN" - }, - "reformulas": { - "Package": "reformulas", - "Version": "0.4.1", - "Source": "Repository", - "Title": "Machinery for Processing Random Effect Formulas", - "Authors@R": "person(given = \"Ben\", family = \"Bolker\", role = c(\"aut\", \"cre\"), email = \"bolker@mcmaster.ca\", comment=c(ORCID=\"0000-0002-2127-0443\"))", - "Description": "Takes formulas including random-effects components (formatted as in 'lme4', 'glmmTMB', etc.) and processes them. Includes various helper functions.", - "URL": "https://github.com/bbolker/reformulas", - "License": "GPL-3", - "Encoding": "UTF-8", - "Imports": [ - "stats", - "methods", - "Matrix", - "Rdpack" - ], - "RdMacros": "Rdpack", - "Suggests": [ - "lme4", - "tinytest", - "glmmTMB" - ], - "RoxygenNote": "7.3.2.9000", - "NeedsCompilation": "no", - "Author": "Ben Bolker [aut, cre] (ORCID: )", - "Maintainer": "Ben Bolker ", - "Repository": "CRAN" - }, "rematch": { "Package": "rematch", "Version": "2.0.0", @@ -7329,7 +6924,7 @@ }, "renv": { "Package": "renv", - "Version": "1.1.4", + "Version": "1.1.5", "Source": "Repository", "Type": "Package", "Title": "Project Environments", @@ -7348,6 +6943,7 @@ "covr", "cpp11", "devtools", + "generics", "gitcreds", "jsonlite", "jsonvalidate", @@ -7376,7 +6972,7 @@ "Config/testthat/parallel": "true", "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes", "NeedsCompilation": "no", - "Author": "Kevin Ushey [aut, cre] (), Hadley Wickham [aut] (), Posit Software, PBC [cph, fnd]", + "Author": "Kevin Ushey [aut, cre] (ORCID: ), Hadley Wickham [aut] (ORCID: ), Posit Software, PBC [cph, fnd]", "Maintainer": "Kevin Ushey ", "Repository": "CRAN" }, diff --git a/renv/activate.R b/renv/activate.R index 90b251ca..2753ae54 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.1.4" + version <- "1.1.5" attr(version, "sha") <- NULL # the project directory From ca2984745006a37f38025b4ef4214900880a5ad9 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Wed, 27 Aug 2025 11:11:00 +0200 Subject: [PATCH 3/7] fix: fixed submenu fold out --- inst/apps/FreesearchR/www/scripts.js | 54 +++++++++++++++++++++------- inst/assets/js/FreesearchR.js | 54 +++++++++++++++++++++------- 2 files changed, 82 insertions(+), 26 deletions(-) diff --git a/inst/apps/FreesearchR/www/scripts.js b/inst/apps/FreesearchR/www/scripts.js index 3382b4e4..f98dffc9 100644 --- a/inst/apps/FreesearchR/www/scripts.js +++ b/inst/apps/FreesearchR/www/scripts.js @@ -6,24 +6,52 @@ $(document).on('shown.bs.tab', '#main_panel', function(e) { $('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false'); }); + $(document).on('shiny:sessioninitialized', function() { -// Function to collapse navbar on mobile -function collapseNavbar() { - var navbar = $('.navbar-collapse'); - if (navbar.hasClass('show')) { - navbar.removeClass('show'); - $('.navbar-toggler').addClass('collapsed'); - $('.navbar-toggler').attr('aria-expanded', 'false'); - } + // Function to collapse navbar on mobile + function collapseNavbar() { + var navbar = $('.navbar-collapse'); + if (navbar.hasClass('show')) { + navbar.removeClass('show'); + $('.navbar-toggler').addClass('collapsed'); + $('.navbar-toggler').attr('aria-expanded', 'false'); + } } - // Add click event to navigation tabs - $(document).on('click', '.nav-link[data-bs-toggle=\"tab\"]', function() { + // Main approach: Handle clicks on nav elements + $(document).on('click', '.navbar-nav .nav-link, .dropdown-item', function(event) { + var $target = $(event.currentTarget); + + // Don't collapse if this is a dropdown toggle + if ($target.hasClass('dropdown-toggle')) { + return; + } + + // Don't collapse if this is inside a dropdown and the dropdown should stay open + if ($target.hasClass('nav-link') && $target.closest('.dropdown').length && + !$target.attr('data-bs-toggle')) { + return; + } + + // Collapse the navbar after a short delay setTimeout(collapseNavbar, 10); }); - // Also handle direct clicks on nav items - $(document).on('click', '.navbar-nav .nav-link', function() { - setTimeout(collapseNavbar, 10); + // Handle tab toggles specifically + $(document).on('click', '.nav-link[data-bs-toggle="tab"]', function() { + if (!$(this).hasClass('dropdown-toggle')) { + setTimeout(collapseNavbar, 10); + } + }); + + // Optional: Handle clicks outside the navbar to close it + $(document).on('click', function(event) { + var navbar = $('.navbar-collapse'); + + // Check if click is outside navbar and navbar is open + if (navbar.hasClass('show') && + !$(event.target).closest('.navbar').length) { + collapseNavbar(); + } }); }); diff --git a/inst/assets/js/FreesearchR.js b/inst/assets/js/FreesearchR.js index 3382b4e4..f98dffc9 100644 --- a/inst/assets/js/FreesearchR.js +++ b/inst/assets/js/FreesearchR.js @@ -6,24 +6,52 @@ $(document).on('shown.bs.tab', '#main_panel', function(e) { $('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false'); }); + $(document).on('shiny:sessioninitialized', function() { -// Function to collapse navbar on mobile -function collapseNavbar() { - var navbar = $('.navbar-collapse'); - if (navbar.hasClass('show')) { - navbar.removeClass('show'); - $('.navbar-toggler').addClass('collapsed'); - $('.navbar-toggler').attr('aria-expanded', 'false'); - } + // Function to collapse navbar on mobile + function collapseNavbar() { + var navbar = $('.navbar-collapse'); + if (navbar.hasClass('show')) { + navbar.removeClass('show'); + $('.navbar-toggler').addClass('collapsed'); + $('.navbar-toggler').attr('aria-expanded', 'false'); + } } - // Add click event to navigation tabs - $(document).on('click', '.nav-link[data-bs-toggle=\"tab\"]', function() { + // Main approach: Handle clicks on nav elements + $(document).on('click', '.navbar-nav .nav-link, .dropdown-item', function(event) { + var $target = $(event.currentTarget); + + // Don't collapse if this is a dropdown toggle + if ($target.hasClass('dropdown-toggle')) { + return; + } + + // Don't collapse if this is inside a dropdown and the dropdown should stay open + if ($target.hasClass('nav-link') && $target.closest('.dropdown').length && + !$target.attr('data-bs-toggle')) { + return; + } + + // Collapse the navbar after a short delay setTimeout(collapseNavbar, 10); }); - // Also handle direct clicks on nav items - $(document).on('click', '.navbar-nav .nav-link', function() { - setTimeout(collapseNavbar, 10); + // Handle tab toggles specifically + $(document).on('click', '.nav-link[data-bs-toggle="tab"]', function() { + if (!$(this).hasClass('dropdown-toggle')) { + setTimeout(collapseNavbar, 10); + } + }); + + // Optional: Handle clicks outside the navbar to close it + $(document).on('click', function(event) { + var navbar = $('.navbar-collapse'); + + // Check if click is outside navbar and navbar is open + if (navbar.hasClass('show') && + !$(event.target).closest('.navbar').length) { + collapseNavbar(); + } }); }); From 898ba128568776572f2fb1726ceee48ddf2e2ab2 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Wed, 27 Aug 2025 11:13:17 +0200 Subject: [PATCH 4/7] chore: updated Overview submenu to Overview and filter --- NEWS.md | 8 ++++++-- R/hosted_version.R | 2 +- R/ui_elements.R | 3 ++- inst/apps/FreesearchR/app.R | 20 +++++++++++++++++--- 4 files changed, 26 insertions(+), 7 deletions(-) diff --git a/NEWS.md b/NEWS.md index fa4f8232..9380dedc 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,10 @@ -# FreesearchR 25.8.2 - DEV +# FreesearchR 25.8.2 -- *NEW* preparing to automatically only show relevant tabs to simplify interface. NOT IMPLEMENTED YET +- *NEW* Including the [NHANES](https://cran.r-project.org/web/packages/NHANES/refman/NHANES.html#NHANES) dataset for experimentation. + +- *BUG* Improved JS to correctly handle menu drop downs on mobile devices + +- *DOCS* Updated "Prepare > Overview" to "Prepare > Overview and filter" to better reflect options. # FreesearchR 25.8.1 diff --git a/R/hosted_version.R b/R/hosted_version.R index a5356f87..9f7d5c78 100644 --- a/R/hosted_version.R +++ b/R/hosted_version.R @@ -1 +1 @@ -hosted_version <- function()'v25.8.1-250808' +hosted_version <- function()'v25.8.1-250827' diff --git a/R/ui_elements.R b/R/ui_elements.R index 1ef55037..7f851c44 100644 --- a/R/ui_elements.R +++ b/R/ui_elements.R @@ -160,10 +160,11 @@ ui_elements <- function(selection) { icon = shiny::icon("pen-to-square"), value = "nav_prepare", bslib::nav_panel( - title = "Overview", + title = "Overview and filter", icon = shiny::icon("eye"), value = "nav_prepare_overview", tags$h3("Overview and filtering"), + # validation_ui("validation_col"), fluidRow( shiny::column( width = 9, diff --git a/inst/apps/FreesearchR/app.R b/inst/apps/FreesearchR/app.R index 1334db3c..750e1f89 100644 --- a/inst/apps/FreesearchR/app.R +++ b/inst/apps/FreesearchR/app.R @@ -3527,7 +3527,8 @@ dummy_Imports <- function() { cardx::all_of(), parameters::ci(), DT::addRow(), - bslib::accordion() + bslib::accordion(), + NHANES::NHANES() ) # https://github.com/hadley/r-pkgs/issues/828 } @@ -4046,7 +4047,7 @@ simple_snake <- function(data){ #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R ######## -hosted_version <- function()'v25.8.1-250808' +hosted_version <- function()'v25.8.1-250827' ######## @@ -8486,10 +8487,11 @@ ui_elements <- function(selection) { icon = shiny::icon("pen-to-square"), value = "nav_prepare", bslib::nav_panel( - title = "Overview", + title = "Overview and filter", icon = shiny::icon("eye"), value = "nav_prepare_overview", tags$h3("Overview and filtering"), + # validation_ui("validation_col"), fluidRow( shiny::column( width = 9, @@ -10963,6 +10965,18 @@ server <- function(input, output, session) { }) + # validation_server(id = "validation_col", + # data = purrr::map2( + # .x = validation_lib()[1], + # .y = list( + # list( + # x = + # reactive(rv$data), + # y = + # reactive(rv$data_variables) + # )), + # make_validation)) + ######### Data filter # IDEAFilter has the least cluttered UI, but might have a License issue # Consider using shinyDataFilter, though not on CRAN From fb8ed79ac94a3b2029d32c7c67e89f48f2064146 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Wed, 27 Aug 2025 12:36:22 +0200 Subject: [PATCH 5/7] updated docs --- CITATION.cff | 28 ++++ R/sysdata.rda | Bin 2676 -> 2676 bytes SESSION.md | 36 ++-- renv.lock | 452 +++++++++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 495 insertions(+), 21 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index d9fdbae7..1ae8f07e 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1002,6 +1002,34 @@ references: email: russell-lenth@uiowa.edu year: '2025' doi: 10.32614/CRAN.package.emmeans +- type: software + title: readxl + abstract: 'readxl: Read Excel Files' + notes: Imports + url: https://readxl.tidyverse.org + repository: https://CRAN.R-project.org/package=readxl + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + orcid: https://orcid.org/0000-0003-4757-117X + - family-names: Bryan + given-names: Jennifer + email: jenny@posit.co + orcid: https://orcid.org/0000-0002-6983-2759 + year: '2025' + doi: 10.32614/CRAN.package.readxl +- type: software + title: NHANES + abstract: 'NHANES: Data from the US National Health and Nutrition Examination Study' + notes: Imports + repository: https://CRAN.R-project.org/package=NHANES + authors: + - family-names: Pruim + given-names: Randall + email: rpruim@calvin.edu + year: '2025' + doi: 10.32614/CRAN.package.NHANES - type: software title: styler abstract: 'styler: Non-Invasive Pretty Printing of R Code' diff --git a/R/sysdata.rda b/R/sysdata.rda index c463a2ac13e3834a10ee66cad307cb30cf2debde..182c9aadc3b2832c7b3539ec33b9f56944b8beb2 100644 GIT binary patch literal 2676 zcmV-)3XAnZT4*^jL0KkKSwIB8fdCmE|HS|QXazw3|KNXb-@w2B|L{Nn0DuSq;0wPO z5aQwBdFUGKpcDao`{+;u=o$xxrXUCgh{R|~u#trssKhlgZ9r(#MvOHx)D2Yp0VPk; zN1-tqWYOr1nrIjakZ1rjX^> z4FCf`00E!|fB*n$L>dNwF$RI413&-(XaLaBpaLZ!CecsS(@Bw_+Ks8E(FU3t0004? 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See http://www.cdc.gov/nchs/nhanes.htm for details.", + "Depends": [ + "R (>= 3.0)" + ], + "Suggests": [ + "mosaic" + ], + "License": "GPL (>= 2)", + "LazyLoad": "yes", + "LazyData": "yes", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, "R.methodsS3": { "Package": "R.methodsS3", "Version": "1.8.2", @@ -689,9 +711,80 @@ "Maintainer": "Dirk Eddelbuettel ", "Repository": "CRAN" }, + "RcppEigen": { + "Package": "RcppEigen", + "Version": "0.3.4.0.2", + "Source": "Repository", + "Type": "Package", + "Title": "'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library", + "Date": "2024-08-23", + "Authors@R": "c(person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Yixuan\", \"Qiu\", role = \"aut\", comment = c(ORCID = \"0000-0003-0109-6692\")), person(\"Authors of\", \"Eigen\", role = \"cph\", comment = \"Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS\"))", + "Copyright": "See the file COPYRIGHTS for various Eigen copyright details", + "Description": "R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library. Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", + "License": "GPL (>= 2) | file LICENSE", + "LazyLoad": "yes", + "Depends": [ + "R (>= 3.6.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp (>= 0.11.0)", + "stats", + "utils" + ], + "Suggests": [ + "Matrix", + "inline", + "tinytest", + "pkgKitten", + "microbenchmark" + ], + "URL": "https://github.com/RcppCore/RcppEigen, https://dirk.eddelbuettel.com/code/rcpp.eigen.html", + "BugReports": "https://github.com/RcppCore/RcppEigen/issues", + "NeedsCompilation": "yes", + "Author": "Doug Bates [aut] (), Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), Yixuan Qiu [aut] (), Authors of Eigen [cph] (Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS)", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "Rdpack": { + "Package": "Rdpack", + "Version": "2.6.4", + "Source": "Repository", + "Type": "Package", + "Title": "Update and Manipulate Rd Documentation Objects", + "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), email = \"georgi.boshnakov@manchester.ac.uk\", comment = c(ORCID = \"0000-0003-2839-346X\")), person(given = \"Duncan\", family = \"Murdoch\", role = \"ctb\", email = \"murdoch.duncan@gmail.com\") )", + "Description": "Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.", + "URL": "https://geobosh.github.io/Rdpack/ (doc), https://github.com/GeoBosh/Rdpack (devel)", + "BugReports": "https://github.com/GeoBosh/Rdpack/issues", + "Depends": [ + "R (>= 2.15.0)", + "methods" + ], + "Imports": [ + "tools", + "utils", + "rbibutils (>= 1.3)" + ], + "Suggests": [ + "grDevices", + "testthat", + "rstudioapi", + "rprojroot", + "gbRd" + ], + "License": "GPL (>= 2)", + "LazyLoad": "yes", + "RoxygenNote": "7.1.1", + "NeedsCompilation": "no", + "Author": "Georgi N. Boshnakov [aut, cre] (), Duncan Murdoch [ctb]", + "Maintainer": "Georgi N. Boshnakov ", + "Repository": "CRAN" + }, "V8": { "Package": "V8", - "Version": "6.0.5", + "Version": "6.0.6", "Source": "Repository", "Type": "Package", "Title": "Embedded JavaScript and WebAssembly Engine for R", @@ -700,7 +793,7 @@ "License": "MIT + file LICENSE", "URL": "https://jeroen.r-universe.dev/V8", "BugReports": "https://github.com/jeroen/v8/issues", - "SystemRequirements": "V8 engine version 6+ is needed for ES6 and WASM support. On Linux you can build against libv8-dev (Debian) or v8-devel (Fedora). We also provide static libv8 binaries for most platforms, see the README for details.", + "SystemRequirements": "On Linux you can build against libv8-dev (Debian) or v8-devel (Fedora). We also provide static libv8 binaries for most platforms, see the README for details.", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "Imports": [ @@ -1083,6 +1176,33 @@ "Maintainer": "Martin Maechler ", "Repository": "CRAN" }, + "boot": { + "Package": "boot", + "Version": "1.3-31", + "Source": "Repository", + "Priority": "recommended", + "Date": "2024-08-28", + "Authors@R": "c(person(\"Angelo\", \"Canty\", role = \"aut\", email = \"cantya@mcmaster.ca\", comment = \"author of original code for S\"), person(\"Brian\", \"Ripley\", role = c(\"aut\", \"trl\"), email = \"ripley@stats.ox.ac.uk\", comment = \"conversion to R, maintainer 1999--2022, author of parallel support\"), person(\"Alessandra R.\", \"Brazzale\", role = c(\"ctb\", \"cre\"), email = \"brazzale@stat.unipd.it\", comment = \"minor bug fixes\"))", + "Maintainer": "Alessandra R. Brazzale ", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Description": "Functions and datasets for bootstrapping from the book \"Bootstrap Methods and Their Application\" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.", + "Title": "Bootstrap Functions (Originally by Angelo Canty for S)", + "Depends": [ + "R (>= 3.0.0)", + "graphics", + "stats" + ], + "Suggests": [ + "MASS", + "survival" + ], + "LazyData": "yes", + "ByteCompile": "yes", + "License": "Unlimited", + "NeedsCompilation": "no", + "Author": "Angelo Canty [aut] (author of original code for S), Brian Ripley [aut, trl] (conversion to R, maintainer 1999--2022, author of parallel support), Alessandra R. Brazzale [ctb, cre] (minor bug fixes)", + "Repository": "CRAN" + }, "brio": { "Package": "brio", "Version": "1.1.5", @@ -1814,6 +1934,23 @@ "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", "Repository": "CRAN" }, + "codetools": { + "Package": "codetools", + "Version": "0.2-20", + "Source": "Repository", + "Priority": "recommended", + "Author": "Luke Tierney ", + "Description": "Code analysis tools for R.", + "Title": "Code Analysis Tools for R", + "Depends": [ + "R (>= 2.1)" + ], + "Maintainer": "Luke Tierney ", + "URL": "https://gitlab.com/luke-tierney/codetools", + "License": "GPL", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, "colorspace": { "Package": "colorspace", "Version": "2.1-1", @@ -3146,6 +3283,41 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, + "foreach": { + "Package": "foreach", + "Version": "1.5.2", + "Source": "Repository", + "Type": "Package", + "Title": "Provides Foreach Looping Construct", + "Authors@R": "c(person(\"Folashade\", \"Daniel\", role=\"cre\", email=\"fdaniel@microsoft.com\"), person(\"Hong\", \"Ooi\", role=\"ctb\"), person(\"Rich\", \"Calaway\", role=\"ctb\"), person(\"Microsoft\", role=c(\"aut\", \"cph\")), person(\"Steve\", \"Weston\", role=\"aut\"))", + "Description": "Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.", + "License": "Apache License (== 2.0)", + "URL": "https://github.com/RevolutionAnalytics/foreach", + "BugReports": "https://github.com/RevolutionAnalytics/foreach/issues", + "Depends": [ + "R (>= 2.5.0)" + ], + "Imports": [ + "codetools", + "utils", + "iterators" + ], + "Suggests": [ + "randomForest", + "doMC", + "doParallel", + "testthat", + "knitr", + "rmarkdown" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "7.1.1", + "Collate": "'callCombine.R' 'foreach.R' 'do.R' 