From dce97598422747e87c253d57d9adade47ed317e2 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 26 Jun 2025 12:33:25 +0200 Subject: [PATCH] cleaning and minor code export polish --- CITATION.cff | 13 + R/data_plots.R | 2 +- R/sysdata.rda | Bin 2769 -> 2817 bytes README.md | 23 +- SESSION.md | 6 + app_docker/Dockerfile | 4 +- app_docker/renv.lock | 2184 ++++++++++++++++++++++++++++++++++- inst/apps/FreesearchR/app.R | 2 +- 8 files changed, 2182 insertions(+), 52 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index fbe8420..dd55e2e 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1259,6 +1259,19 @@ references: orcid: https://orcid.org/0000-0001-8457-4658 year: '2025' doi: 10.32614/CRAN.package.cffr +- type: software + title: shiny2docker + abstract: 'shiny2docker: Generate Dockerfiles for ''Shiny'' Applications' + notes: Suggests + url: https://github.com/VincentGuyader/shiny2docker + repository: https://CRAN.R-project.org/package=shiny2docker + authors: + - family-names: Guyader + given-names: Vincent + email: vincent@thinkr.fr + orcid: https://orcid.org/0000-0003-0671-9270 + year: '2025' + doi: 10.32614/CRAN.package.shiny2docker - type: software title: 'R: A Language and Environment for Statistical Computing' notes: Depends diff --git a/R/data_plots.R b/R/data_plots.R index 1b07f43..ba56697 100644 --- a/R/data_plots.R +++ b/R/data_plots.R @@ -340,7 +340,7 @@ data_visuals_server <- function(id, rv$plot <- rlang::exec(create_plot, !!!append_list(data(), parameters, "data")) }) - rv$code <- glue::glue("FreesearchR::create_plot(data,{list2str(parameters)})") + rv$code <- glue::glue("FreesearchR::create_plot(df,{list2str(parameters)})") }, # warning = function(warn) { # showNotification(paste0(warn), type = "warning") diff --git a/R/sysdata.rda b/R/sysdata.rda index e24deec4ecb011461697641b10e8b02eeacf8de7..83be4d5d48b3b9ef967620a1a1b06904b859a0ad 100644 GIT binary patch literal 2817 zcmV+c3;y&%T4*^jL0KkKS>^YO+W;F4f5QL&Xazw3|KNXb-@w2B|L{Nn0DuSq;0&LA zZYe^?d;`H1c2Efl4tNhh2!fP6H8KE0L7_5gZA}Iw(W#oI^)vv`1T#qTn@P5yYIy-9 zOhHZPk?FMpX`lcNGynhqJwc(yhJm9@jWlVH7?>ac8UsLSkQfsnNu-34H4T)HQ%y7g z27!MBms~_kxeP+o~NNQ8Ug5oKmY&$ z8fX9jVwQ6gOru2%##&PMrByJ9fbsS<%OU_@o`B*)LUF-^{C>|v9S|M|uUx-)sv_GG zDUx24sAdd06QzcsY!D1^Kn37H54K-swqIwy9^AY8$=>hRK~L^9cu>ZuSm+vujSEdh zBW19cwZq)^+at%h65MENg^v>PL&=g0!+9l~)k(E%S)l{c*6M0*AQ1jIXA(s_rh74% zg5l-Lc+9-xBs;rP+W{gjL1#sr)zdu7QCNF5VN{? 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Any data.frame available in the global environment will be accessible from the interface. Just follow the below steps: +The ***FreesearchR*** app can also run on your own machine with no data transmitted anywhere. Blow are the available options. + +### Run from R (or RStduio) + +Working with data in R, FreesearchR is a quick and easy tool to get overview and perform the first explorative analyses to get you going. + +Any data available in the your R session will be available to the FreesearchR app. Just follow the below steps to get going: 1. **Requirement:** You need to have [*R* installed](https://www.r-project.org/) and possibly an editor like [RStudio](https://posit.co/download/rstudio-desktop/). @@ -43,6 +49,21 @@ The ***FreesearchR*** app can also run on your own machine with no data transmit launch_FreesearchR() ``` +### Running with docker compose + +For advanced users, wanting to deploy the FreesearchR app to run anywhere, a docker image is available. + +Below is the minimal `docker_compose.yml` file: + +``` +services: + freesearchr: + image: ghcr.io/agdamsbo/freesearchr:latest + ports: + - '3838:3838' + restart: on-failure +``` + ## Code of Conduct Please note that the ***FreesearchR*** project is published with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms. diff --git a/SESSION.md b/SESSION.md index 61ceed7..700f8d2 100644 --- a/SESSION.md +++ b/SESSION.md @@ -26,6 +26,8 @@ |apexcharter |0.4.4 |2024-09-06 |CRAN (R 4.4.1) | |askpass |1.2.1 |2024-10-04 |CRAN (R 4.4.1) | |assertthat |0.2.1 |2019-03-21 |CRAN (R 4.4.1) | +|attachment |0.4.5 |2025-03-14 |CRAN (R 4.4.1) | +|attempt |0.3.1 |2020-05-03 |CRAN (R 4.4.1) | |backports |1.5.0 |2024-05-23 |CRAN (R 4.4.1) | |base64enc |0.1-3 |2015-07-28 |CRAN (R 4.4.1) | |bayestestR |0.15.3 |2025-04-28 |CRAN (R 4.4.1) | @@ -62,6 +64,7 @@ |devtools |2.4.5 |2022-10-11 |CRAN (R 4.4.0) | |DHARMa |0.4.7 |2024-10-18 |CRAN (R 4.4.1) | |digest |0.6.37 |2024-08-19 |CRAN (R 4.4.1) | +|dockerfiler |0.2.5 |2025-05-07 |CRAN (R 4.4.1) | |doParallel |1.0.17 |2022-02-07 |CRAN (R 4.4.0) | |dplyr |1.1.4 |2023-11-17 |CRAN (R 4.4.0) | |DT |0.33 |2024-04-04 |CRAN (R 4.4.0) | @@ -139,6 +142,7 @@ |opdisDownsampling |1.0.1 |2024-04-15 |CRAN (R 4.4.0) | |openssl |2.3.2 |2025-02-03 |CRAN (R 4.4.1) | |openxlsx2 |1.15 |2025-04-25 |CRAN (R 4.4.1) | +|pak |0.8.0.2 |2025-04-08 |CRAN (R 4.4.1) | |parameters |0.24.2 |2025-03-04 |CRAN (R 4.4.1) | |patchwork |1.3.0 |2024-09-16 |CRAN (R 4.4.1) | |pbmcapply |1.5.1 |2022-04-28 |CRAN (R 4.4.1) | @@ -198,6 +202,7 @@ |see |0.11.0 |2025-03-11 |CRAN (R 4.4.1) | |sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.4.1) | |shiny |1.10.0 |2024-12-14 |CRAN (R 4.4.1) | +|shiny2docker |0.0.2 |2025-02-09 |CRAN (R 4.4.1) | |shinybusy |0.3.3 |2024-03-09 |CRAN (R 4.4.0) | |shinyjs |2.1.0 |2021-12-23 |CRAN (R 4.4.0) | |shinyTime |1.0.3 |2022-08-19 |CRAN (R 4.4.0) | @@ -231,4 +236,5 @@ |xml2 |1.3.8 |2025-03-14 |CRAN (R 4.4.1) | |xtable |1.8-4 |2019-04-21 |CRAN (R 4.4.1) | |yaml |2.3.10 |2024-07-26 |CRAN (R 4.4.1) | +|yesno |0.1.3 |2024-07-26 |CRAN (R 4.4.1) | |zip |2.3.2 |2025-02-01 |CRAN (R 4.4.1) | diff --git a/app_docker/Dockerfile b/app_docker/Dockerfile index 47eaca4..201620a 100644 --- a/app_docker/Dockerfile +++ b/app_docker/Dockerfile @@ -1,9 +1,9 @@ FROM rocker/geospatial:4.4.1 -RUN apt-get update -y && apt-get install -y make pandoc zlib1g-dev libicu-dev libcurl4-openssl-dev libsecret-1-dev libxml2-dev libssl-dev libx11-dev libfontconfig1-dev libfreetype6-dev git libsodium-dev && rm -rf /var/lib/apt/lists/* +RUN apt-get update -y && apt-get install -y cmake make libcurl4-openssl-dev libicu-dev libssl-dev pandoc zlib1g-dev libsecret-1-dev libxml2-dev libx11-dev libcairo2-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libjpeg-dev libpng-dev libtiff-dev libfftw3-dev libsodium-dev && rm -rf /var/lib/apt/lists/* 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 = "1.0.3")' +RUN R -e 'remotes::install_version("renv", version = "1.1.4")' 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/renv.lock b/app_docker/renv.lock index be472d7..074b3f4 100644 --- a/app_docker/renv.lock +++ b/app_docker/renv.lock @@ -9,6 +9,87 @@ ] }, "Packages": { + "DEoptimR": { + "Package": "DEoptimR", + "Version": "1.1-3-1", + "Source": "Repository", + "Date": "2024-11-23", + "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", + "Description": "Differential Evolution (DE) stochastic heuristic algorithms for global optimization of problems with and without general constraints. The aim is to curate a collection of its variants that (1) do not sacrifice simplicity of design, (2) are essentially tuning-free, and (3) can be efficiently implemented directly in the R language. Currently, it provides implementations of the algorithms 'jDE' by Brest et al. (2006) for single-objective optimization and 'NCDE' by Qu et al. (2012) for multimodal optimization (single-objective problems with multiple solutions).", + "Imports": [ + "stats" + ], + "Enhances": [ + "robustbase" + ], + "License": "GPL (>= 2)", + "Author": "Eduardo L. T. Conceicao [aut, cre], Martin Maechler [ctb] ()", + "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", + "NeedsCompilation": "no" + }, + "DHARMa": { + "Package": "DHARMa", + "Version": "0.4.7", + "Source": "Repository", + "Title": "Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models", + "Date": "2024-10-16", + "Authors@R": "c(person(\"Florian\", \"Hartig\", email = \"florian.hartig@biologie.uni-regensburg.de\", role = c(\"aut\", \"cre\"), comment=c(ORCID=\"0000-0002-6255-9059\")), person(\"Lukas\", \"Lohse\", role = \"ctb\"), person(\"Melina\", \"de Souza leite\", role = \"ctb\"))", + "Description": "The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Currently supported are linear and generalized linear (mixed) models from 'lme4' (classes 'lmerMod', 'glmerMod'), 'glmmTMB', 'GLMMadaptive', and 'spaMM'; phylogenetic linear models from 'phylolm' (classes 'phylolm' and 'phyloglm'); generalized additive models ('gam' from 'mgcv'); 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model classes. Moreover, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problems, such as over/underdispersion, zero-inflation, and residual spatial, phylogenetic and temporal autocorrelation.", + "Depends": [ + "R (>= 3.0.2)" + ], + "Imports": [ + "stats", + "graphics", + "utils", + "grDevices", + "Matrix", + "parallel", + "gap", + "lmtest", + "ape", + "qgam (>= 1.3.2)", + "lme4" + ], + "Suggests": [ + "knitr", + "testthat (>= 3.0.0)", + "rmarkdown", + "KernSmooth", + "sfsmisc", + "MASS", + "mgcv", + "mgcViz (>= 0.1.9)", + "spaMM (>= 3.2.0)", + "GLMMadaptive", + "glmmTMB (>= 1.1.2.3)", + "phylolm (>= 2.6.5)" + ], + "Enhances": [ + "phyr", + "rstan", + "rjags", + "BayesianTools" + ], + "License": "GPL (>= 3)", + "URL": "http://florianhartig.github.io/DHARMa/", + "LazyData": "TRUE", + "BugReports": "https://github.com/florianhartig/DHARMa/issues", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Florian Hartig [aut, cre] (), Lukas Lohse [ctb], Melina de Souza leite [ctb]", + "Maintainer": "Florian Hartig ", + "Repository": "CRAN" + }, "DT": { "Package": "DT", "Version": "0.33", @@ -645,6 +726,40 @@ "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": "6.0.3", @@ -681,6 +796,48 @@ "Maintainer": "Jeroen Ooms ", "Repository": "CRAN" }, + "ape": { + "Package": "ape", + "Version": "5.8-1", + "Source": "Repository", + "Date": "2024-12-10", + "Title": "Analyses of Phylogenetics and Evolution", + "Authors@R": "c(person(\"Emmanuel\", \"Paradis\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Emmanuel.Paradis@ird.fr\", comment = c(ORCID = \"0000-0003-3092-2199\")), person(\"Simon\", \"Blomberg\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-1062-0839\")), person(\"Ben\", \"Bolker\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-2127-0443\")), person(\"Joseph\", \"Brown\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-3835-8062\")), person(\"Santiago\", \"Claramunt\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-8926-5974\")), person(\"Julien\", \"Claude\", role = c(\"aut\", \"cph\"), , comment = c(ORCID = \"0000-0002-9267-1228\")), person(\"Hoa Sien\", \"Cuong\", role = c(\"aut\", \"cph\")), person(\"Richard\", \"Desper\", role = c(\"aut\", \"cph\")), person(\"Gilles\", \"Didier\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-0596-9112\")), person(\"Benoit\", \"Durand\", role = c(\"aut\", \"cph\")), person(\"Julien\", \"Dutheil\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-7753-4121\")), person(\"RJ\", \"Ewing\", role = c(\"aut\", \"cph\")), person(\"Olivier\", \"Gascuel\", role = c(\"aut\", \"cph\")), person(\"Thomas\", \"Guillerme\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-4325-1275\")), person(\"Christoph\", \"Heibl\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-7655-3299\")), person(\"Anthony\", \"Ives\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-9375-9523\")), person(\"Bradley\", \"Jones\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-4498-1069\")), person(\"Franz\", \"Krah\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-7866-7508\")), person(\"Daniel\", \"Lawson\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-5311-6213\")), person(\"Vincent\", \"Lefort\", role = c(\"aut\", \"cph\")), person(\"Pierre\", \"Legendre\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-3838-3305\")), person(\"Jim\", \"Lemon\", role = c(\"aut\", \"cph\")), person(\"Guillaume\", \"Louvel\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-7745-0785\")), person(\"Federico\", \"Marotta\", role = c(\"aut\", \"cph\")), person(\"Eric\", \"Marcon\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-5249-321X\")), person(\"Rosemary\", \"McCloskey\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-9772-8553\")), person(\"Johan\", \"Nylander\", role = c(\"aut\", \"cph\")), person(\"Rainer\", \"Opgen-Rhein\", role = c(\"aut\", \"cph\")), person(\"Andrei-Alin\", \"Popescu\", role = c(\"aut\", \"cph\")), person(\"Manuela\", \"Royer-Carenzi\", role = c(\"aut\", \"cph\")), person(\"Klaus\", \"Schliep\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-2941-0161\")), person(\"Korbinian\", \"Strimmer\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-7917-2056\")), person(\"Damien\", \"de Vienne\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-9532-5251\")))", + "Depends": [ + "R (>= 3.2.0)" + ], + "Suggests": [ + "gee", + "expm", + "igraph", + "phangorn", + "xml2" + ], + "Imports": [ + "nlme", + "lattice", + "graphics", + "methods", + "stats", + "utils", + "parallel", + "Rcpp (>= 0.12.0)", + "digest" + ], + "LinkingTo": [ + "Rcpp" + ], + "ZipData": "no", + "Description": "Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.", + "License": "GPL-2 | GPL-3", + "URL": "https://github.com/emmanuelparadis/ape", + "BugReports": "https://github.com/emmanuelparadis/ape/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Emmanuel Paradis [aut, cre, cph] (), Simon Blomberg [aut, cph] (), Ben Bolker [aut, cph] (), Joseph Brown [aut, cph] (), Santiago Claramunt [aut, cph] (), Julien Claude [aut, cph] (), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (), Christoph Heibl [aut, cph] (), Anthony Ives [aut, cph] (), Bradley Jones [aut, cph] (), Franz Krah [aut, cph] (), Daniel Lawson [aut, cph] (), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (), Federico Marotta [aut, cph], Eric Marcon [aut, cph] (), Rosemary McCloskey [aut, cph] (), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (), Korbinian Strimmer [aut, cph] (), Damien de Vienne [aut, cph] ()", + "Maintainer": "Emmanuel Paradis ", + "Repository": "CRAN" + }, "apexcharter": { "Package": "apexcharter", "Version": "0.4.4", @@ -997,6 +1154,59 @@ "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", + "Source": "Repository", + "Title": "Basic R Input Output", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Functions to handle basic input output, these functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.", + "License": "MIT + file LICENSE", + "URL": "https://brio.r-lib.org, https://github.com/r-lib/brio", + "BugReports": "https://github.com/r-lib/brio/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut] (), Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, "broom": { "Package": "broom", "Version": "1.0.8", @@ -1304,6 +1514,31 @@ "Maintainer": "Carson Sievert ", "Repository": "CRAN" }, + "caTools": { + "Package": "caTools", + "Version": "1.18.3", + "Source": "Repository", + "Type": "Package", + "Title": "Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc", + "Date": "2024-09-04", + "Authors@R": "c(person(given = \"Jarek\", family = \"Tuszynski\", role = \"aut\", email = \"jaroslaw.w.tuszynski@saic.com\"), person(given = \"Michael\", family = \"Dietze\", role = \"cre\", email = \"michael.dietze@uni-goettingen.de\"))", + "Maintainer": "Michael Dietze ", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "bitops" + ], + "Suggests": [ + "MASS", + "rpart" + ], + "Description": "Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.", + "License": "GPL-3", + "NeedsCompilation": "yes", + "Repository": "CRAN", + "Author": "Jarek Tuszynski [aut], Michael Dietze [cre]" + }, "cachem": { "Package": "cachem", "Version": "1.1.0", @@ -1676,6 +1911,23 @@ "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", @@ -1754,6 +2006,64 @@ "Maintainer": "Jeroen Ooms ", "Repository": "CRAN" }, + "correlation": { + "Package": "correlation", + "Version": "0.8.7", + "Source": "Repository", + "Type": "Package", + "Title": "Methods for Correlation Analysis", + "Authors@R": "c(person(given = \"Dominique\", family = \"Makowski\", role = c(\"aut\", \"inv\"), email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = c(\"aut\", \"cre\"), email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Daniel\", family = \"Lüdecke\", role = \"aut\", email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = \"aut\", email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Rémi\", family = \"Thériault\", role = c(\"aut\"), email = \"remi.theriault@mail.mcgill.ca\", comment = c(ORCID = \"0000-0003-4315-6788\")), person(given = \"Mark\", family = \"White\", email = \"markhwhiteii@gmail.com\", role = \"rev\"), person(given = \"Maximilian M.\", family = \"Rabe\", email = \"maximilian.rabe@uni-potsdam.de\", role = \"rev\", comment = c(ORCID = \"0000-0002-2556-5644\")))", + "Maintainer": "Brenton M. Wiernik ", + "Description": "Lightweight package for computing different kinds of correlations, such as partial correlations, Bayesian correlations, multilevel correlations, polychoric correlations, biweight correlations, distance correlations and more. Part of the 'easystats' ecosystem. References: Makowski et al. (2020) .", + "License": "MIT + file LICENSE", + "URL": "https://easystats.github.io/correlation/", + "BugReports": "https://github.com/easystats/correlation/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "bayestestR (>= 0.15.0)", + "datasets", + "datawizard (>= 1.0.0)", + "insight (>= 1.0.0)", + "parameters (>= 0.24.0)", + "stats" + ], + "Suggests": [ + "BayesFactor", + "energy", + "ggplot2", + "ggraph", + "gt", + "Hmisc", + "knitr", + "lme4", + "MASS", + "mbend", + "polycor", + "poorman", + "ppcor", + "psych", + "rmarkdown", + "rmcorr", + "rstanarm", + "see (>= 0.8.1)", + "testthat (>= 3.2.1)", + "tidygraph", + "wdm", + "WRS2", + "openxlsx2 (>= 1.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/Needs/website": "rstudio/bslib, r-lib/pkgdown, easystats/easystatstemplate", + "NeedsCompilation": "no", + "Author": "Dominique Makowski [aut, inv] (), Brenton M. Wiernik [aut, cre] (), Indrajeet Patil [aut] (), Daniel Lüdecke [aut] (), Mattan S. Ben-Shachar [aut] (), Rémi Thériault [aut] (), Mark White [rev], Maximilian M. Rabe [rev] ()", + "Repository": "CRAN" + }, "cpp11": { "Package": "cpp11", "Version": "0.5.2", @@ -2042,6 +2352,44 @@ "Author": "Indrajeet Patil [aut] (), Etienne Bacher [aut, cre] (), Dominique Makowski [aut] (), Daniel Lüdecke [aut] (), Mattan S. Ben-Shachar [aut] (), Brenton M. Wiernik [aut] (), Rémi Thériault [ctb] (), Thomas J. Faulkenberry [rev], Robert Garrett [rev]", "Repository": "CRAN" }, + "desc": { + "Package": "desc", + "Version": "1.4.3", + "Source": "Repository", + "Title": "Manipulate DESCRIPTION Files", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", role = \"aut\"), person(\"Jim\", \"Hester\", , \"james.f.hester@gmail.com\", role = \"aut\"), person(\"Maëlle\", \"Salmon\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2815-0399\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Maintainer": "Gábor Csárdi ", + "Description": "Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.", + "License": "MIT + file LICENSE", + "URL": "https://desc.r-lib.org/, https://github.com/r-lib/desc", + "BugReports": "https://github.com/r-lib/desc/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "cli", + "R6", + "utils" + ], + "Suggests": [ + "callr", + "covr", + "gh", + "spelling", + "testthat", + "whoami", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "Collate": "'assertions.R' 'authors-at-r.R' 'built.R' 'classes.R' 'collate.R' 'constants.R' 'deps.R' 'desc-package.R' 'description.R' 'encoding.R' 'find-package-root.R' 'latex.R' 'non-oo-api.R' 'package-archives.R' 'read.R' 'remotes.R' 'str.R' 'syntax_checks.R' 'urls.R' 'utils.R' 'validate.R' 'version.