'foreach-ext.R' 'foreach-pkg.R' 'getDoPar.R' 'getDoSeq.R' 'getsyms.R' 'iter.R' 'nextElem.R' 'onLoad.R' 'setDoPar.R' 'setDoSeq.R' 'times.R' 'utils.R'", + "NeedsCompilation": "no", + "Author": "Folashade Daniel [cre], Hong Ooi [ctb], Rich Calaway [ctb], Microsoft [aut, cph], Steve Weston [aut]", + "Maintainer": "Folashade Daniel ", + "Repository": "CRAN" + }, "foreign": { "Package": "foreign", "Version": "0.8-90", @@ -4494,6 +4666,29 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, + "iterators": { + "Package": "iterators", + "Version": "1.0.14", + "Source": "Repository", + "Type": "Package", + "Title": "Provides Iterator Construct", + "Authors@R": "c(person(\"Folashade\", \"Daniel\", role=\"cre\", email=\"fdaniel@microsoft.com\"), person(\"Revolution\", \"Analytics\", role=c(\"aut\", \"cph\")), person(\"Steve\", \"Weston\", role=\"aut\"))", + "Description": "Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.", + "URL": "https://github.com/RevolutionAnalytics/iterators", + "Depends": [ + "R (>= 2.5.0)", + "utils" + ], + "Suggests": [ + "RUnit", + "foreach" + ], + "License": "Apache License (== 2.0)", + "NeedsCompilation": "no", + "Author": "Folashade Daniel [cre], Revolution Analytics [aut, cph], Steve Weston [aut]", + "Maintainer": "Folashade Daniel ", + "Repository": "CRAN" + }, "jquerylib": { "Package": "jquerylib", "Version": "0.1.4", @@ -4911,6 +5106,70 @@ "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, + "lme4": { + "Package": "lme4", + "Version": "1.1-37", + "Source": "Repository", + "Title": "Linear Mixed-Effects Models using 'Eigen' and S4", + "Authors@R": "c( person(\"Douglas\",\"Bates\", role=\"aut\", comment=c(ORCID=\"0000-0001-8316-9503\")), person(\"Martin\",\"Maechler\", role=\"aut\", comment=c(ORCID=\"0000-0002-8685-9910\")), person(\"Ben\",\"Bolker\",email=\"bbolker+lme4@gmail.com\", role=c(\"aut\",\"cre\"), comment=c(ORCID=\"0000-0002-2127-0443\")), person(\"Steven\",\"Walker\",role=\"aut\", comment=c(ORCID=\"0000-0002-4394-9078\")), person(\"Rune Haubo Bojesen\",\"Christensen\", role=\"ctb\", comment=c(ORCID=\"0000-0002-4494-3399\")), person(\"Henrik\",\"Singmann\", role=\"ctb\", comment=c(ORCID=\"0000-0002-4842-3657\")), person(\"Bin\", \"Dai\", role=\"ctb\"), person(\"Fabian\", \"Scheipl\", role=\"ctb\", comment=c(ORCID=\"0000-0001-8172-3603\")), person(\"Gabor\", \"Grothendieck\", role=\"ctb\"), person(\"Peter\", \"Green\", role=\"ctb\", comment=c(ORCID=\"0000-0002-0238-9852\")), person(\"John\", \"Fox\", role=\"ctb\"), person(\"Alexander\", \"Bauer\", role=\"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role=c(\"ctb\",\"cph\"), comment=c(ORCID=\"0000-0002-9101-3362\", \"shared copyright on simulate.formula\")), person(\"Emi\", \"Tanaka\", role = \"ctb\", comment = c(ORCID=\"0000-0002-1455-259X\")), person(\"Mikael\", \"Jagan\", role = \"ctb\", comment = c(ORCID=\"0000-0002-3542-2938\")), person(\"Ross D.\", \"Boylan\", email=\"ross.boylan@ucsf.edu\", role=(\"ctb\"), comment = c(ORCID=\"0009-0003-4123-8090\")) )", + "Description": "Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' \"glue\".", + "Depends": [ + "R (>= 3.6.0)", + "Matrix", + "methods", + "stats" + ], + "LinkingTo": [ + "Rcpp (>= 0.10.5)", + "RcppEigen (>= 0.3.3.9.4)", + "Matrix (>= 1.2-3)" + ], + "Imports": [ + "graphics", + "grid", + "splines", + "utils", + "parallel", + "MASS", + "lattice", + "boot", + "nlme (>= 3.1-123)", + "minqa (>= 1.1.15)", + "nloptr (>= 1.0.4)", + "reformulas (>= 0.3.0)" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "MEMSS", + "testthat (>= 0.8.1)", + "ggplot2", + "mlmRev", + "optimx (>= 2013.8.6)", + "gamm4", + "pbkrtest", + "HSAUR3", + "numDeriv", + "car", + "dfoptim", + "mgcv", + "statmod", + "rr2", + "semEff", + "tibble", + "merDeriv" + ], + "VignetteBuilder": "knitr", + "LazyData": "yes", + "License": "GPL (>= 2)", + "URL": "https://github.com/lme4/lme4/", + "BugReports": "https://github.com/lme4/lme4/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Douglas Bates [aut] (), Martin Maechler [aut] (), Ben Bolker [aut, cre] (), Steven Walker [aut] (), Rune Haubo Bojesen Christensen [ctb] (), Henrik Singmann [ctb] (), Bin Dai [ctb], Fabian Scheipl [ctb] (), Gabor Grothendieck [ctb], Peter Green [ctb] (), John Fox [ctb], Alexander Bauer [ctb], Pavel N. Krivitsky [ctb, cph] (, shared copyright on simulate.formula), Emi Tanaka [ctb] (), Mikael Jagan [ctb] (), Ross D. Boylan [ctb] ()", + "Maintainer": "Ben Bolker ", + "Repository": "CRAN" + }, "lmtest": { "Package": "lmtest", "Version": "0.9-40", @@ -5136,6 +5395,28 @@ "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, + "minqa": { + "Package": "minqa", + "Version": "1.2.8", + "Source": "Repository", + "Type": "Package", + "Title": "Derivative-Free Optimization Algorithms by Quadratic Approximation", + "Authors@R": "c(person(given = \"Douglas\", family = \"Bates\", role = \"aut\"), person(given = c(\"Katharine\", \"M.\"), family = \"Mullen\", role = c(\"aut\", \"cre\"), email = \"katharine.mullen@stat.ucla.edu\"), person(given = c(\"John\", \"C.\"), family = \"Nash\", role = \"aut\"), person(given = \"Ravi\", family = \"Varadhan\", role = \"aut\"))", + "Maintainer": "Katharine M. Mullen ", + "Description": "Derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.", + "License": "GPL-2", + "URL": "http://optimizer.r-forge.r-project.org", + "Imports": [ + "Rcpp (>= 0.9.10)" + ], + "LinkingTo": [ + "Rcpp" + ], + "SystemRequirements": "GNU make", + "NeedsCompilation": "yes", + "Repository": "CRAN", + "Author": "Douglas Bates [aut], Katharine M. Mullen [aut, cre], John C. Nash [aut], Ravi Varadhan [aut]" + }, "minty": { "Package": "minty", "Version": "0.0.5", @@ -5267,6 +5548,31 @@ "Author": "Dominique Makowski [aut, cre] (ORCID: ), Daniel Lüdecke [aut] (ORCID: ), Mattan S. Ben-Shachar [aut] (ORCID: ), Indrajeet Patil [aut] (ORCID: ), Rémi Thériault [aut] (ORCID: )", "Repository": "CRAN" }, + "mvtnorm": { + "Package": "mvtnorm", + "Version": "1.3-3", + "Source": "Repository", + "Title": "Multivariate Normal and t Distributions", + "Date": "2025-01-09", + "Authors@R": "c(person(\"Alan\", \"Genz\", role = \"aut\"), person(\"Frank\", \"Bretz\", role = \"aut\"), person(\"Tetsuhisa\", \"Miwa\", role = \"aut\"), person(\"Xuefei\", \"Mi\", role = \"aut\"), person(\"Friedrich\", \"Leisch\", role = \"ctb\"), person(\"Fabian\", \"Scheipl\", role = \"ctb\"), person(\"Bjoern\", \"Bornkamp\", role = \"ctb\", comment = c(ORCID = \"0000-0002-6294-8185\")), person(\"Martin\", \"Maechler\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Torsten\", \"Hothorn\", role = c(\"aut\", \"cre\"), email = \"Torsten.Hothorn@R-project.org\", comment = c(ORCID = \"0000-0001-8301-0471\")))", + "Description": "Computes multivariate normal and t probabilities, quantiles, random deviates, and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae parameterised by Cholesky factors of covariance or precision matrices are implemented for interval-censored and exact data, or a mix thereof. Score functions for these log-likelihoods are available. A class representing multiple lower triangular matrices and corresponding methods are part of this package.", + "Imports": [ + "stats" + ], + "Depends": [ + "R(>= 3.5.0)" + ], + "Suggests": [ + "qrng", + "numDeriv" + ], + "License": "GPL-2", + "URL": "http://mvtnorm.R-forge.R-project.org", + "NeedsCompilation": "yes", + "Author": "Alan Genz [aut], Frank Bretz [aut], Tetsuhisa Miwa [aut], Xuefei Mi [aut], Friedrich Leisch [ctb], Fabian Scheipl [ctb], Bjoern Bornkamp [ctb] (), Martin Maechler [ctb] (), Torsten Hothorn [aut, cre] ()", + "Maintainer": "Torsten Hothorn ", + "Repository": "CRAN" + }, "nlme": { "Package": "nlme", "Version": "3.1-168", @@ -5301,6 +5607,33 @@ "Maintainer": "R Core Team ", "Repository": "CRAN" }, + "nloptr": { + "Package": "nloptr", + "Version": "2.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "R Interface to NLopt", + "Authors@R": "c(person(\"Jelmer\", \"Ypma\", role = \"aut\", email = \"uctpjyy@ucl.ac.uk\"), person(c(\"Steven\", \"G.\"), \"Johnson\", role = \"aut\", comment = \"author of the NLopt C library\"), person(\"Aymeric\", \"Stamm\", role = c(\"ctb\", \"cre\"), email = \"aymeric.stamm@cnrs.fr\", comment = c(ORCID = \"0000-0002-8725-3654\")), person(c(\"Hans\", \"W.