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Kirill Müller [aut], Jim Hester [aut], Maëlle Salmon [ctb] (), Posit Software, PBC [cph, fnd]", + "Repository": "CRAN" + }, "digest": { "Package": "digest", "Version": "0.6.37", @@ -2070,6 +2418,83 @@ "Maintainer": "Dirk Eddelbuettel ", "Repository": "CRAN" }, + "doParallel": { + "Package": "doParallel", + "Version": "1.0.17", + "Source": "Repository", + "Type": "Package", + "Title": "Foreach Parallel Adaptor for the 'parallel' Package", + "Authors@R": "c(person(\"Folashade\", \"Daniel\", role=\"cre\", email=\"fdaniel@microsoft.com\"), person(\"Microsoft\", \"Corporation\", role=c(\"aut\", \"cph\")), person(\"Steve\", \"Weston\", role=\"aut\"), person(\"Dan\", \"Tenenbaum\", role=\"ctb\"))", + "Description": "Provides a parallel backend for the %dopar% function using the parallel package.", + "Depends": [ + "R (>= 2.14.0)", + "foreach (>= 1.2.0)", + "iterators (>= 1.0.0)", + "parallel", + "utils" + ], + "Suggests": [ + "caret", + "mlbench", + "rpart", + "RUnit" + ], + "Enhances": [ + "compiler" + ], + "License": "GPL-2", + "URL": "https://github.com/RevolutionAnalytics/doparallel", + "BugReports": "https://github.com/RevolutionAnalytics/doparallel/issues", + "NeedsCompilation": "no", + "Author": "Folashade Daniel [cre], Microsoft Corporation [aut, cph], Steve Weston [aut], Dan Tenenbaum [ctb]", + "Maintainer": "Folashade Daniel ", + "Repository": "CRAN" + }, + "downlit": { + "Package": "downlit", + "Version": "0.4.4", + "Source": "Repository", + "Title": "Syntax Highlighting and Automatic Linking", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Syntax highlighting of R code, specifically designed for the needs of 'RMarkdown' packages like 'pkgdown', 'hugodown', and 'bookdown'. It includes linking of function calls to their documentation on the web, and automatic translation of ANSI escapes in output to the equivalent HTML.", + "License": "MIT + file LICENSE", + "URL": "https://downlit.r-lib.org/, https://github.com/r-lib/downlit", + "BugReports": "https://github.com/r-lib/downlit/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Imports": [ + "brio", + "desc", + "digest", + "evaluate", + "fansi", + "memoise", + "rlang", + "vctrs", + "withr", + "yaml" + ], + "Suggests": [ + "covr", + "htmltools", + "jsonlite", + "MASS", + "MassSpecWavelet", + "pkgload", + "rmarkdown", + "testthat (>= 3.0.0)", + "xml2" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, "dplyr": { "Package": "dplyr", "Version": "1.1.4", @@ -2168,6 +2593,277 @@ "Maintainer": "David Meyer ", "Repository": "CRAN" }, + "easystats": { + "Package": "easystats", + "Version": "0.7.4", + "Source": "Repository", + "Type": "Package", + "Title": "Framework for Easy Statistical Modeling, Visualization, and Reporting", + "Authors@R": "c(person(given = \"Daniel\", family = \"Lüdecke\", role = c(\"aut\", \"cre\"), email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Dominique\", family = \"Makowski\", role = \"aut\", email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = \"aut\", email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"aut\", email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(\"Etienne\", \"Bacher\", , \"etienne.bacher@protonmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-9271-5075\")), person(given = \"Rémi\", family = \"Thériault\", role = \"aut\", email = \"remi.theriault@mail.mcgill.ca\", comment = c(ORCID = \"0000-0003-4315-6788\")))", + "Maintainer": "Daniel Lüdecke ", + "Description": "A meta-package that installs and loads a set of packages from 'easystats' ecosystem in a single step. This collection of packages provide a unifying and consistent framework for statistical modeling, visualization, and reporting. Additionally, it provides articles targeted at instructors for teaching 'easystats', and a dashboard targeted at new R users for easily conducting statistical analysis by accessing summary results, model fit indices, and visualizations with minimal programming.", + "License": "MIT + file LICENSE", + "URL": "https://easystats.github.io/easystats/", + "BugReports": "https://github.com/easystats/easystats/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "bayestestR (>= 0.15.1)", + "correlation (>= 0.8.6)", + "datawizard (>= 1.0.0)", + "effectsize (>= 1.0.0)", + "insight (>= 1.0.1)", + "modelbased (>= 0.9.0)", + "parameters (>= 0.24.1)", + "performance (>= 0.13.0)", + "report (>= 0.6.0)", + "see (>= 0.10.0)", + "tools", + "utils" + ], + "Suggests": [ + "collapse", + "DHARMa", + "DT", + "flexdashboard (>= 0.6.2)", + "Formula", + "ggplot2", + "glmmTMB", + "httr", + "jsonlite", + "knitr", + "marginaleffects (>= 0.25.0)", + "mockery", + "pak", + "patchwork", + "rmarkdown", + "testthat (>= 3.2.1)", + "withr", + "xml2" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/Needs/website": "easystats/easystatstemplate", + "NeedsCompilation": "no", + "Author": "Daniel Lüdecke [aut, cre] (), Dominique Makowski [aut] (), Mattan S. Ben-Shachar [aut] (), Indrajeet Patil [aut] (), Brenton M. Wiernik [aut] (), Etienne Bacher [aut] (), Rémi Thériault [aut] ()", + "Repository": "CRAN" + }, + "effectsize": { + "Package": "effectsize", + "Version": "1.0.0", + "Source": "Repository", + "Type": "Package", + "Title": "Indices of Effect Size", + "Authors@R": "c(person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = c(\"aut\", \"cre\"), email = \"mattansb@msbstats.info\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Dominique\", family = \"Makowski\", role = \"aut\", email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Daniel\", family = \"Lüdecke\", role = \"aut\", email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"aut\", email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Rémi\", family = \"Thériault\", role = \"aut\", email = \"remi.theriault@mail.mcgill.ca\", comment = c(ORCID = \"0000-0003-4315-6788\")), person(given = \"Ken\", family = \"Kelley\", role = \"ctb\"), person(given = \"David\", family = \"Stanley\", role = \"ctb\"), person(given = \"Aaron\", family = \"Caldwell\", role = \"ctb\", email = \"arcaldwell49@gmail.com\", comment = c(ORCID = \"0000-0002-4541-6283\")), person(given = \"Jessica\", family = \"Burnett\", role = \"rev\", email = \"jburnett@usgs.gov\", comment = c(ORCID = \"0000-0002-0896-5099\")), person(given = \"Johannes\", family = \"Karreth\", role = \"rev\", email = \"jkarreth@ursinus.edu\", comment = c(ORCID = \"0000-0003-4586-7153\")), person(given = \"Philip\", family = \"Waggoner\", role = c(\"aut\", \"ctb\"), email = \"philip.waggoner@gmail.com\", comment = c(ORCID = \"0000-0002-7825-7573\")))", + "Maintainer": "Mattan S. Ben-Shachar ", + "Description": "Provide utilities to work with indices of effect size for a wide variety of models and hypothesis tests (see list of supported models using the function 'insight::supported_models()'), allowing computation of and conversion between indices such as Cohen's d, r, odds, etc. References: Ben-Shachar et al. (2020) .", + "License": "MIT + file LICENSE", + "URL": "https://easystats.github.io/effectsize/", + "BugReports": "https://github.com/easystats/effectsize/issues/", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "bayestestR (>= 0.15.0)", + "insight (>= 1.0.0)", + "parameters (>= 0.24.0)", + "performance (>= 0.12.4)", + "datawizard (>= 0.13.0)", + "stats", + "utils" + ], + "Suggests": [ + "correlation (>= 0.8.4)", + "see (>= 0.8.0)", + "afex", + "BayesFactor", + "boot", + "brms", + "car", + "emmeans", + "gt", + "knitr", + "lavaan", + "lme4", + "lmerTest", + "mgcv", + "parsnip", + "pwr", + "rmarkdown", + "rms", + "rstanarm", + "rstantools", + "testthat (>= 3.1.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/Needs/website": "rstudio/bslib, r-lib/pkgdown, easystats/easystatstemplate", + "NeedsCompilation": "no", + "Author": "Mattan S. Ben-Shachar [aut, cre] (), Dominique Makowski [aut] (), Daniel Lüdecke [aut] (), Indrajeet Patil [aut] (), Brenton M. Wiernik [aut] (), Rémi Thériault [aut] (), Ken Kelley [ctb], David Stanley [ctb], Aaron Caldwell [ctb] (), Jessica Burnett [rev] (), Johannes Karreth [rev] (), Philip Waggoner [aut, ctb] ()", + "Repository": "CRAN" + }, + "emmeans": { + "Package": "emmeans", + "Version": "1.11.1", + "Source": "Repository", + "Type": "Package", + "Title": "Estimated Marginal Means, aka Least-Squares Means", + "Date": "2025-05-03", + "Authors@R": "c(person(\"Russell V.\", \"Lenth\", role = c(\"aut\", \"cre\", \"cph\"), email = \"russell-lenth@uiowa.edu\"), person(\"Balazs\", \"Banfai\", role = \"ctb\"), person(\"Ben\", \"Bolker\", role = \"ctb\"), person(\"Paul\", \"Buerkner\", role = \"ctb\"), person(\"Iago\", \"Giné-Vázquez\", role = \"ctb\"), person(\"Maxime\", \"Herve\", role = \"ctb\"), person(\"Maarten\", \"Jung\", role = \"ctb\"), person(\"Jonathon\", \"Love\", role = \"ctb\"), person(\"Fernando\", \"Miguez\", role = \"ctb\"), person(\"Julia\", \"Piaskowski\", role = \"ctb\"), person(\"Hannes\", \"Riebl\", role = \"ctb\"), person(\"Henrik\", \"Singmann\", role = \"ctb\"))", + "Depends": [ + "R (>= 4.1.0)" + ], + "Imports": [ + "estimability (>= 1.4.1)", + "graphics", + "methods", + "mvtnorm", + "numDeriv", + "stats", + "utils" + ], + "Suggests": [ + "bayesplot", + "bayestestR", + "biglm", + "brms", + "car", + "coda (>= 0.17)", + "compositions", + "ggplot2", + "knitr", + "lattice", + "lme4", + "lmerTest (>= 2.0.32)", + "logspline", + "MASS", + "mediation", + "mgcv", + "multcomp", + "multcompView", + "MuMIn", + "nlme", + "ordinal (>= 2014.11-12)", + "pbkrtest (>= 0.4-1)", + "rmarkdown", + "rsm", + "sandwich", + "scales", + "splines", + "testthat", + "tibble", + "xtable (>= 1.8-2)" + ], + "Enhances": [ + "CARBayes", + "coxme", + "gee", + "geepack", + "MCMCglmm", + "MCMCpack", + "mice", + "nnet", + "pscl", + "rstanarm", + "sommer", + "survival" + ], + "URL": "https://rvlenth.github.io/emmeans/,https://rvlenth.github.io/emmeans/", + "BugReports": "https://github.com/rvlenth/emmeans/issues", + "LazyData": "yes", + "ByteCompile": "yes", + "Description": "Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. Least-squares means are discussed, and the term \"estimated marginal means\" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 .", + "License": "GPL-2 | GPL-3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "knitr", + "NeedsCompilation": "no", + "Author": "Russell V. Lenth [aut, cre, cph], Balazs Banfai [ctb], Ben Bolker [ctb], Paul Buerkner [ctb], Iago Giné-Vázquez [ctb], Maxime Herve [ctb], Maarten Jung [ctb], Jonathon Love [ctb], Fernando Miguez [ctb], Julia Piaskowski [ctb], Hannes Riebl [ctb], Henrik Singmann [ctb]", + "Maintainer": "Russell V. Lenth ", + "Repository": "CRAN" + }, + "esquisse": { + "Package": "esquisse", + "Version": "2.1.0", + "Source": "Repository", + "Type": "Package", + "Title": "Explore and Visualize Your Data Interactively", + "Authors@R": "c(person(\"Fanny\", \"Meyer\", role = c(\"aut\")), person(\"Victor\", \"Perrier\", email = \"victor.perrier@dreamrs.fr\", role = c(\"aut\", \"cre\")), person(\"Ian\", \"Carroll\", comment = \"Faceting support\", role = \"ctb\"), person(\"Xiangnan\", \"Dang\", comment = \"Facets rows and cols, X/Y limits\", role = \"ctb\"), person(\"Nicolas\", \"Bevacqua\", role = \"cph\", comment = \"author of dragula JavaScript library\"), person(\"Daybrush (Younkue Choi)\", role = \"cph\", comment = \"author of moveable JavaScript library\"), person(\"Zeno\", \"Rocha\", role = \"cph\", comment = \"author of clipboard JavaScript library\"))", + "Description": "A 'shiny' gadget to create 'ggplot2' figures interactively with drag-and-drop to map your variables to different aesthetics. You can quickly visualize your data accordingly to their type, export in various formats, and retrieve the code to reproduce the plot.", + "URL": "https://dreamrs.github.io/esquisse/, https://github.com/dreamRs/esquisse", + "BugReports": "https://github.com/dreamRs/esquisse/issues", + "License": "GPL-3 | file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Imports": [ + "bslib", + "datamods (>= 1.5.1)", + "downlit", + "ggplot2 (>= 3.0.0)", + "grDevices", + "htmltools (>= 0.5.0)", + "jsonlite", + "phosphoricons (>= 0.2.1)", + "rlang (>= 0.3.1)", + "rstudioapi", + "scales", + "shiny (>= 1.1.0)", + "shinybusy", + "shinyWidgets (>= 0.6.0)", + "zip" + ], + "Suggests": [ + "officer", + "rvg", + "rio", + "testthat (>= 2.1.0)", + "knitr", + "rmarkdown", + "ggthemes", + "hrbrthemes", + "plotly" + ], + "VignetteBuilder": "knitr", + "NeedsCompilation": "no", + "Author": "Fanny Meyer [aut], Victor Perrier [aut, cre], Ian Carroll [ctb] (Faceting support), Xiangnan Dang [ctb] (Facets rows and cols, X/Y limits), Nicolas Bevacqua [cph] (author of dragula JavaScript library), Daybrush (Younkue Choi) [cph] (author of moveable JavaScript library), Zeno Rocha [cph] (author of clipboard JavaScript library)", + "Maintainer": "Victor Perrier ", + "Repository": "CRAN" + }, + "estimability": { + "Package": "estimability", + "Version": "1.5.1", + "Source": "Repository", + "Type": "Package", + "Title": "Tools for Assessing Estimability of Linear Predictions", + "Date": "2024-05-12", + "Authors@R": "c(person(\"Russell\", \"Lenth\", role = c(\"aut\", \"cre\", \"cph\"), email = \"russell-lenth@uiowa.edu\"))", + "Depends": [ + "stats", + "R(>= 4.1.0)" + ], + "Suggests": [ + "knitr", + "rmarkdown" + ], + "Description": "Provides tools for determining estimability of linear functions of regression coefficients, and 'epredict' methods that handle non-estimable cases correctly. Estimability theory is discussed in many linear-models textbooks including Chapter 3 of Monahan, JF (2008), \"A Primer on Linear Models\", Chapman and Hall (ISBN 978-1-4200-6201-4).", + "URL": "https://github.com/rvlenth/estimability, https://rvlenth.github.io/estimability/", + "BugReports": "https://github.com/rvlenth/estimability/issues", + "ByteCompile": "yes", + "License": "GPL (>= 3)", + "VignetteBuilder": "knitr", + "NeedsCompilation": "no", + "Author": "Russell Lenth [aut, cre, cph]", + "Maintainer": "Russell Lenth ", + "Repository": "CRAN" + }, "eulerr": { "Package": "eulerr", "Version": "7.0.2", @@ -2350,8 +3046,110 @@ "NeedsCompilation": "yes", "Author": "Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd]", "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" + }, + "flextable": { + "Package": "flextable", + "Version": "0.9.7", + "Source": "Repository", + "Type": "Package", + "Title": "Functions for Tabular Reporting", + "Authors@R": "c( person(\"David\", \"Gohel\", , \"david.gohel@ardata.fr\", role = c(\"aut\", \"cre\")), person(\"ArData\", role = \"cph\"), person(\"Clementine\", \"Jager\", role = \"ctb\"), person(\"Eli\", \"Daniels\", role = \"ctb\"), person(\"Panagiotis\", \"Skintzos\", , \"panagiotis.skintzos@ardata.fr\", role = \"aut\"), person(\"Quentin\", \"Fazilleau\", role = \"ctb\"), person(\"Maxim\", \"Nazarov\", role = \"ctb\"), person(\"Titouan\", \"Robert\", role = \"ctb\"), person(\"Michael\", \"Barrowman\", role = \"ctb\"), person(\"Atsushi\", \"Yasumoto\", role = \"ctb\"), person(\"Paul\", \"Julian\", role = \"ctb\"), person(\"Sean\", \"Browning\", role = \"ctb\"), person(\"Rémi\", \"Thériault\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4315-6788\")), person(\"Samuel\", \"Jobert\", role = \"ctb\"), person(\"Keith\", \"Newman\", role = \"ctb\") )", + "Description": "Use a grammar for creating and customizing pretty tables. The following formats are supported: 'HTML', 'PDF', 'RTF', 'Microsoft Word', 'Microsoft PowerPoint' and R 'Grid Graphics'. 'R Markdown', 'Quarto' and the package 'officer' can be used to produce the result files. The syntax is the same for the user regardless of the type of output to be produced. A set of functions allows the creation, definition of cell arrangement, addition of headers or footers, formatting and definition of cell content with text and or images. The package also offers a set of high-level functions that allow tabular reporting of statistical models and the creation of complex cross tabulations.", + "License": "GPL-3", + "URL": "https://ardata-fr.github.io/flextable-book/, https://davidgohel.github.io/flextable/", + "BugReports": "https://github.com/davidgohel/flextable/issues", + "Imports": [ + "data.table (>= 1.13.0)", + "gdtools (>= 0.4.0)", + "graphics", + "grDevices", + "grid", + "htmltools", + "knitr", + "officer (>= 0.6.7)", + "ragg", + "rlang", + "rmarkdown (>= 2.0)", + "stats", + "utils", + "uuid (>= 0.1-4)", + "xml2" + ], + "Suggests": [ + "bookdown (>= 0.40)", + "broom", + "broom.mixed", + "chromote", + "cluster", + "commonmark", + "doconv (>= 0.3.0)", + "equatags", + "ggplot2", + "lme4", + "magick", + "mgcv", + "nlme", + "officedown", + "pdftools", + "pkgdown (>= 2.0.0)", + "scales", + "svglite", + "tables (>= 0.9.17)", + "testthat (>= 3.0.0)", + "webshot2", + "withr", + "xtable" + ], + "VignetteBuilder": "knitr", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "David Gohel [aut, cre], ArData [cph], Clementine Jager [ctb], Eli Daniels [ctb], Panagiotis Skintzos [aut], Quentin Fazilleau [ctb], Maxim Nazarov [ctb], Titouan Robert [ctb], Michael Barrowman [ctb], Atsushi Yasumoto [ctb], Paul Julian [ctb], Sean Browning [ctb], Rémi Thériault [ctb] (), Samuel Jobert [ctb], Keith Newman [ctb]", + "Maintainer": "David Gohel ", "Repository": "CRAN" }, + "fontBitstreamVera": { + "Package": "fontBitstreamVera", + "Version": "0.1.1", + "Source": "Repository", + "Title": "Fonts with 'Bitstream Vera Fonts' License", + "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel.hry@gmail.com\", c(\"cre\", \"aut\")), person(\"Bitstream\", role = \"cph\"))", + "Description": "Provides fonts licensed under the 'Bitstream Vera Fonts' license for the 'fontquiver' package.", + "Depends": [ + "R (>= 3.0.0)" + ], + "License": "file LICENCE", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "5.0.1", + "NeedsCompilation": "no", + "Author": "Lionel Henry [cre, aut], Bitstream [cph]", + "Maintainer": "Lionel Henry ", + "License_is_FOSS": "yes", + "Repository": "CRAN" + }, + "fontLiberation": { + "Package": "fontLiberation", + "Version": "0.1.0", + "Source": "Repository", + "Title": "Liberation Fonts", + "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel@rstudio.com\", \"cre\"), person(\"Pravin Satpute\", role = \"aut\"), person(\"Steve Matteson\", role = \"aut\"), person(\"Red Hat, Inc\", role = \"cph\"), person(\"Google Corporation\", role = \"cph\"))", + "Description": "A placeholder for the Liberation fontset intended for the `fontquiver` package. This fontset covers the 12 combinations of families (sans, serif, mono) and faces (plain, bold, italic, bold italic) supported in R graphics devices.", + "Depends": [ + "R (>= 3.0)" + ], + "License": "file LICENSE", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "5.0.1", + "NeedsCompilation": "no", + "Author": "Lionel Henry [cre], Pravin Satpute [aut], Steve Matteson [aut], Red Hat, Inc [cph], Google Corporation [cph]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN", + "License_is_FOSS": "yes" + }, "fontawesome": { "Package": "fontawesome", "Version": "0.5.3", @@ -2387,6 +3185,34 @@ "Maintainer": "Richard Iannone ", "Repository": "CRAN" }, + "fontquiver": { + "Package": "fontquiver", + "Version": "0.2.1", + "Source": "Repository", + "Title": "Set of Installed Fonts", + "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel@rstudio.com\", c(\"cre\", \"aut\")), person(\"RStudio\", role = \"cph\"), person(\"George Douros\", role = \"cph\", comment = \"Symbola font\"))", + "Description": "Provides a set of fonts with permissive licences. This is useful when you want to avoid system fonts to make sure your outputs are reproducible.", + "Depends": [ + "R (>= 3.0.0)" + ], + "Imports": [ + "fontBitstreamVera (>= 0.1.0)", + "fontLiberation (>= 0.1.0)" + ], + "Suggests": [ + "testthat", + "htmltools" + ], + "License": "GPL-3 | file LICENSE", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "5.0.1", + "Collate": "'font-getters.R' 'fontset.R' 'fontset-bitstream-vera.R' 'fontset-dejavu.R' 'fontset-liberation.R' 'fontset-symbola.R' 'html-dependency.R' 'utils.R'", + "NeedsCompilation": "no", + "Author": "Lionel Henry [cre, aut], RStudio [cph], George Douros [cph] (Symbola font)", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" + }, "forcats": { "Package": "forcats", "Version": "1.0.0", @@ -2429,6 +3255,41 @@ "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", @@ -2501,6 +3362,140 @@ "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" }, + "gap": { + "Package": "gap", + "Version": "1.6", + "Source": "Repository", + "Type": "Package", + "Title": "Genetic Analysis Package", + "Date": "2024-8-26", + "Authors@R": "c( person(\"Jing Hua\", \"Zhao\", role = c(\"aut\", \"cre\"), email = \"jinghuazhao@hotmail.com\", comment = c(ORCID = \"0000-0002-1463-5870\", \"0000-0003-4930-3582\")), person(\"Kurt\", \"Hornik\", role = \"ctb\"), person(\"Brian\", \"Ripley\", role = \"ctb\"), person(\"Uwe\", \"Ligges\", role = \"ctb\"), person(\"Achim\", \"Zeileis\", role = \"ctb\") )", + "Description": "As first reported [Zhao, J. H. 2007. \"gap: Genetic Analysis Package\". J Stat Soft 23(8):1-18. ], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).", + "License": "GPL (>= 2)", + "URL": "https://github.com/jinghuazhao/R", + "BugReports": "https://github.com/jinghuazhao/R/issues", + "Depends": [ + "R (>= 2.10)", + "gap.datasets (>= 0.0.6)" + ], + "Imports": [ + "dplyr", + "ggplot2", + "plotly", + "Rdpack" + ], + "Suggests": [ + "BradleyTerry2", + "DiagrammeR", + "DOT", + "MASS", + "Matrix", + "MCMCglmm", + "R2jags", + "bdsmatrix", + "bookdown", + "calibrate", + "circlize", + "coda", + "cowplot", + "coxme", + "foreign", + "genetics", + "grid", + "haplo.stats", + "htmlwidgets", + "jsonlite", + "kinship2", + "knitr", + "lattice", + "magic", + "manhattanly", + "matrixStats", + "meta", + "metafor", + "nlme", + "pedigree", + "pedigreemm", + "plotrix", + "readr", + "reshape", + "rmarkdown", + "rms", + "survival", + "valr" + ], + "Enhances": [ + "shiny" + ], + "LazyData": "Yes", + "LazyLoad": "Yes", + "NeedsCompilation": "yes", + "Encoding": "UTF-8", + "VignetteBuilder": "knitr", + "RoxygenNote": "7.3.2", + "RdMacros": "Rdpack", + "Author": "Jing Hua Zhao [aut, cre] (, 0000-0003-4930-3582), Kurt Hornik [ctb], Brian Ripley [ctb], Uwe Ligges [ctb], Achim Zeileis [ctb]", + "Maintainer": "Jing Hua Zhao ", + "Repository": "CRAN" + }, + "gap.datasets": { + "Package": "gap.datasets", + "Version": "0.0.6", + "Source": "Repository", + "Date": "2023-8-14", + "Title": "Datasets for 'gap'", + "Authors@R": "c(person(\"Jing Hua\", \"Zhao\", role = c(\"aut\", \"cre\"), email=\"jinghuazhao@hotmail.com\"), person(\"Swetlana\", \"Herbrandt\", role = \"ctb\"))", + "Description": "Datasets associated with the 'gap' package. Currently, it includes an example data for regional association plot (CDKN), an example data for a genomewide association meta-analysis (OPG), data in studies of Parkinson's diease (PD), ALHD2 markers and alcoholism (aldh2), APOE/APOC1 markers and Schizophrenia (apoeapoc), cystic fibrosis (cf), a Olink/INF panel (inf1), Manhattan plots with (hr1420, mhtdata) and without (w4) gene annotations.", + "LazyData": "Yes", + "LazyLoad": "Yes", + "License": "GPL (>= 2)", + "URL": "https://jinghuazhao.github.io/R/", + "NeedsCompilation": "no", + "Depends": [ + "R (>= 2.10)" + ], + "RoxygenNote": "7.1.2", + "Author": "Jing Hua Zhao [aut, cre], Swetlana Herbrandt [ctb]", + "Maintainer": "Jing Hua Zhao ", + "Repository": "CRAN" + }, + "gdtools": { + "Package": "gdtools", + "Version": "0.4.2", + "Source": "Repository", + "Title": "Utilities for Graphical Rendering and Fonts Management", + "Authors@R": "c( person(\"David\", \"Gohel\", , \"david.gohel@ardata.fr\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@rstudio.com\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", , \"jeroen@berkeley.edu\", role = \"aut\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Yixuan\", \"Qiu\", role = \"ctb\"), person(\"R Core Team\", role = \"cph\", comment = \"Cairo code from X11 device\"), person(\"ArData\", role = \"cph\"), person(\"RStudio\", role = \"cph\") )", + "Description": "Tools are provided to compute metrics of formatted strings and to check the availability of a font. Another set of functions is provided to support the collection of fonts from 'Google Fonts' in a cache. Their use is simple within 'R Markdown' documents and 'shiny' applications but also with graphic productions generated with the 'ggiraph', 'ragg' and 'svglite' packages or with tabular productions from the 'flextable' package.", + "License": "GPL-3 | file LICENSE", + "URL": "https://davidgohel.github.io/gdtools/", + "BugReports": "https://github.com/davidgohel/gdtools/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Imports": [ + "fontquiver (>= 0.2.0)", + "htmltools", + "Rcpp (>= 0.12.12)", + "systemfonts (>= 1.1.0)", + "tools" + ], + "Suggests": [ + "curl", + "gfonts", + "methods", + "testthat" + ], + "LinkingTo": [ + "Rcpp" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "cairo, freetype2, fontconfig", + "NeedsCompilation": "yes", + "Author": "David Gohel [aut, cre], Hadley Wickham [aut], Lionel Henry [aut], Jeroen Ooms [aut] (), Yixuan Qiu [ctb], R Core Team [cph] (Cairo code from X11 device), ArData [cph], RStudio [cph]", + "Maintainer": "David Gohel ", + "Repository": "CRAN" + }, "generics": { "Package": "generics", "Version": "0.1.3", @@ -3643,6 +4638,29 @@ "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", @@ -4063,6 +5081,102 @@ "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", + "Source": "Repository", + "Title": "Testing Linear Regression Models", + "Date": "2022-03-21", + "Authors@R": "c(person(given = \"Torsten\", family = \"Hothorn\", role = \"aut\", email = \"Torsten.Hothorn@R-project.org\", comment = c(ORCID = \"0000-0001-8301-0471\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = c(\"Richard\", \"W.\"), family = \"Farebrother\", role = \"aut\", comment = \"pan.f\"), person(given = \"Clint\", family = \"Cummins\", role = \"aut\", comment = \"pan.f\"), person(given = \"Giovanni\", family = \"Millo\", role = \"ctb\"), person(given = \"David\", family = \"Mitchell\", role = \"ctb\"))", + "Description": "A collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.", + "LazyData": "yes", + "Depends": [ + "R (>= 3.0.0)", + "stats", + "zoo" + ], + "Suggests": [ + "car", + "strucchange", + "sandwich", + "dynlm", + "stats4", + "survival", + "AER" + ], + "Imports": [ + "graphics" + ], + "License": "GPL-2 | GPL-3", + "NeedsCompilation": "yes", + "Author": "Torsten Hothorn [aut] (), Achim Zeileis [aut, cre] (), Richard W. Farebrother [aut] (pan.f), Clint Cummins [aut] (pan.f), Giovanni Millo [ctb], David Mitchell [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" + }, "lubridate": { "Package": "lubridate", "Version": "1.9.4", @@ -4256,6 +5370,28 @@ "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", @@ -4295,6 +5431,114 @@ "Maintainer": "Chung-hong Chan ", "Repository": "CRAN" }, + "modelbased": { + "Package": "modelbased", + "Version": "0.10.0", + "Source": "Repository", + "Type": "Package", + "Title": "Estimation of Model-Based Predictions, Contrasts and Means", + "Authors@R": "c(person(given = \"Dominique\", family = \"Makowski\", role = c(\"aut\", \"cre\"), email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Daniel\", family = \"Lüdecke\", role = \"aut\", email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = \"aut\", email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Rémi\", family = \"Thériault\", role = \"aut\", email = \"remi.theriault@mail.mcgill.ca\", comment = c(ORCID = \"0000-0003-4315-6788\")))", + "Maintainer": "Dominique Makowski ", + "Description": "Implements a general interface for model-based estimations for a wide variety of models, used in the computation of marginal means, contrast analysis and predictions. For a list of supported models, see 'insight::supported_models()'.", + "License": "GPL-3", + "URL": "https://easystats.github.io/modelbased/", + "BugReports": "https://github.com/easystats/modelbased/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "bayestestR (>= 0.15.1)", + "datawizard (>= 1.0.0)", + "insight (>= 1.0.1)", + "parameters (>= 0.24.1)", + "graphics", + "stats", + "tools", + "utils" + ], + "Suggests": [ + "BH", + "betareg", + "bootES", + "brms", + "coda", + "collapse", + "correlation", + "curl", + "easystats", + "effectsize (>= 1.0.0)", + "emmeans (>= 1.10.2)", + "Formula", + "gamm4", + "gganimate", + "ggplot2", + "glmmTMB", + "httr2", + "knitr", + "lme4", + "lmerTest", + "logspline", + "MASS", + "Matrix", + "marginaleffects (>= 0.25.0)", + "mice", + "mgcv", + "nanoparquet", + "ordinal", + "performance (>= 0.13.0)", + "patchwork", + "pbkrtest", + "poorman", + "pscl", + "RcppEigen", + "report", + "rmarkdown", + "rstanarm", + "rtdists", + "sandwich", + "see (>= 0.9.0)", + "testthat (>= 3.2.1)", + "vdiffr", + "withr" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/Needs/check": "stan-dev/cmdstanr", + "Config/Needs/website": "easystats/easystatstemplate", + "LazyData": "true", + "NeedsCompilation": "no", + "Author": "Dominique Makowski [aut, cre] (), Daniel Lüdecke [aut] (), Mattan S. Ben-Shachar [aut] (), Indrajeet Patil [aut] (), Rémi Thériault [aut] ()", + "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", @@ -4329,6 +5573,33 @@ "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", @@ -4354,6 +5625,104 @@ "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": "0.6.8", + "Source": "Repository", + "Type": "Package", + "Title": "Manipulation of Microsoft Word and PowerPoint Documents", + "Authors@R": "c( person(\"David\", \"Gohel\", , \"david.gohel@ardata.fr\", role = c(\"aut\", \"cre\")), person(\"Stefan\", \"Moog\", , \"moogs@gmx.de\", role = \"aut\"), person(\"Mark\", \"Heckmann\", , \"heckmann.mark@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-0736-7417\")), person(\"ArData\", role = \"cph\"), person(\"Frank\", \"Hangler\", , \"frank@plotandscatter.com\", role = \"ctb\", comment = \"function body_replace_all_text\"), person(\"Liz\", \"Sander\", , \"lsander@civisanalytics.com\", role = \"ctb\", comment = \"several documentation fixes\"), person(\"Anton\", \"Victorson\", , \"anton@victorson.se\", role = \"ctb\", comment = \"fixes xml structures\"), person(\"Jon\", \"Calder\", , \"jonmcalder@gmail.com\", role = \"ctb\", comment = \"update vignettes\"), person(\"John\", \"Harrold\", , \"john.m.harrold@gmail.com\", role = \"ctb\", comment = \"function annotate_base\"), person(\"John\", \"Muschelli\", , \"muschellij2@gmail.com\", role = \"ctb\", comment = \"google doc compatibility\"), person(\"Bill\", \"Denney\", , \"wdenney@humanpredictions.