\"), \"Borchers\", role = \"ctb\", email = \"hwborchers@googlemail.com\"), person(\"Dirk\", \"Eddelbuettel\", role = \"ctb\", email = \"edd@debian.org\"), person(\"Brian\", \"Ripley\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Kurt\", \"Hornik\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Julien\", \"Chiquet\", role = \"ctb\"), person(\"Avraham\", \"Adler\", role = \"ctb\", email = \"Avraham.Adler@gmail.com\", comment = c(ORCID = \"0000-0002-3039-0703\")), person(\"Xiongtao\", \"Dai\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\", email = \"jeroen@berkeley.edu\"), person(\"Tomas\", \"Kalibera\", role = \"ctb\"), person(\"Mikael\", \"Jagan\", role = \"ctb\"))", + "Description": "Solve optimization problems using an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See for more information on the available algorithms. Building from included sources requires 'CMake'. On Linux and 'macOS', if a suitable system build of NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from included sources via 'CMake'. On Windows, NLopt is obtained through 'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for 'R >= 4.2.0'.", + "License": "LGPL (>= 3)", + "SystemRequirements": "cmake (>= 3.2.0) which is used only on Linux or macOS systems when no system build of nlopt (>= 2.7.0) can be found.", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Suggests": [ + "knitr", + "rmarkdown", + "covr", + "tinytest" + ], + "VignetteBuilder": "knitr", + "URL": "https://github.com/astamm/nloptr, https://astamm.github.io/nloptr/", + "BugReports": "https://github.com/astamm/nloptr/issues", + "NeedsCompilation": "yes", + "UseLTO": "yes", + "Author": "Jelmer Ypma [aut], Steven G. Johnson [aut] (author of the NLopt C library), Aymeric Stamm [ctb, cre] (), Hans W. Borchers [ctb], Dirk Eddelbuettel [ctb], Brian Ripley [ctb] (build process on multiple OS), Kurt Hornik [ctb] (build process on multiple OS), Julien Chiquet [ctb], Avraham Adler [ctb] (), Xiongtao Dai [ctb], Jeroen Ooms [ctb], Tomas Kalibera [ctb], Mikael Jagan [ctb]", + "Maintainer": "Aymeric Stamm ", + "Repository": "CRAN" + }, "nnet": { "Package": "nnet", "Version": "7.3-20", @@ -5326,6 +5659,25 @@ "Maintainer": "Brian Ripley ", "Repository": "CRAN" }, + "numDeriv": { + "Package": "numDeriv", + "Version": "2016.8-1.1", + "Source": "Repository", + "Title": "Accurate Numerical Derivatives", + "Description": "Methods for calculating (usually) accurate numerical first and second order derivatives. Accurate calculations are done using 'Richardson''s' extrapolation or, when applicable, a complex step derivative is available. A simple difference method is also provided. Simple difference is (usually) less accurate but is much quicker than 'Richardson''s' extrapolation and provides a useful cross-check. Methods are provided for real scalar and vector valued functions.", + "Depends": [ + "R (>= 2.11.1)" + ], + "LazyLoad": "yes", + "ByteCompile": "yes", + "License": "GPL-2", + "Copyright": "2006-2011, Bank of Canada. 2012-2016, Paul Gilbert", + "Author": "Paul Gilbert and Ravi Varadhan", + "Maintainer": "Paul Gilbert ", + "URL": "http://optimizer.r-forge.r-project.org/", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, "officer": { "Package": "officer", "Version": "0.6.10", @@ -6665,6 +7017,34 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, + "rbibutils": { + "Package": "rbibutils", + "Version": "2.3", + "Source": "Repository", + "Type": "Package", + "Title": "Read 'Bibtex' Files and Convert Between Bibliography Formats", + "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), \t email = \"georgi.boshnakov@manchester.ac.uk\", comment = \"R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)\" ), person(given = \"Chris\", family = \"Putman\", role = \"aut\", comment = \"src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/\"), person(given = \"Richard\", family = \"Mathar\", role = \"ctb\", comment = \"src/addsout.c\"), person(given = \"Johannes\", family = \"Wilm\", role = \"ctb\", comment = \"src/biblatexin.c, src/bltypes.c\"), person(\"R Core Team\", role = \"ctb\", comment = \"base R's bibentry and bibstyle implementation\") )", + "Description": "Read and write 'Bibtex' files. Convert between bibliography formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam . Supports all bibliography formats and character encodings implemented in 'bibutils'.", + "License": "GPL-2", + "URL": "https://geobosh.github.io/rbibutils/ (doc), https://github.com/GeoBosh/rbibutils (devel)", + "BugReports": "https://github.com/GeoBosh/rbibutils/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Imports": [ + "utils", + "tools" + ], + "Suggests": [ + "testthat" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Config/Needs/memcheck": "devtools, rcmdcheck", + "Author": "Georgi N. Boshnakov [aut, cre] (R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)), Chris Putman [aut] (src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/), Richard Mathar [ctb] (src/addsout.c), Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c), R Core Team [ctb] (base R's bibentry and bibstyle implementation)", + "Maintainer": "Georgi N. Boshnakov ", + "Repository": "CRAN" + }, "reactR": { "Package": "reactR", "Version": "0.6.1", @@ -6842,6 +7222,74 @@ "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, + "readxl": { + "Package": "readxl", + "Version": "1.4.5", + "Source": "Repository", + "Title": "Read Excel Files", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = \"Copyright holder of all R code and all C/C++ code without explicit copyright attribution\"), person(\"Marcin\", \"Kalicinski\", role = c(\"ctb\", \"cph\"), comment = \"Author of included RapidXML code\"), person(\"Komarov Valery\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Christophe Leitienne\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Bob Colbert\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"David Hoerl\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Evan Miller\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\") )", + "Description": "Import excel files into R. Supports '.xls' via the embedded 'libxls' C library and '.xlsx' via the embedded 'RapidXML' C++ library . Works on Windows, Mac and Linux without external dependencies.", + "License": "MIT + file LICENSE", + "URL": "https://readxl.tidyverse.org, https://github.com/tidyverse/readxl", + "BugReports": "https://github.com/tidyverse/readxl/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cellranger", + "tibble (>= 2.0.1)", + "utils" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "testthat (>= 3.1.6)", + "withr" + ], + "LinkingTo": [ + "cpp11 (>= 0.4.0)", + "progress" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate, tidyverse", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Note": "libxls v1.6.3 c199d13", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Posit, PBC [cph, fnd] (Copyright holder of all R code and all C/C++ code without explicit copyright attribution), Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Komarov Valery [ctb, cph] (Author of included libxls code), Christophe Leitienne [ctb, cph] (Author of included libxls code), Bob Colbert [ctb, cph] (Author of included libxls code), David Hoerl [ctb, cph] (Author of included libxls code), Evan Miller [ctb, cph] (Author of included libxls code)", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "reformulas": { + "Package": "reformulas", + "Version": "0.4.1", + "Source": "Repository", + "Title": "Machinery for Processing Random Effect Formulas", + "Authors@R": "person(given = \"Ben\", family = \"Bolker\", role = c(\"aut\", \"cre\"), email = \"bolker@mcmaster.ca\", comment=c(ORCID=\"0000-0002-2127-0443\"))", + "Description": "Takes formulas including random-effects components (formatted as in 'lme4', 'glmmTMB', etc.) and processes them. Includes various helper functions.", + "URL": "https://github.com/bbolker/reformulas", + "License": "GPL-3", + "Encoding": "UTF-8", + "Imports": [ + "stats", + "methods", + "Matrix", + "Rdpack" + ], + "RdMacros": "Rdpack", + "Suggests": [ + "lme4", + "tinytest", + "glmmTMB" + ], + "RoxygenNote": "7.3.2.9000", + "NeedsCompilation": "no", + "Author": "Ben Bolker [aut, cre] (ORCID: )", + "Maintainer": "Ben Bolker ", + "Repository": "CRAN" + }, "rematch": { "Package": "rematch", "Version": "2.0.0", From 42cc9e7660e5d7b6493630560ac372bda45324c3 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Wed, 27 Aug 2025 12:45:02 +0200 Subject: [PATCH 6/7] ready for docker update --- app_docker/Dockerfile | 2 +- app_docker/app.R | 20 +++++- app_docker/renv.lock | 130 +++++++++++++++++++++++++------------- app_docker/www/scripts.js | 54 ++++++++++++---- 4 files changed, 146 insertions(+), 60 deletions(-) diff --git a/app_docker/Dockerfile b/app_docker/Dockerfile index 877787fd..a4f31bcf 100644 --- a/app_docker/Dockerfile +++ b/app_docker/Dockerfile @@ -3,7 +3,7 @@ RUN apt-get update -y && apt-get install -y cmake make libcurl4-openssl-dev lib RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/ RUN echo "options(renv.config.pak.enabled = FALSE, repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site RUN R -e 'install.packages("remotes")' -RUN R -e 'remotes::install_version("renv", version = "1.1.4")' +RUN R -e 'remotes::install_version("renv", version = "1.1.5")' COPY renv.lock renv.lock RUN --mount=type=cache,id=renv-cache,target=/root/.cache/R/renv R -e 'renv::restore()' WORKDIR /srv/shiny-server/ diff --git a/app_docker/app.R b/app_docker/app.R index ac51ad58..b57e14a4 100644 --- a/app_docker/app.R +++ b/app_docker/app.R @@ -3527,7 +3527,8 @@ dummy_Imports <- function() { cardx::all_of(), parameters::ci(), DT::addRow(), - bslib::accordion() + bslib::accordion(), + NHANES::NHANES() ) # https://github.com/hadley/r-pkgs/issues/828 } @@ -4046,7 +4047,7 @@ simple_snake <- function(data){ #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R ######## -hosted_version <- function()'v25.8.1-250808' +hosted_version <- function()'v25.8.1-250827' ######## @@ -8486,10 +8487,11 @@ ui_elements <- function(selection) { icon = shiny::icon("pen-to-square"), value = "nav_prepare", bslib::nav_panel( - title = "Overview", + title = "Overview and filter", icon = shiny::icon("eye"), value = "nav_prepare_overview", tags$h3("Overview and filtering"), + # validation_ui("validation_col"), fluidRow( shiny::column( width = 9, @@ -10964,6 +10966,18 @@ server <- function(input, output, session) { }) + # validation_server(id = "validation_col", + # data = purrr::map2( + # .x = validation_lib()[1], + # .y = list( + # list( + # x = + # reactive(rv$data), + # y = + # reactive(rv$data_variables) + # )), + # make_validation)) + ######### Data filter # IDEAFilter has the least cluttered UI, but might have a License issue # Consider using shinyDataFilter, though not on CRAN diff --git a/app_docker/renv.lock b/app_docker/renv.lock index 57077d00..0735cef6 100644 --- a/app_docker/renv.lock +++ b/app_docker/renv.lock @@ -4,16 +4,16 @@ "Repositories": [ { "Name": "CRAN", - "URL": "https://cloud.r-project.org" + "URL": "https://mirrors.dotsrc.org/cran" } ] }, "Packages": { "DEoptimR": { "Package": "DEoptimR", - "Version": "1.1-3-1", + "Version": "1.1-4", "Source": "Repository", - "Date": "2024-11-23", + "Date": "2025-07-27", "Title": "Differential Evolution Optimization in Pure R", "Authors@R": "c( person(c(\"Eduardo\", \"L. T.\"), \"Conceicao\", role = c(\"aut\", \"cre\"), email = \"mail@eduardoconceicao.org\"), person(\"Martin\", \"Maechler\", role = \"ctb\", email = \"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) )", "URL": "svn://svn.r-forge.r-project.org/svnroot/robustbase/pkg/DEoptimR", @@ -25,12 +25,12 @@ "robustbase" ], "License": "GPL (>= 2)", - "Author": "Eduardo L. T. Conceicao [aut, cre], Martin Maechler [ctb] ()", + "Author": "Eduardo L. T. Conceicao [aut, cre], Martin Maechler [ctb] (ORCID: )", "Maintainer": "Eduardo L. T. Conceicao ", "Repository": "CRAN", "Repository/R-Forge/Project": "robustbase", - "Repository/R-Forge/Revision": "1008", - "Repository/R-Forge/DateTimeStamp": "2024-11-23 19:13:45", + "Repository/R-Forge/Revision": "1009", + "Repository/R-Forge/DateTimeStamp": "2025-07-27 18:16:52", "NeedsCompilation": "no" }, "DHARMa": { @@ -241,7 +241,7 @@ }, "IDEAFilter": { "Package": "IDEAFilter", - "Version": "0.2.0", + "Version": "0.2.1", "Source": "Repository", "Type": "Package", "Title": "Agnostic, Idiomatic Data Filter Module for Shiny", @@ -251,7 +251,7 @@ "URL": "https://biogen-inc.github.io/IDEAFilter/, https://github.com/Biogen-Inc/IDEAFilter", "BugReports": "https://github.com/Biogen-Inc/IDEAFilter/issues", "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "Imports": [ "crayon", "ggplot2", @@ -276,7 +276,7 @@ "R (>= 2.10)" ], "NeedsCompilation": "no", - "Author": "Aaron Clark [aut, cre] (), Jeff Thompson [aut], Doug Kelkhoff [ctb, cph] (Author of shinyDataFilter), Maya Gans [ctb], SortableJS contributors [ctb] (SortableJS library), Biogen [cph]", + "Author": "Aaron Clark [aut, cre] (ORCID: ), Jeff Thompson [aut], Doug Kelkhoff [ctb, cph] (Author of shinyDataFilter), Maya Gans [ctb], SortableJS contributors [ctb] (SortableJS library), Biogen [cph]", "Maintainer": "Aaron Clark ", "Repository": "CRAN" }, @@ -386,6 +386,28 @@ "Maintainer": "Martin Maechler ", "Repository": "CRAN" }, + "NHANES": { + "Package": "NHANES", + "Version": "2.1.0", + "Source": "Repository", + "Type": "Package", + "Title": "Data from the US National Health and Nutrition Examination Study", + "Date": "2015-07-02", + "Author": "Randall Pruim ", + "Maintainer": "Randall Pruim ", + "Description": "Body Shape and related measurements from the US National Health and Nutrition Examination Survey (NHANES, 1999-2004). See http://www.cdc.gov/nchs/nhanes.htm for details.", + "Depends": [ + "R (>= 3.0)" + ], + "Suggests": [ + "mosaic" + ], + "License": "GPL (>= 2)", + "LazyLoad": "yes", + "LazyData": "yes", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, "R.methodsS3": { "Package": "R.methodsS3", "Version": "1.8.2", @@ -575,7 +597,7 @@ }, "REDCapR": { "Package": "REDCapR", - "Version": "1.4.0", + "Version": "1.5.0", "Source": "Repository", "Title": "Interaction Between R and REDCap", "Description": "Encapsulates functions to streamline calls from R to the REDCap API. REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.", @@ -583,7 +605,7 @@ "URL": "https://ouhscbbmc.github.io/REDCapR/, https://github.com/OuhscBbmc/REDCapR, https://www.ouhsc.edu/bbmc/, https://projectredcap.org", "BugReports": "https://github.com/OuhscBbmc/REDCapR/issues", "Depends": [ - "R(>= 3.5.0)" + "R (>= 4.1.0)" ], "Imports": [ "checkmate (>= 2.0)", @@ -618,7 +640,7 @@ "Config/testthat/edition": "3", "Language": "en-US", "NeedsCompilation": "no", - "Author": "Will Beasley [aut, cre] (), David Bard [ctb] (), Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb] (), Benjamin Nutter [ctb], Andrew Peters [ctb] (), Hao Zhu [ctb] (), Janosch Linkersdörfer [ctb] (), Jonathan Mang [ctb] (), Felix Torres [ctb], Philip Chase [ctb] (), Victor Castro [ctb] (), Greg Botwin [ctb], Stephan Kadauke [ctb] (), Ezra Porter [ctb] (), Matthew Schuelke [ctb] ()", + "Author": "Will Beasley [aut, cre] (ORCID: ), David Bard [ctb] (ORCID: ), Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb] (ORCID: ), Benjamin Nutter [ctb], Andrew Peters [ctb] (ORCID: ), Hao Zhu [ctb] (ORCID: ), Janosch Linkersdörfer [ctb] (ORCID: ), Jonathan Mang [ctb] (ORCID: ), Felix Torres [ctb], Philip Chase [ctb] (ORCID: ), Victor Castro [ctb] (ORCID: ), Greg Botwin [ctb], Stephan Kadauke [ctb] (ORCID: ), Ezra Porter [ctb] (ORCID: ), Matthew Schuelke [ctb] (ORCID: )", "Maintainer": "Will Beasley ", "Repository": "CRAN" }, @@ -762,7 +784,7 @@ }, "V8": { "Package": "V8", - "Version": "6.0.4", + "Version": "6.0.6", "Source": "Repository", "Type": "Package", "Title": "Embedded JavaScript and WebAssembly Engine for R", @@ -771,7 +793,7 @@ "License": "MIT + file LICENSE", "URL": "https://jeroen.r-universe.dev/V8", "BugReports": "https://github.com/jeroen/v8/issues", - "SystemRequirements": "V8 engine version 6+ is needed for ES6 and WASM support. On Linux you can build against libv8-dev (Debian) or v8-devel (Fedora). We also provide static libv8 binaries for most platforms, see the README for details.", + "SystemRequirements": "On Linux you can build against libv8-dev (Debian) or v8-devel (Fedora). We also provide static libv8 binaries for most platforms, see the README for details.", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "Imports": [ @@ -1209,17 +1231,17 @@ }, "broom": { "Package": "broom", - "Version": "1.0.8", + "Version": "1.0.9", "Source": "Repository", "Type": "Package", "Title": "Convert Statistical Objects into Tidy Tibbles", - "Authors@R": "c(person(given = \"David\", family = \"Robinson\", role = \"aut\", email = \"admiral.david@gmail.com\"), person(given = \"Alex\", family = \"Hayes\", role = \"aut\", email = \"alexpghayes@gmail.com\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(given = \"Simon\", family = \"Couch\", role = c(\"aut\", \"cre\"), email = \"simon.couch@posit.co\", comment = c(ORCID = \"0000-0001-5676-5107\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"ctb\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = 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\"Shiro\", family = \"Kuriwaki\", role = \"ctb\", email = \"shirokuriwaki@gmail.com\", comment = c(ORCID = \"0000-0002-5687-2647\")), person(given = \"Lukas\", family = \"Wallrich\", role = \"ctb\", email = \"lukas.wallrich@gmail.com\", comment = c(ORCID = \"0000-0003-2121-5177\")), person(given = \"James\", family = \"Martherus\", role = \"ctb\", email = \"james@martherus.com\", comment = c(ORCID = \"0000-0002-8285-3300\")), person(given = \"Chuliang\", family = \"Xiao\", role = \"ctb\", email = \"cxiao@umich.edu\", comment = c(ORCID = \"0000-0002-8466-9398\")), person(given = \"Joseph\", family = \"Larmarange\", role = \"ctb\", email = \"joseph@larmarange.net\"), person(given = \"Max\", family = \"Kuhn\", role = \"ctb\", email = \"max@posit.co\"), person(given = \"Michal\", family = \"Bojanowski\", role = \"ctb\", email = \"michal2992@gmail.com\"), person(given = \"Hakon\", family = \"Malmedal\", role = \"ctb\", email = \"hmalmedal@gmail.com\"), person(given = \"Clara\", family = \"Wang\", role = \"ctb\"), person(given = \"Sergio\", family = \"Oller\", role = \"ctb\", email = \"sergioller@gmail.com\"), person(given = \"Luke\", family = \"Sonnet\", role = \"ctb\", email = \"luke.sonnet@gmail.com\"), person(given = \"Jim\", family = \"Hester\", role = \"ctb\", email = \"jim.hester@posit.co\"), person(given = \"Ben\", family = \"Schneider\", role = \"ctb\", email = \"benjamin.julius.schneider@gmail.com\"), person(given = \"Bernie\", family = \"Gray\", role = \"ctb\", email = \"bfgray3@gmail.com\", comment = c(ORCID = \"0000-0001-9190-6032\")), person(given = \"Mara\", family = \"Averick\", role = \"ctb\", email = \"mara@posit.co\"), person(given = \"Aaron\", family = \"Jacobs\", role = \"ctb\", email = \"atheriel@gmail.com\"), person(given = \"Andreas\", family = \"Bender\", role = \"ctb\", email = \"bender.at.R@gmail.com\"), person(given = \"Sven\", family = \"Templer\", role = \"ctb\", email = \"sven.templer@gmail.com\"), person(given = \"Paul-Christian\", family = \"Buerkner\", role = \"ctb\", email = \"paul.buerkner@gmail.com\"), person(given = \"Matthew\", family = \"Kay\", role = \"ctb\", email = \"mjskay@umich.edu\"), person(given = \"Erwan\", family = \"Le Pennec\", role = \"ctb\", email = \"lepennec@gmail.com\"), person(given = \"Johan\", family = \"Junkka\", role = \"ctb\", email = \"johan.junkka@umu.se\"), person(given = \"Hao\", family = \"Zhu\", role = \"ctb\", email = \"haozhu233@gmail.com\"), person(given = \"Benjamin\", family = \"Soltoff\", role = \"ctb\", email = \"soltoffbc@uchicago.edu\"), person(given = \"Zoe\", family = \"Wilkinson Saldana\", role = \"ctb\", email = \"zoewsaldana@gmail.com\"), person(given = \"Tyler\", family = \"Littlefield\", role = \"ctb\", email = \"tylurp1@gmail.com\"), person(given = \"Charles T.