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\", \"function as.matrix.rpptx\")), person(\"Nikolai\", \"Beck\", , \"beck.nikolai@gmail.com\", role = \"ctb\", comment = \"set speaker notes for .pptx documents\"), person(\"Greg\", \"Leleu\", , \"gregoire.leleu@gmail.com\", role = \"ctb\", comment = \"fields functionality in ppt\"), person(\"Majid\", \"Eismann\", role = \"ctb\"), person(\"Hongyuan\", \"Jia\", , \"hongyuanjia@cqust.edu.cn\", role = \"ctb\", comment = c(ORCID = \"0000-0002-0075-8183\")) )", + "Description": "Access and manipulate 'Microsoft Word', 'RTF' and 'Microsoft PowerPoint' documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. The package does not require any installation of Microsoft products to be able to write Microsoft files.", + "License": "MIT + file LICENSE", + "URL": "https://ardata-fr.github.io/officeverse/, https://davidgohel.github.io/officer/", + "BugReports": "https://github.com/davidgohel/officer/issues", + "Imports": [ + "cli", + "graphics", + "grDevices", + "openssl", + "R6", + "ragg", + "stats", + "utils", + "uuid", + "xml2 (>= 1.1.0)", + "zip (>= 2.1.0)" + ], + "Suggests": [ + "devEMF", + "doconv (>= 0.3.0)", + "gdtools", + "ggplot2", + "knitr", + "magick", + "rmarkdown", + "rsvg", + "testthat", + "withr" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'core_properties.R' 'custom_properties.R' 'defunct.R' 'dev-utils.R' 'docx_add.R' 'docx_comments.R' 'docx_cursor.R' 'docx_part.R' 'docx_replace.R' 'docx_section.R' 'docx_settings.R' 'empty_content.R' 'formatting_properties.R' 'fortify_docx.R' 'fortify_pptx.R' 'knitr_utils.R' 'officer.R' 'ooxml.R' 'ooxml_block_objects.R' 'ooxml_run_objects.R' 'openxml_content_type.R' 'openxml_document.R' 'pack_folder.R' 'ph_location.R' 'post-proc.R' 'ppt_class_dir_collection.R' 'ppt_classes.R' 'ppt_notes.R' 'ppt_ph_dedupe_layout.R' 'ppt_ph_manipulate.R' 'ppt_ph_rename_layout.R' 'ppt_ph_with_methods.R' 'pptx_informations.R' 'pptx_layout_helper.R' 'pptx_matrix.R' 'utils.R' 'pptx_slide_manip.R' 'read_docx.R' 'read_docx_styles.R' 'read_pptx.R' 'read_xlsx.R' 'relationship.R' 'rtf.R' 'shape_properties.R' 'shorcuts.R'", + "NeedsCompilation": "no", + "Author": "David Gohel [aut, cre], Stefan Moog [aut], Mark Heckmann [aut] (), ArData [cph], Frank Hangler [ctb] (function body_replace_all_text), Liz Sander [ctb] (several documentation fixes), Anton Victorson [ctb] (fixes xml structures), Jon Calder [ctb] (update vignettes), John Harrold [ctb] (function annotate_base), John Muschelli [ctb] (google doc compatibility), Bill Denney [ctb] (, function as.matrix.rpptx), Nikolai Beck [ctb] (set speaker notes for .pptx documents), Greg Leleu [ctb] (fields functionality in ppt), Majid Eismann [ctb], Hongyuan Jia [ctb] ()", + "Maintainer": "David Gohel ", + "Repository": "CRAN" + }, + "opdisDownsampling": { + "Package": "opdisDownsampling", + "Version": "1.0.1", + "Source": "Repository", + "Type": "Package", + "Title": "Optimal Distribution Preserving Down-Sampling of Bio-Medical Data", + "Description": "An optimized method for distribution-preserving class-proportional down-sampling of bio-medical data.", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "parallel", + "graphics", + "methods", + "stats", + "caTools", + "pracma", + "twosamples", + "doParallel", + "pbmcapply", + "foreach" + ], + "LazyData": "true", + "Suggests": [ + "testthat" + ], + "License": "GPL-3", + "URL": "https://cran.r-project.org/package=opdisDownsampling", + "Encoding": "UTF-8", + "Author": "Jorn Lotsch [aut,cre] (), Sebastian Malkusch [aut] (), Alfred Ultsch [aut] ()", + "Maintainer": "Jorn Lotsch ", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, "openssl": { "Package": "openssl", "Version": "2.3.2", @@ -4645,6 +6014,27 @@ "Author": "Thomas Lin Pedersen [cre, aut] ()", "Repository": "CRAN" }, + "pbmcapply": { + "Package": "pbmcapply", + "Version": "1.5.1", + "Source": "Repository", + "Type": "Package", + "Title": "Tracking the Progress of Mc*pply with Progress Bar", + "Author": "Kevin Kuang (aut), Quyu Kong (ctb), Francesco Napolitano (ctb)", + "Maintainer": "Kevin kuang ", + "Description": "A light-weight package helps you track and visualize the progress of parallel version of vectorized R functions (mc*apply). Parallelization (mc.core > 1) works only on *nix (Linux, Unix such as macOS) system due to the lack of fork() functionality, which is essential for mc*apply, on Windows.", + "Depends": [ + "utils", + "parallel" + ], + "BugReports": "https://github.com/kvnkuang/pbmcapply/issues", + "URL": "https://github.com/kvnkuang/pbmcapply", + "License": "MIT + file LICENSE", + "RoxygenNote": "6.1.1", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, "performance": { "Package": "performance", "Version": "0.13.0", @@ -4859,6 +6249,82 @@ "NeedsCompilation": "no", "Repository": "CRAN" }, + "plotly": { + "Package": "plotly", + "Version": "4.10.4", + "Source": "Repository", + "Title": "Create Interactive Web Graphics via 'plotly.js'", + "Authors@R": "c(person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"cpsievert1@gmail.com\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Chris\", \"Parmer\", role = \"aut\", email = \"chris@plot.ly\"), person(\"Toby\", \"Hocking\", role = \"aut\", email = \"tdhock5@gmail.com\"), person(\"Scott\", \"Chamberlain\", role = \"aut\", email = \"myrmecocystus@gmail.com\"), person(\"Karthik\", \"Ram\", role = \"aut\", email = \"karthik.ram@gmail.com\"), person(\"Marianne\", \"Corvellec\", role = \"aut\", email = \"marianne.corvellec@igdore.org\", comment = c(ORCID = \"0000-0002-1994-3581\")), person(\"Pedro\", \"Despouy\", role = \"aut\", email = \"pedro@plot.ly\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Plotly Technologies Inc.\", role = \"cph\"))", + "License": "MIT + file LICENSE", + "Description": "Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.", + "URL": "https://plotly-r.com, https://github.com/plotly/plotly.R, https://plotly.com/r/", + "BugReports": "https://github.com/plotly/plotly.R/issues", + "Depends": [ + "R (>= 3.2.0)", + "ggplot2 (>= 3.0.0)" + ], + "Imports": [ + "tools", + "scales", + "httr (>= 1.3.0)", + "jsonlite (>= 1.6)", + "magrittr", + "digest", + "viridisLite", + "base64enc", + "htmltools (>= 0.3.6)", + "htmlwidgets (>= 1.5.2.9001)", + "tidyr (>= 1.0.0)", + "RColorBrewer", + "dplyr", + "vctrs", + "tibble", + "lazyeval (>= 0.2.0)", + "rlang (>= 0.4.10)", + "crosstalk", + "purrr", + "data.table", + "promises" + ], + "Suggests": [ + "MASS", + "maps", + "hexbin", + "ggthemes", + "GGally", + "ggalluvial", + "testthat", + "knitr", + "shiny (>= 1.1.0)", + "shinytest (>= 1.3.0)", + "curl", + "rmarkdown", + "Cairo", + "broom", + "webshot", + "listviewer", + "dendextend", + "sf", + "png", + "IRdisplay", + "processx", + "plotlyGeoAssets", + "forcats", + "withr", + "palmerpenguins", + "rversions", + "reticulate", + "rsvg" + ], + "LazyData": "true", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "Config/Needs/check": "tidyverse/ggplot2, rcmdcheck, devtools, reshape2", + "NeedsCompilation": "no", + "Author": "Carson Sievert [aut, cre] (), Chris Parmer [aut], Toby Hocking [aut], Scott Chamberlain [aut], Karthik Ram [aut], Marianne Corvellec [aut] (), Pedro Despouy [aut], Salim Brüggemann [ctb] (), Plotly Technologies Inc. [cph]", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, "plyr": { "Package": "plyr", "Version": "1.8.9", @@ -4951,6 +6417,36 @@ "Maintainer": "Johan Larsson ", "Repository": "CRAN" }, + "pracma": { + "Package": "pracma", + "Version": "2.4.4", + "Source": "Repository", + "Type": "Package", + "Date": "2023-11-08", + "Title": "Practical Numerical Math Functions", + "Authors@R": "person(\"Hans W.\", \"Borchers\", email=\"hwborchers@googlemail.com\", role=c(\"aut\", \"cre\"))", + "Depends": [ + "R (>= 3.1.0)" + ], + "Imports": [ + "graphics", + "grDevices", + "stats", + "utils" + ], + "Suggests": [ + "NlcOptim", + "quadprog" + ], + "Description": "Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.", + "License": "GPL (>= 3)", + "ByteCompile": "true", + "LazyData": "yes", + "NeedsCompilation": "no", + "Author": "Hans W. Borchers [aut, cre]", + "Maintainer": "Hans W. Borchers ", + "Repository": "CRAN" + }, "prettyunits": { "Package": "prettyunits", "Version": "1.2.0", @@ -5203,6 +6699,119 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, + "qgam": { + "Package": "qgam", + "Version": "2.0.0", + "Source": "Repository", + "Type": "Package", + "Title": "Smooth Additive Quantile Regression Models", + "Date": "2025-04-10", + "Authors@R": "c(person(\"Matteo\", \"Fasiolo\", email = \"matteo.fasiolo@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Ben\", \"Griffiths\", role = c(\"aut\")), person(\"Simon\", \"N. 