\", family = \"Gray\", role = \"ctb\", email = \"charlestigray@gmail.com\"), person(given = \"Shabbh E.\", family = \"Banks\", role = \"ctb\"), person(given = \"Serina\", family = \"Robinson\", role = \"ctb\", email = \"robi0916@umn.edu\"), person(given = \"Roger\", family = \"Bivand\", role = \"ctb\", email = \"Roger.Bivand@nhh.no\"), person(given = \"Riinu\", family = \"Ots\", role = \"ctb\", email = \"riinuots@gmail.com\"), person(given = \"Nicholas\", family = \"Williams\", role = \"ctb\", email = \"ntwilliams.personal@gmail.com\"), person(given = \"Nina\", family = \"Jakobsen\", role = \"ctb\"), person(given = \"Michael\", family = \"Weylandt\", role = \"ctb\", email = \"michael.weylandt@gmail.com\"), person(given = \"Lisa\", family = \"Lendway\", role = \"ctb\", email = \"llendway@macalester.edu\"), person(given = \"Karl\", family = \"Hailperin\", role = \"ctb\", email = \"khailper@gmail.com\"), person(given = \"Josue\", family = \"Rodriguez\", role = \"ctb\", email = \"jerrodriguez@ucdavis.edu\"), person(given = \"Jenny\", family = \"Bryan\", role = \"ctb\", email = \"jenny@posit.co\"), person(given = \"Chris\", family = \"Jarvis\", role = \"ctb\", email = \"Christopher1.jarvis@gmail.com\"), person(given = \"Greg\", family = \"Macfarlane\", role = \"ctb\", email = \"gregmacfarlane@gmail.com\"), person(given = \"Brian\", family = \"Mannakee\", role = \"ctb\", email = \"bmannakee@gmail.com\"), person(given = \"Drew\", family = \"Tyre\", role = \"ctb\", email = \"atyre2@unl.edu\"), person(given = \"Shreyas\", family = \"Singh\", role = \"ctb\", email = \"shreyas.singh.298@gmail.com\"), person(given = \"Laurens\", family = \"Geffert\", role = \"ctb\", email = \"laurensgeffert@gmail.com\"), person(given = \"Hong\", family = \"Ooi\", role = \"ctb\", email = \"hongooi@microsoft.com\"), person(given = \"Henrik\", family = \"Bengtsson\", role = \"ctb\", email = \"henrikb@braju.com\"), person(given = \"Eduard\", family = \"Szocs\", role = \"ctb\", email = \"eduardszoecs@gmail.com\"), person(given = \"David\", family = \"Hugh-Jones\", role = \"ctb\", email = \"davidhughjones@gmail.com\"), person(given = \"Matthieu\", family = \"Stigler\", role = \"ctb\", email = \"Matthieu.Stigler@gmail.com\"), person(given = \"Hugo\", family = \"Tavares\", role = \"ctb\", email = \"hm533@cam.ac.uk\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(given = \"R. Willem\", family = \"Vervoort\", role = \"ctb\", email = \"Willemvervoort@gmail.com\"), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"ctb\", email = \"brenton@wiernik.org\"), person(given = \"Josh\", family = \"Yamamoto\", role = \"ctb\", email = \"joshuayamamoto5@gmail.com\"), person(given = \"Jasme\", family = \"Lee\", role = \"ctb\"), person(given = \"Taren\", family = \"Sanders\", role = \"ctb\", email = \"taren.sanders@acu.edu.au\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(given = \"Ilaria\", family = \"Prosdocimi\", role = \"ctb\", email = \"prosdocimi.ilaria@gmail.com\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(given = \"Daniel D.\", family = \"Sjoberg\", role = \"ctb\", email = \"danield.sjoberg@gmail.com\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(given = \"Alex\", family = \"Reinhart\", role = \"ctb\", email = \"areinhar@stat.cmu.edu\", comment = c(ORCID = \"0000-0002-6658-514X\")))", - "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", + "Authors@R": "c( person(\"David\", \"Robinson\", , \"admiral.david@gmail.com\", role = \"aut\"), person(\"Alex\", \"Hayes\", , \"alexpghayes@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(\"Simon\", \"Couch\", , \"simon.couch@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5676-5107\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(\"Indrajeet\", \"Patil\", , \"patilindrajeet.science@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(\"Derek\", \"Chiu\", , \"dchiu@bccrc.ca\", role = \"ctb\"), person(\"Matthieu\", \"Gomez\", , \"mattg@princeton.edu\", role = \"ctb\"), person(\"Boris\", \"Demeshev\", , \"boris.demeshev@gmail.com\", role = \"ctb\"), person(\"Dieter\", \"Menne\", , \"dieter.menne@menne-biomed.de\", role = \"ctb\"), person(\"Benjamin\", \"Nutter\", , \"nutter@battelle.org\", role = \"ctb\"), person(\"Luke\", \"Johnston\", , \"luke.johnston@mail.utoronto.ca\", role = \"ctb\"), person(\"Ben\", \"Bolker\", , \"bolker@mcmaster.ca\", role = \"ctb\"), person(\"Francois\", \"Briatte\", , \"f.briatte@gmail.com\", role = \"ctb\"), person(\"Jeffrey\", \"Arnold\", , \"jeffrey.arnold@gmail.com\", role = \"ctb\"), person(\"Jonah\", \"Gabry\", , \"jsg2201@columbia.edu\", role = \"ctb\"), person(\"Luciano\", \"Selzer\", , \"luciano.selzer@gmail.com\", role = \"ctb\"), person(\"Gavin\", \"Simpson\", , \"ucfagls@gmail.com\", role = \"ctb\"), person(\"Jens\", \"Preussner\", , \"jens.preussner@mpi-bn.mpg.de\", role = \"ctb\"), person(\"Jay\", \"Hesselberth\", , \"jay.hesselberth@gmail.com\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"ctb\"), person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = \"ctb\"), person(\"Alessandro\", \"Gasparini\", , \"ag475@leicester.ac.uk\", role = \"ctb\"), person(\"Lukasz\", \"Komsta\", , \"lukasz.komsta@umlub.pl\", role = \"ctb\"), person(\"Frederick\", \"Novometsky\", role = \"ctb\"), person(\"Wilson\", \"Freitas\", role = \"ctb\"), person(\"Michelle\", \"Evans\", role = \"ctb\"), person(\"Jason Cory\", \"Brunson\", , \"cornelioid@gmail.com\", role = \"ctb\"), person(\"Simon\", \"Jackson\", , \"drsimonjackson@gmail.com\", role = \"ctb\"), person(\"Ben\", \"Whalley\", , \"ben.whalley@plymouth.ac.uk\", role = \"ctb\"), person(\"Karissa\", \"Whiting\", , \"karissa.whiting@gmail.com\", role = \"ctb\"), person(\"Yves\", \"Rosseel\", , \"yrosseel@gmail.com\", role = \"ctb\"), person(\"Michael\", \"Kuehn\", , \"mkuehn10@gmail.com\", role = \"ctb\"), person(\"Jorge\", \"Cimentada\", , \"cimentadaj@gmail.com\", role = \"ctb\"), person(\"Erle\", \"Holgersen\", , \"erle.holgersen@gmail.com\", role = \"ctb\"), person(\"Karl\", \"Dunkle Werner\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0523-7309\")), person(\"Ethan\", \"Christensen\", , \"christensen.ej@gmail.com\", role = \"ctb\"), person(\"Steven\", \"Pav\", , \"shabbychef@gmail.com\", role = \"ctb\"), person(\"Paul\", \"PJ\", , \"pjpaul.stephens@gmail.com\", role = \"ctb\"), person(\"Ben\", \"Schneider\", , \"benjamin.julius.schneider@gmail.com\", role = \"ctb\"), person(\"Patrick\", \"Kennedy\", , \"pkqstr@protonmail.com\", role = \"ctb\"), person(\"Lily\", \"Medina\", , \"lilymiru@gmail.com\", role = \"ctb\"), person(\"Brian\", \"Fannin\", , \"captain@pirategrunt.com\", role = \"ctb\"), person(\"Jason\", \"Muhlenkamp\", , \"jason.muhlenkamp@gmail.com\", role = \"ctb\"), person(\"Matt\", \"Lehman\", role = \"ctb\"), person(\"Bill\", \"Denney\", , \"wdenney@humanpredictions.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\")), person(\"Nic\", \"Crane\", role = \"ctb\"), person(\"Andrew\", \"Bates\", role = \"ctb\"), person(\"Vincent\", \"Arel-Bundock\", , \"vincent.arel-bundock@umontreal.ca\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2042-7063\")), person(\"Hideaki\", \"Hayashi\", role = \"ctb\"), person(\"Luis\", \"Tobalina\", role = \"ctb\"), person(\"Annie\", \"Wang\", , \"anniewang.uc@gmail.com\", role = \"ctb\"), person(\"Wei Yang\", \"Tham\", , \"weiyang.tham@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", , \"clara.wang.94@gmail.com\", role = \"ctb\"), person(\"Abby\", \"Smith\", , \"als1@u.northwestern.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3207-0375\")), person(\"Jasper\", \"Cooper\", , \"jaspercooper@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8639-3188\")), person(\"E Auden\", \"Krauska\", , \"krauskae@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1466-5850\")), person(\"Alex\", \"Wang\", , \"x249wang@uwaterloo.ca\", role = \"ctb\"), person(\"Malcolm\", \"Barrett\", , \"malcolmbarrett@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(\"Charles\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9978-011X\")), person(\"Jared\", \"Wilber\", role = \"ctb\"), person(\"Vilmantas\", \"Gegzna\", , \"GegznaV@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9500-5167\")), person(\"Eduard\", \"Szoecs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"Frederik\", \"Aust\", , \"frederik.aust@uni-koeln.de\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4900-788X\")), person(\"Angus\", \"Moore\", , \"angusmoore9@gmail.com\", role = \"ctb\"), person(\"Nick\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Marius\", \"Barth\", , \"marius.barth.uni.koeln@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3421-6665\")), person(\"Bruna\", \"Wundervald\", , \"brunadaviesw@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8163-220X\")), person(\"Joyce\", \"Cahoon\", , \"joyceyu48@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7217-4702\")), person(\"Grant\", \"McDermott\", , \"grantmcd@uoregon.