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The main function is qgam() which is similar to gam() in 'mgcv', but fits non-parametric quantile regression models.", + "License": "GPL (>= 2)", + "Depends": [ + "R (>= 4.0)", + "mgcv (>= 1.9)" + ], + "Imports": [ + "shiny", + "plyr", + "doParallel", + "parallel", + "grDevices" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "MASS", + "RhpcBLASctl", + "testthat" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Matteo Fasiolo [aut, cre], Ben Griffiths [aut], Simon N. Wood [ctb], Margaux Zaffran [ctb], Yannig Goude [ctb], Raphael Nedellec [ctb]", + "Repository": "CRAN" + }, + "qqconf": { + "Package": "qqconf", + "Version": "1.3.2", + "Source": "Repository", + "Type": "Package", + "Title": "Creates Simultaneous Testing Bands for QQ-Plots", + "Authors@R": "c( person(\"Eric\", \"Weine\", email = \"ericweine15@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Mary Sara\", \"McPeek\", email = \"mcpeek@uchicago.edu\", role = \"aut\"), person(\"Abney\", \"Mark\", email = \"abney@uchicago.edu\", role = \"aut\"))", + "Description": "Provides functionality for creating Quantile-Quantile (QQ) and Probability-Probability (PP) plots with simultaneous testing bands to asses significance of sample deviation from a reference distribution .", + "License": "GPL-3", + "Depends": [ + "R (>= 4.0.0)" + ], + "SystemRequirements": "fftw3 (>= 3.1.2)", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "Imports": [ + "MASS (>= 7.3-50)", + "robustbase (>= 0.93-4)", + "Rcpp" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "distr (>= 2.8.0)" + ], + "Collate": "'one_sided.R' 'ppplot.R' 'qqconf-package.R' 'qqplot.R' 'RcppExports.R' 'two_sided.R' 'utils.R'", + "VignetteBuilder": "knitr", + "LinkingTo": [ + "Rcpp" + ], + "URL": "https://github.com/eweine/qqconf", + "BugReports": "https://github.com/eweine/qqconf/issues", + "NeedsCompilation": "yes", + "Author": "Eric Weine [aut, cre], Mary Sara McPeek [aut], Abney Mark [aut]", + "Maintainer": "Eric Weine ", + "Repository": "CRAN" + }, + "qqplotr": { + "Package": "qqplotr", + "Version": "0.0.6", + "Source": "Repository", + "Type": "Package", + "Title": "Quantile-Quantile Plot Extensions for 'ggplot2'", + "Description": "Extensions of 'ggplot2' Q-Q plot functionalities.", + "Authors@R": "c(person(\"Alexandre\", \"Almeida\", email = \"almeida.xan@gmail.com\", role = c(\"aut\")), person(\"Adam\", \"Loy\", email = \"loyad01@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Heike\", \"Hofmann\", role = \"aut\"))", + "URL": "https://github.com/aloy/qqplotr", + "BugReports": "https://github.com/aloy/qqplotr/issues", + "License": "GPL-3 | file LICENSE", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.2.2", + "Collate": "'data.R' 'geom_qq_band.R' 'qqplotr.R' 'runShinyExample.R' 'stat_pp_band.R' 'stat_pp_line.R' 'stat_pp_point.R' 'stat_qq_line.R' 'stat_qq_band.R' 'stat_qq_point.R'", + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.1)", + "ggplot2 (>= 2.2)" + ], + "Imports": [ + "dplyr", + "robustbase", + "MASS", + "opdisDownsampling", + "qqconf (>= 1.3.1)" + ], + "Suggests": [ + "shiny", + "devtools", + "lattice", + "shinyBS", + "knitr", + "rmarkdown" + ], + "NeedsCompilation": "no", + "Author": "Alexandre Almeida [aut], Adam Loy [aut, cre], Heike Hofmann [aut]", + "Maintainer": "Adam Loy ", + "Repository": "CRAN" + }, "quarto": { "Package": "quarto", "Version": "1.4.4", @@ -5246,6 +6855,42 @@ "Maintainer": "Christophe Dervieux ", "Repository": "CRAN" }, + "ragg": { + "Package": "ragg", + "Version": "1.4.0", + "Source": "Repository", + "Type": "Package", + "Title": "Graphic Devices Based on AGG", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Maxim\", \"Shemanarev\", role = c(\"aut\", \"cph\"), comment = \"Author of AGG\"), person(\"Tony\", \"Juricic\", , \"tonygeek@yahoo.com\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Milan\", \"Marusinec\", , \"milan@marusinec.sk\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Spencer\", \"Garrett\", role = \"ctb\", comment = \"Contributor to AGG\"), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Maintainer": "Thomas Lin Pedersen ", + "Description": "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The 'ragg' package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://ragg.r-lib.org, https://github.com/r-lib/ragg", + "BugReports": "https://github.com/r-lib/ragg/issues", + "Imports": [ + "systemfonts (>= 1.0.3)", + "textshaping (>= 0.3.0)" + ], + "Suggests": [ + "covr", + "graphics", + "grid", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "systemfonts", + "textshaping" + ], + "Config/Needs/website": "ggplot2, devoid, magick, bench, tidyr, ggridges, hexbin, sessioninfo, pkgdown, tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "freetype2, libpng, libtiff, libjpeg", + "Config/testthat/edition": "3", + "Config/build/compilation-database": "true", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Maxim Shemanarev [aut, cph] (Author of AGG), Tony Juricic [ctb, cph] (Contributor to AGG), Milan Marusinec [ctb, cph] (Contributor to AGG), Spencer Garrett [ctb] (Contributor to AGG), Posit, PBC [cph, fnd]", + "Repository": "CRAN" + }, "rankinPlot": { "Package": "rankinPlot", "Version": "1.1.0", @@ -5302,6 +6947,34 @@ "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", @@ -5519,6 +7192,33 @@ "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, + "reformulas": { + "Package": "reformulas", + "Version": "0.4.0", + "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" + ], + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Ben Bolker [aut, cre] ()", + "Maintainer": "Ben Bolker ", + "Repository": "CRAN" + }, "rematch": { "Package": "rematch", "Version": "2.0.0", @@ -5539,53 +7239,6 @@ "NeedsCompilation": "no", "Repository": "CRAN" }, - "remotes": { - "Package": "remotes", - "Version": "2.5.0", - "Source": "Repository", - "Title": "R Package Installation from Remote Repositories, Including 'GitHub'", - "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Martin\", \"Morgan\", role = \"aut\"), person(\"Dan\", \"Tenenbaum\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Ascent Digital Services\", role = \"cph\") )", - "Description": "Download and install R packages stored in 'GitHub', 'GitLab', 'Bitbucket', 'Bioconductor', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.", - "License": "MIT + file LICENSE", - "URL": "https://remotes.r-lib.org, https://github.com/r-lib/remotes#readme", - "BugReports": "https://github.com/r-lib/remotes/issues", - "Depends": [ - "R (>= 3.0.0)" - ], - "Imports": [ - "methods", - "stats", - "tools", - "utils" - ], - "Suggests": [ - "brew", - "callr", - "codetools", - "covr", - "curl", - "git2r (>= 0.23.0)", - "knitr", - "mockery", - "pingr", - "pkgbuild (>= 1.0.1)", - "rmarkdown", - "rprojroot", - "testthat (>= 3.0.0)", - "webfakes", - "withr" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", - "SystemRequirements": "Subversion for install_svn, git for install_git", - "NeedsCompilation": "no", - "Author": "Gábor Csárdi [aut, cre], Jim Hester [aut], Hadley Wickham [aut], Winston Chang [aut], Martin Morgan [aut], Dan Tenenbaum [aut], Posit Software, PBC [cph, fnd], Ascent Digital Services [cph]", - "Maintainer": "Gábor Csárdi ", - "Repository": "CRAN" - }, "rempsyc": { "Package": "rempsyc", "Version": "0.1.9", @@ -5646,6 +7299,116 @@ "Maintainer": "Rémi Thériault ", "Repository": "CRAN" }, + "renv": { + "Package": "renv", + "Version": "1.1.4", + "Source": "Repository", + "Type": "Package", + "Title": "Project Environments", + "Authors@R": "c( person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"kevin@rstudio.com\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Hadley\", \"Wickham\", role = c(\"aut\"), email = \"hadley@rstudio.com\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.", + "License": "MIT + file LICENSE", + "URL": "https://rstudio.github.io/renv/, https://github.com/rstudio/renv", + "BugReports": "https://github.com/rstudio/renv/issues", + "Imports": [ + "utils" + ], + "Suggests": [ + "BiocManager", + "cli", + "compiler", + "covr", + "cpp11", + "devtools", + "gitcreds", + "jsonlite", + "jsonvalidate", + "knitr", + "miniUI", + "modules", + "packrat", + "pak", + "R6", + "remotes", + "reticulate", + "rmarkdown", + "rstudioapi", + "shiny", + "testthat", + "uuid", + "waldo", + "yaml", + "webfakes" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "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]", + "Maintainer": "Kevin Ushey ", + "Repository": "CRAN" + }, + "report": { + "Package": "report", + "Version": "0.6.1", + "Source": "Repository", + "Type": "Package", + "Title": "Automated Reporting of Results and Statistical Models", + "Authors@R": "c(person(given = \"Dominique\", family = \"Makowski\", role = \"aut\", email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Daniel\", family = \"Lüdecke\", role = \"aut\", email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Rémi\", family = \"Thériault\", role = c(\"aut\", \"cre\"), email = \"remi.theriault@mail.mcgill.ca\", comment = c(ORCID = \"0000-0003-4315-6788\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = \"aut\", email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"aut\", email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Rudolf\", family = \"Siegel\", role = \"ctb\", email = \"mutlusun@users.noreply.github.com\", comment = c(ORCID = \"0000-0002-6021-804X\")), person(given = \"Camden\", family = \"Bock\", role = \"ctb\", email = \"camden.bock@maine.edu\", comment = c(ORCID = \"0000-0002-3907-7748\")))", + "Maintainer": "Rémi Thériault ", + "Description": "The aim of the 'report' package is to bridge the gap between R’s output and the formatted results contained in your manuscript. This package converts statistical models and data frames into textual reports suited for publication, ensuring standardization and quality in results reporting.", + "License": "MIT + file LICENSE", + "URL": "https://easystats.github.io/report/", + "BugReports": "https://github.com/easystats/report/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "bayestestR (>= 0.15.0)", + "effectsize (>= 1.0.0)", + "insight (>= 1.0.1)", + "parameters (>= 0.24.1)", + "performance (>= 0.13.0)", + "datawizard (>= 1.0.0)", + "stats", + "tools", + "utils" + ], + "Suggests": [ + "BayesFactor", + "brms", + "collapse", + "ivreg", + "knitr", + "lavaan", + "lme4", + "dplyr", + "Formula", + "rmarkdown", + "rstanarm", + "survival", + "modelbased (>= 0.9.0)", + "emmeans", + "marginaleffects (>= 0.25.0)", + "RcppEigen", + "BH", + "testthat (>= 3.2.1)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/Needs/website": "rstudio/bslib, r-lib/pkgdown, easystats/easystatstemplate", + "Collate": "'cite_easystats.R' 'format_algorithm.R' 'format_citation.R' 'format_formula.R' 'format_model.R' 'reexports.R' 'report-package.R' 'report.BFBayesFactor.R' 