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7883-8573\")), person(\"Kevin\", \"Zarca\", , \"kevin.zarca@gmail.com\", role = \"ctb\"), person(\"Shiro\", \"Kuriwaki\", , \"shirokuriwaki@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5687-2647\")), person(\"Lukas\", \"Wallrich\", , \"lukas.wallrich@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2121-5177\")), person(\"James\", \"Martherus\", , \"james@martherus.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8285-3300\")), person(\"Chuliang\", \"Xiao\", , \"cxiao@umich.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8466-9398\")), person(\"Joseph\", \"Larmarange\", , \"joseph@larmarange.net\", role = \"ctb\"), person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", , \"michal2992@gmail.com\", role = \"ctb\"), person(\"Hakon\", \"Malmedal\", , \"hmalmedal@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", role = \"ctb\"), person(\"Sergio\", \"Oller\", , \"sergioller@gmail.com\", role = \"ctb\"), person(\"Luke\", \"Sonnet\", , \"luke.sonnet@gmail.com\", role = \"ctb\"), person(\"Jim\", \"Hester\", , \"jim.hester@posit.co\", role = \"ctb\"), person(\"Ben\", \"Schneider\", , \"benjamin.julius.schneider@gmail.com\", role = \"ctb\"), person(\"Bernie\", \"Gray\", , \"bfgray3@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9190-6032\")), person(\"Mara\", \"Averick\", , \"mara@posit.co\", role = \"ctb\"), person(\"Aaron\", \"Jacobs\", , \"atheriel@gmail.com\", role = \"ctb\"), person(\"Andreas\", \"Bender\", , \"bender.at.R@gmail.com\", role = \"ctb\"), person(\"Sven\", \"Templer\", , \"sven.templer@gmail.com\", role = \"ctb\"), person(\"Paul-Christian\", \"Buerkner\", , \"paul.buerkner@gmail.com\", role = \"ctb\"), person(\"Matthew\", \"Kay\", , \"mjskay@umich.edu\", role = \"ctb\"), person(\"Erwan\", \"Le Pennec\", , \"lepennec@gmail.com\", role = \"ctb\"), person(\"Johan\", \"Junkka\", , \"johan.junkka@umu.se\", role = \"ctb\"), person(\"Hao\", \"Zhu\", , \"haozhu233@gmail.com\", role = \"ctb\"), person(\"Benjamin\", \"Soltoff\", , \"soltoffbc@uchicago.edu\", role = \"ctb\"), person(\"Zoe\", \"Wilkinson Saldana\", , \"zoewsaldana@gmail.com\", role = \"ctb\"), person(\"Tyler\", \"Littlefield\", , \"tylurp1@gmail.com\", role = \"ctb\"), person(\"Charles T.\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\"), person(\"Shabbh E.\", \"Banks\", role = \"ctb\"), person(\"Serina\", \"Robinson\", , \"robi0916@umn.edu\", role = \"ctb\"), person(\"Roger\", \"Bivand\", , \"Roger.Bivand@nhh.no\", role = \"ctb\"), person(\"Riinu\", \"Ots\", , \"riinuots@gmail.com\", role = \"ctb\"), person(\"Nicholas\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Nina\", \"Jakobsen\", role = \"ctb\"), person(\"Michael\", \"Weylandt\", , \"michael.weylandt@gmail.com\", role = \"ctb\"), person(\"Lisa\", \"Lendway\", , \"llendway@macalester.edu\", role = \"ctb\"), person(\"Karl\", \"Hailperin\", , \"khailper@gmail.com\", role = \"ctb\"), person(\"Josue\", \"Rodriguez\", , \"jerrodriguez@ucdavis.edu\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", , \"jenny@posit.co\", role = \"ctb\"), person(\"Chris\", \"Jarvis\", , \"Christopher1.jarvis@gmail.com\", role = \"ctb\"), person(\"Greg\", \"Macfarlane\", , \"gregmacfarlane@gmail.com\", role = \"ctb\"), person(\"Brian\", \"Mannakee\", , \"bmannakee@gmail.com\", role = \"ctb\"), person(\"Drew\", \"Tyre\", , \"atyre2@unl.edu\", role = \"ctb\"), person(\"Shreyas\", \"Singh\", , \"shreyas.singh.298@gmail.com\", role = \"ctb\"), person(\"Laurens\", \"Geffert\", , \"laurensgeffert@gmail.com\", role = \"ctb\"), person(\"Hong\", \"Ooi\", , \"hongooi@microsoft.com\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", , \"henrikb@braju.com\", role = \"ctb\"), person(\"Eduard\", \"Szocs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", , \"davidhughjones@gmail.com\", role = \"ctb\"), person(\"Matthieu\", \"Stigler\", , \"Matthieu.Stigler@gmail.com\", role = \"ctb\"), person(\"Hugo\", \"Tavares\", , \"hm533@cam.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(\"R. Willem\", \"Vervoort\", , \"Willemvervoort@gmail.com\", role = \"ctb\"), person(\"Brenton M.\", \"Wiernik\", , \"brenton@wiernik.org\", role = \"ctb\"), person(\"Josh\", \"Yamamoto\", , \"joshuayamamoto5@gmail.com\", role = \"ctb\"), person(\"Jasme\", \"Lee\", role = \"ctb\"), person(\"Taren\", \"Sanders\", , \"taren.sanders@acu.edu.au\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(\"Ilaria\", \"Prosdocimi\", , \"prosdocimi.ilaria@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(\"Alex\", \"Reinhart\", , \"areinhar@stat.cmu.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-6658-514X\")) )", + "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", "License": "MIT + file LICENSE", "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", "BugReports": "https://github.com/tidymodels/broom/issues", "Depends": [ - "R (>= 3.5)" + "R (>= 4.1)" ], "Imports": [ "backports", @@ -1253,7 +1275,7 @@ "drc", "e1071", "emmeans", - "epiR", + "epiR (>= 2.0.85)", "ergm (>= 3.10.4)", "fixest (>= 0.9.0)", "gam (>= 1.15)", @@ -1264,8 +1286,8 @@ "glmnetUtils", "gmm", "Hmisc", - "irlba", "interp", + "irlba", "joineRML", "Kendall", "knitr", @@ -1304,8 +1326,8 @@ "robustbase", "rsample", "sandwich", - "spdep (>= 1.1)", "spatialreg", + "spdep (>= 1.1)", "speedglm", "spelling", "survey", @@ -1318,13 +1340,14 @@ ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "Language": "en-US", - "Collate": "'aaa-documentation-helper.R' 'null-and-default.R' 'aer.R' 'auc.R' 'base.R' 'bbmle.R' 'betareg.R' 'biglm.R' 'bingroup.R' 'boot.R' 'broom-package.R' 'broom.R' 'btergm.R' 'car.R' 'caret.R' 'cluster.R' 'cmprsk.R' 'data-frame.R' 'deprecated-0-7-0.R' 'drc.R' 'emmeans.R' 'epiR.R' 'ergm.R' 'fixest.R' 'gam.R' 'geepack.R' 'glmnet-cv-glmnet.R' 'glmnet-glmnet.R' 'gmm.R' 'hmisc.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'joinerml.R' 'kendall.R' 'ks.R' 'lavaan.R' 'leaps.R' 'lfe.R' 'list-irlba.R' 'list-optim.R' 'list-svd.R' 'list-xyz.R' 'list.R' 'lm-beta.R' 'lmodel2.R' 'lmtest.R' 'maps.R' 'margins.R' 'mass-fitdistr.R' 'mass-negbin.R' 'mass-polr.R' 'mass-ridgelm.R' 'stats-lm.R' 'mass-rlm.R' 'mclust.R' 'mediation.R' 'metafor.R' 'mfx.R' 'mgcv.R' 'mlogit.R' 'muhaz.R' 'multcomp.R' 'nnet.R' 'nobs.R' 'ordinal-clm.R' 'ordinal-clmm.R' 'plm.R' 'polca.R' 'psych.R' 'stats-nls.R' 'quantreg-nlrq.R' 'quantreg-rq.R' 'quantreg-rqs.R' 'robust-glmrob.R' 'robust-lmrob.R' 'robustbase-glmrob.R' 'robustbase-lmrob.R' 'sp.R' 'spdep.R' 'speedglm-speedglm.R' 'speedglm-speedlm.R' 'stats-anova.R' 'stats-arima.R' 'stats-decompose.R' 'stats-factanal.R' 'stats-glm.R' 'stats-htest.R' 'stats-kmeans.R' 'stats-loess.R' 'stats-mlm.R' 'stats-prcomp.R' 'stats-smooth.spline.R' 'stats-summary-lm.R' 'stats-time-series.R' 'survey.R' 'survival-aareg.R' 'survival-cch.R' 'survival-coxph.R' 'survival-pyears.R' 'survival-survdiff.R' 'survival-survexp.R' 'survival-survfit.R' 'survival-survreg.R' 'systemfit.R' 'tseries.R' 'utilities.R' 'vars.R' 'zoo.R' 'zzz.R'", "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-25", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Collate": "'aaa-documentation-helper.R' 'null-and-default.R' 'aer.R' 'auc.R' 'base.R' 'bbmle.R' 'betareg.R' 'biglm.R' 'bingroup.R' 'boot.R' 'broom-package.R' 'broom.R' 'btergm.R' 'car.R' 'caret.R' 'cluster.R' 'cmprsk.R' 'data-frame.R' 'deprecated-0-7-0.R' 'drc.R' 'emmeans.R' 'epiR.R' 'ergm.R' 'fixest.R' 'gam.R' 'geepack.R' 'glmnet-cv-glmnet.R' 'glmnet-glmnet.R' 'gmm.R' 'hmisc.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'joinerml.R' 'kendall.R' 'ks.R' 'lavaan.R' 'leaps.R' 'lfe.R' 'list-irlba.R' 'list-optim.R' 'list-svd.R' 'list-xyz.R' 'list.R' 'lm-beta.R' 'lmodel2.R' 'lmtest.R' 'maps.R' 'margins.R' 'mass-fitdistr.R' 'mass-negbin.R' 'mass-polr.R' 'mass-ridgelm.R' 'stats-lm.R' 'mass-rlm.R' 'mclust.R' 'mediation.R' 'metafor.R' 'mfx.R' 'mgcv.R' 'mlogit.R' 'muhaz.R' 'multcomp.R' 'nnet.R' 'nobs.R' 'ordinal-clm.R' 'ordinal-clmm.R' 'plm.R' 'polca.R' 'psych.R' 'stats-nls.R' 'quantreg-nlrq.R' 'quantreg-rq.R' 'quantreg-rqs.R' 'robust-glmrob.R' 'robust-lmrob.R' 'robustbase-glmrob.R' 'robustbase-lmrob.R' 'sp.R' 'spdep.R' 'speedglm-speedglm.R' 'speedglm-speedlm.R' 'stats-anova.R' 'stats-arima.R' 'stats-decompose.R' 'stats-factanal.R' 'stats-glm.R' 'stats-htest.R' 'stats-kmeans.R' 'stats-loess.R' 'stats-mlm.R' 'stats-prcomp.R' 'stats-smooth.spline.R' 'stats-summary-lm.R' 'stats-time-series.R' 'survey.R' 'survival-aareg.R' 'survival-cch.R' 'survival-coxph.R' 'survival-pyears.R' 'survival-survdiff.R' 'survival-survexp.R' 'survival-survfit.R' 'survival-survreg.R' 'systemfit.R' 'tseries.R' 'utilities.R' 'vars.R' 'zoo.R' 'zzz.R'", "NeedsCompilation": "no", - "Author": "David Robinson [aut], Alex Hayes [aut] (), Simon Couch [aut, cre] (), Posit Software, PBC [cph, fnd], Indrajeet Patil [ctb] (), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (), Jasper Cooper [ctb] (), E Auden Krauska [ctb] (), Alex Wang [ctb], Malcolm Barrett [ctb] (), Charles Gray [ctb] (), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (), Eduard Szoecs [ctb], Frederik Aust [ctb] (), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (), Bruna Wundervald [ctb] (), Joyce Cahoon [ctb] (), Grant McDermott [ctb] (), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (), Lukas Wallrich [ctb] (), James Martherus [ctb] (), Chuliang Xiao [ctb] (), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (), Ilaria Prosdocimi [ctb] (), Daniel D. Sjoberg [ctb] (), Alex Reinhart [ctb] ()", + "Author": "David Robinson [aut], Alex Hayes [aut] (ORCID: ), Simon Couch [aut, cre] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: ), Indrajeet Patil [ctb] (ORCID: ), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (ORCID: ), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (ORCID: ), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (ORCID: ), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (ORCID: ), Jasper Cooper [ctb] (ORCID: ), E Auden Krauska [ctb] (ORCID: ), Alex Wang [ctb], Malcolm Barrett [ctb] (ORCID: ), Charles Gray [ctb] (ORCID: ), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (ORCID: ), Eduard Szoecs [ctb], Frederik Aust [ctb] (ORCID: ), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (ORCID: ), Bruna Wundervald [ctb] (ORCID: ), Joyce Cahoon [ctb] (ORCID: ), Grant McDermott [ctb] (ORCID: ), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (ORCID: ), Lukas Wallrich [ctb] (ORCID: ), James Martherus [ctb] (ORCID: ), Chuliang Xiao [ctb] (ORCID: ), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (ORCID: ), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (ORCID: ), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (ORCID: ), Ilaria Prosdocimi [ctb] (ORCID: ), Daniel D. Sjoberg [ctb] (ORCID: ), Alex Reinhart [ctb] (ORCID: )", "Maintainer": "Simon Couch ", "Repository": "CRAN" }, @@ -3051,7 +3074,7 @@ "NeedsCompilation": "yes", "Author": "Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd]", "Maintainer": "Gábor Csárdi ", - "Repository": "RSPM" + "Repository": "CRAN" }, "flextable": { "Package": "flextable", @@ -4445,7 +4468,7 @@ }, "insight": { "Package": "insight", - "Version": "1.3.1", + "Version": "1.4.0", "Source": "Repository", "Type": "Package", "Title": "Easy Access to Model Information for Various Model Objects", @@ -4491,7 +4514,7 @@ "cplm", "crch", "curl", - "datawizard", + "datawizard (>= 1.2.0)", "dbarts", "effectsize", "emmeans", @@ -4547,6 +4570,7 @@ "modelbased (>= 0.9.0)", "multgee", "MuMIn", + "mvtnorm", "nestedLogit", "nlme", "nnet", @@ -4559,7 +4583,6 @@ "performance", "phylolm", "plm", - "poorman", "PROreg (>= 1.3.0)", "pscl", "psych", @@ -4577,6 +4600,7 @@ "RWiener", "sandwich", "sdmTMB", + "sampleSelection", "serp", "speedglm", "splines", @@ -5652,8 +5676,7 @@ "Maintainer": "Paul Gilbert ", "URL": "http://optimizer.r-forge.r-project.org/", "NeedsCompilation": "no", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "officer": { "Package": "officer", @@ -5768,7 +5791,7 @@ }, "openxlsx2": { "Package": "openxlsx2", - "Version": "1.17", + "Version": "1.18", "Source": "Repository", "Type": "Package", "Title": "Read, Write and Edit 'xlsx' Files", @@ -6841,36 +6864,56 @@ }, "quarto": { "Package": "quarto", - "Version": "1.4.4", + "Version": "1.5.0", "Source": "Repository", "Title": "R Interface to 'Quarto' Markdown Publishing System", - "Authors@R": "c( person(\"JJ\", \"Allaire\", , \"jj@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"JJ\", \"Allaire\", , \"jj@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Gordon\", \"Woodhull\", role = \"ctb\") )", "Description": "Convert R Markdown documents and 'Jupyter' notebooks to a variety of output formats using 'Quarto'.", - "License": "GPL (>= 2)", + "License": "MIT + file LICENSE", "URL": "https://github.com/quarto-dev/quarto-r, https://quarto-dev.github.io/quarto-r/", "BugReports": "https://github.com/quarto-dev/quarto-r/issues", "Depends": [ - "R (>= 3.6)" + "R (>= 4.1.0)" ], "Imports": [ "cli", + "fs", + "htmltools", "jsonlite", "later", + "lifecycle", "processx", "rlang", "rmarkdown", "rstudioapi", "tools", "utils", - "yaml" + "xfun", + "yaml (>= 2.3.10)" ], "Suggests": [ + "bslib", + "callr", "curl", + "dplyr", + "flextable", + "ggiraph", + "ggplot2", + "gt", + "heatmaply", + "kableExtra", "knitr", + "palmerpenguins", + "patchwork", + "pkgload", + "plotly", "rsconnect (>= 0.8.26)", "testthat (>= 3.1.7)", - "withr", - "xfun" + "thematic", + "tidyverse", + "tinytable", + "whoami", + "withr" ], "VignetteBuilder": "quarto", "Config/testthat/edition": "3", @@ -6878,7 +6921,7 @@ "RoxygenNote": "7.3.2", "SystemRequirements": "Quarto command line tool ().", "NeedsCompilation": "no", - "Author": "JJ Allaire [aut] (), Christophe Dervieux [cre, aut] (), Posit Software, PBC [cph, fnd]", + "Author": "JJ Allaire [aut] (ORCID: ), Christophe Dervieux [cre, aut] (ORCID: ), Posit Software, PBC [cph, fnd], Gordon Woodhull [ctb]", "Maintainer": "Christophe Dervieux ", "Repository": "CRAN" }, @@ -7329,7 +7372,7 @@ }, "renv": { "Package": "renv", - "Version": "1.1.4", + "Version": "1.1.5", "Source": "Repository", "Type": "Package", "Title": "Project Environments", @@ -7348,6 +7391,7 @@ "covr", "cpp11", "devtools", + "generics", "gitcreds", "jsonlite", "jsonvalidate", @@ -7376,7 +7420,7 @@ "Config/testthat/parallel": "true", "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes", "NeedsCompilation": "no", - "Author": "Kevin Ushey [aut, cre] (), Hadley Wickham [aut] (), Posit Software, PBC [cph, fnd]", + "Author": "Kevin Ushey [aut, cre] (ORCID: ), Hadley Wickham [aut] (ORCID: ), Posit Software, PBC [cph, fnd]", "Maintainer": "Kevin Ushey ", "Repository": "CRAN" }, diff --git a/app_docker/www/scripts.js b/app_docker/www/scripts.js index 3382b4e4..f98dffc9 100644 --- a/app_docker/www/scripts.js +++ b/app_docker/www/scripts.js @@ -6,24 +6,52 @@ $(document).on('shown.bs.tab', '#main_panel', function(e) { $('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false'); }); + $(document).on('shiny:sessioninitialized', function() { -// Function to collapse navbar on mobile -function collapseNavbar() { - var navbar = $('.navbar-collapse'); - if (navbar.hasClass('show')) { - navbar.removeClass('show'); - $('.navbar-toggler').addClass('collapsed'); - $('.navbar-toggler').attr('aria-expanded', 'false'); - } + // Function to collapse navbar on mobile + function collapseNavbar() { + var navbar = $('.navbar-collapse'); + if (navbar.hasClass('show')) { + navbar.removeClass('show'); + $('.navbar-toggler').addClass('collapsed'); + $('.navbar-toggler').attr('aria-expanded', 'false'); + } } - // Add click event to navigation tabs - $(document).on('click', '.nav-link[data-bs-toggle=\"tab\"]', function() { + // Main approach: Handle clicks on nav elements + $(document).on('click', '.navbar-nav .nav-link, .dropdown-item', function(event) { + var $target = $(event.currentTarget); + + // Don't collapse if this is a dropdown toggle + if ($target.hasClass('dropdown-toggle')) { + return; + } + + // Don't collapse if this is inside a dropdown and the dropdown should stay open + if ($target.hasClass('nav-link') && $target.closest('.dropdown').length && + !$target.attr('data-bs-toggle')) { + return; + } + + // Collapse the navbar after a short delay setTimeout(collapseNavbar, 10); }); - // Also handle direct clicks on nav items - $(document).on('click', '.navbar-nav .nav-link', function() { - setTimeout(collapseNavbar, 10); + // Handle tab toggles specifically + $(document).on('click', '.nav-link[data-bs-toggle="tab"]', function() { + if (!$(this).hasClass('dropdown-toggle')) { + setTimeout(collapseNavbar, 10); + } + }); + + // Optional: Handle clicks outside the navbar to close it + $(document).on('click', function(event) { + var navbar = $('.navbar-collapse'); + + // Check if click is outside navbar and navbar is open + if (navbar.hasClass('show') && + !$(event.target).closest('.navbar').length) { + collapseNavbar(); + } }); }); From 7fde4bde46c2498291208124c41b0bca1189531c Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Wed, 27 Aug 2025 12:46:44 +0200 Subject: [PATCH 7/7] version bump --- CITATION.cff | 2 +- DESCRIPTION | 2 +- R/app_version.R | 2 +- R/hosted_version.R | 2 +- R/sysdata.rda | Bin 2676 -> 2803 bytes SESSION.md | 20 ++++++++++++++++++-- app_docker/app.R | 4 ++-- 7 files changed, 24 insertions(+), 8 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 1ae8f07e..86a98725 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -9,7 +9,7 @@ type: software license: AGPL-3.0-or-later title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers with publication ready output' -version: 25.8.1 +version: 25.8.2 doi: 10.5281/zenodo.14527429 identifiers: - type: url diff --git a/DESCRIPTION b/DESCRIPTION index c43b72ae..46200944 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: FreesearchR Title: A free and open-source browser based data analysis tool for researchers with publication ready output -Version: 25.8.1 +Version: 25.8.2 Authors@R: c( person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7559-1154")), diff --git a/R/app_version.R b/R/app_version.R index 9942e6fc..433f5276 100644 --- a/R/app_version.R +++ b/R/app_version.R @@ -1 +1 @@ -app_version <- function()'25.8.1' +app_version <- function()'25.8.2' diff --git a/R/hosted_version.R b/R/hosted_version.R index 9f7d5c78..8f6fca33 100644 --- a/R/hosted_version.R +++ b/R/hosted_version.R @@ -1 +1 @@ -hosted_version <- function()'v25.8.1-250827' +hosted_version <- function()'v25.8.2-250827' diff --git a/R/sysdata.rda b/R/sysdata.rda index 182c9aadc3b2832c7b3539ec33b9f56944b8beb2..7544231672e57f77267496f5334a8fc8208165b0 100644 GIT binary patch literal 2803 zcmVH|lp(@g=Ungca7XaN$5Pe7-s;*5rks67$t zXaE3c05tUhkPWG+D&i(Wh5<1cXbqN75F22snX_w^L;%zGxK%|O)P@fa*6vAg3!!&| z-KT)WC$)Vj6s0GM?0`cMpuOAP8FDdExD3RerGD-55yTQ@qAphA^N58wUvzjTAg`O$IXvq?> zz@)djQ4_QRm}-@5C^aZ-!NV?*g#ty^X;g;kBx4lK8!3Z@!h&HbC6 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