'utils_combine_tables.R' 'report.lm.R' 'report.MixMod.R' 'report_text.R' 'report.R' 'report.htest.R' 'report.aov.R' 'report.bayesfactor_models.R' 'report.lme4.R' 'report.stanreg.R' 'report.brmsfit.R' 'report.character.R' 'report.compare.loo.R' 'report.compare_performance.R' 'report.coxph.R' 'report.data.frame.R' 'report.default.R' 'report.estimate_contrasts.R' 'report.factor.R' 'report.glm.R' 'report.glmmTMB.R' 'report.ivreg.R' 'report.lavaan.R' 'report.lme.R' 'report.numeric.R' 'report.sessionInfo.R' 'report.survreg.R' 'report.test_performance.R' 'report.zeroinfl.R' 'report_effectsize.R' 'report_htest_chi2.R' 'report_htest_cor.R' 'report_htest_fisher.R' 'report_htest_friedman.R' 'report_htest_kruskal.R' 'report_htest_ttest.R' 'report_htest_wilcox.R' 'report_info.R' 'report_intercept.R' 'report_misc.R' 'report_model.R' 'report_parameters.R' 'report_participants.R' 'report_performance.R' 'report_priors.R' 'report_random.R' 'report_s.R' 'report_sample.R' 'report_statistics.R' 'report_table.R' 'utils_error_message.R' 'utils_grouped_df.R' 'utils_misspelled_variables.R' 'zzz.R'", + "NeedsCompilation": "no", + "Author": "Dominique Makowski [aut] (), Daniel Lüdecke [aut] (), Indrajeet Patil [aut] (), Rémi Thériault [aut, cre] (), Mattan S. Ben-Shachar [aut] (), Brenton M. Wiernik [aut] (), Rudolf Siegel [ctb] (), Camden Bock [ctb] ()", + "Repository": "CRAN" + }, "reshape2": { "Package": "reshape2", "Version": "1.4.4", @@ -5846,6 +7609,64 @@ "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, + "robustbase": { + "Package": "robustbase", + "Version": "0.99-4-1", + "Source": "Repository", + "VersionNote": "Released 0.99-4 on 2024-08-19, 0.99-3 on 2024-07-01 and 0.99-2 on 2024-01-27 to CRAN", + "Date": "2024-09-24", + "Title": "Basic Robust Statistics", + "Authors@R": "c(person(\"Martin\",\"Maechler\", role=c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) , person(\"Peter\", \"Rousseeuw\", role=\"ctb\", comment = \"Qn and Sn\") , person(\"Christophe\", \"Croux\", role=\"ctb\", comment = \"Qn and Sn\") , person(\"Valentin\", \"Todorov\", role = \"aut\", email = \"valentin.todorov@chello.at\", comment = \"most robust Cov\") , person(\"Andreas\", \"Ruckstuhl\", role = \"aut\", email = \"andreas.ruckstuhl@zhaw.ch\", comment = \"nlrob, anova, glmrob\") , person(\"Matias\", \"Salibian-Barrera\", role = \"aut\", email = \"matias@stat.ubc.ca\", comment = \"lmrob orig.\") , person(\"Tobias\", \"Verbeke\", role = c(\"ctb\",\"fnd\"), email = \"tobias.verbeke@openanalytics.eu\", comment = \"mc, adjbox\") , person(\"Manuel\", \"Koller\", role = \"aut\", email = \"koller.manuel@gmail.com\", comment = \"mc, lmrob, psi-func.\") , person(c(\"Eduardo\", \"L. T.\"), \"Conceicao\", role = \"aut\", email = \"mail@eduardoconceicao.org\", comment = \"MM-, tau-, CM-, and MTL- nlrob\") , person(\"Maria\", \"Anna di Palma\", role = \"ctb\", comment = \"initial version of Comedian\") )", + "URL": "https://robustbase.R-forge.R-project.org/, https://R-forge.R-project.org/R/?group_id=59, https://R-forge.R-project.org/scm/viewvc.php/pkg/robustbase/?root=robustbase, svn://svn.r-forge.r-project.org/svnroot/robustbase/pkg/robustbase", + "BugReports": "https://R-forge.R-project.org/tracker/?atid=302&group_id=59", + "Description": "\"Essential\" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book \"Robust Statistics, Theory and Methods\" by 'Maronna, Martin and Yohai'; Wiley 2006.", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "stats", + "graphics", + "utils", + "methods", + "DEoptimR" + ], + "Suggests": [ + "grid", + "MASS", + "lattice", + "boot", + "cluster", + "Matrix", + "robust", + "fit.models", + "MPV", + "xtable", + "ggplot2", + "GGally", + "RColorBrewer", + "reshape2", + "sfsmisc", + "catdata", + "doParallel", + "foreach", + "skewt" + ], + "SuggestsNote": "mostly only because of vignette graphics and simulation", + "Enhances": [ + "robustX", + "rrcov", + "matrixStats", + "quantreg", + "Hmisc" + ], + "EnhancesNote": "linked to in man/*.Rd", + "LazyData": "yes", + "NeedsCompilation": "yes", + "License": "GPL (>= 2)", + "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [ctb] (Qn and Sn), Christophe Croux [ctb] (Qn and Sn), Valentin Todorov [aut] (most robust Cov), Andreas Ruckstuhl [aut] (nlrob, anova, glmrob), Matias Salibian-Barrera [aut] (lmrob orig.), Tobias Verbeke [ctb, fnd] (mc, adjbox), Manuel Koller [aut] (mc, lmrob, psi-func.), Eduardo L. T. Conceicao [aut] (MM-, tau-, CM-, and MTL- nlrob), Maria Anna di Palma [ctb] (initial version of Comedian)", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" + }, "rpart": { "Package": "rpart", "Version": "4.1.24", @@ -6011,6 +7832,90 @@ "Maintainer": "Thomas Lin Pedersen ", "Repository": "CRAN" }, + "see": { + "Package": "see", + "Version": "0.11.0", + "Source": "Repository", + "Type": "Package", + "Title": "Model Visualisation Toolbox for 'easystats' and 'ggplot2'", + "Authors@R": "c(person(given = \"Daniel\", family = \"Lüdecke\", role = c(\"aut\", \"ctb\"), email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Dominique\", family = \"Makowski\", role = c(\"aut\", \"inv\"), email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Indrajeet\", family = \"Patil\", role = c(\"aut\", \"cre\"), email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = c(\"aut\", \"ctb\"), email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = c(\"aut\", \"ctb\"), email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Philip\", family = \"Waggoner\", role = c(\"aut\", \"ctb\"), email = \"philip.waggoner@gmail.com\", comment = c(ORCID = \"0000-0002-7825-7573\")), person(given = \"Jeffrey R.\", family = \"Stevens\", role = \"ctb\", email = \"jeffrey.r.stevens@gmail.com\", comment = c(ORCID = \"0000-0003-2375-1360\")), person(given = \"Matthew\", family = \"Smith\", role = \"rev\", email = \"M.Smith3@napier.ac.uk\"), person(given = \"Jakob\", family = \"Bossek\", role = \"rev\", email = \"bossek@wi.uni-muenster.de\"))", + "Maintainer": "Indrajeet Patil ", + "Description": "Provides plotting utilities supporting packages in the 'easystats' ecosystem () and some extra themes, geoms, and scales for 'ggplot2'. Color scales are based on . References: Lüdecke et al. (2021) .", + "License": "MIT + file LICENSE", + "URL": "https://easystats.github.io/see/", + "BugReports": "https://github.com/easystats/see/issues", + "Depends": [ + "graphics", + "grDevices", + "R (>= 4.0)", + "stats" + ], + "Imports": [ + "bayestestR (>= 0.15.2)", + "correlation (>= 0.8.7)", + "datawizard (>= 1.0.1)", + "effectsize (>= 1.0.0)", + "ggplot2 (>= 3.5.1)", + "insight (>= 1.1.0)", + "modelbased (>= 0.10.0)", + "patchwork (>= 1.3.0)", + "parameters (>= 0.24.2)", + "performance (>= 0.13.0)" + ], + "Suggests": [ + "BH", + "brms", + "collapse", + "curl", + "DHARMa", + "emmeans", + "factoextra", + "Formula", + "ggdag", + "ggdist", + "ggraph", + "ggrepel", + "ggridges", + "ggside", + "glmmTMB", + "grid", + "httr2", + "lavaan", + "lme4", + "logspline", + "marginaleffects", + "MASS", + "mclogit", + "mclust", + "merDeriv", + "mgcv", + "metafor", + "NbClust", + "nFactors", + "psych", + "qqplotr (>= 0.0.6)", + "randomForest", + "RcppEigen", + "rlang", + "rmarkdown", + "rstanarm", + "scales (>= 1.3.0)", + "splines", + "testthat (>= 3.2.1)", + "tidygraph", + "vdiffr (>= 1.0.8)" + ], + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/Needs/website": "easystats/easystatstemplate", + "Config/rcmdcheck/ignore-inconsequential-notes": "true", + "NeedsCompilation": "no", + "Author": "Daniel Lüdecke [aut, ctb] (), Dominique Makowski [aut, inv] (), Indrajeet Patil [aut, cre] (), Mattan S. Ben-Shachar [aut, ctb] (), Brenton M. Wiernik [aut, ctb] (), Philip Waggoner [aut, ctb] (), Jeffrey R. Stevens [ctb] (), Matthew Smith [rev], Jakob Bossek [rev]", + "Repository": "CRAN" + }, "shiny": { "Package": "shiny", "Version": "1.10.0", @@ -6397,6 +8302,107 @@ "Maintainer": "Thomas Lin Pedersen ", "Repository": "CRAN" }, + "textshaping": { + "Package": "textshaping", + "Version": "1.0.0", + "Source": "Repository", + "Title": "Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text Shaping", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides access to the text shaping functionality in the 'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi' library. 'textshaping' is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the 'systemfonts' package.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/textshaping", + "BugReports": "https://github.com/r-lib/textshaping/issues", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ + "lifecycle", + "stats", + "stringi", + "systemfonts (>= 1.1.0)", + "utils" + ], + "Suggests": [ + "covr", + "grDevices", + "grid", + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.1)", + "systemfonts (>= 1.0.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "freetype2, harfbuzz, fribidi", + "Config/build/compilation-database": "true", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Posit, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "thematic": { + "Package": "thematic", + "Version": "0.1.6", + "Source": "Repository", + "Title": "Unified and Automatic 'Theming' of 'ggplot2', 'lattice', and 'base' R Graphics", + "Authors@R": "c( person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Theme 'ggplot2', 'lattice', and 'base' graphics based on a few choices, including foreground color, background color, accent color, and font family. Fonts that aren't available on the system, but are available via download on 'Google Fonts', can be automatically downloaded, cached, and registered for use with the 'showtext' and 'ragg' packages.", + "License": "MIT + file LICENSE", + "URL": "https://rstudio.github.io/thematic/, https://github.com/rstudio/thematic", + "BugReports": "https://github.com/rstudio/thematic/issues", + "Depends": [ + "R (>= 3.0.0)" + ], + "Imports": [ + "farver", + "ggplot2 (>= 3.3.0)", + "graphics", + "grDevices", + "grid", + "rappdirs", + "rlang", + "rstudioapi (>= 0.8)", + "scales", + "utils" + ], + "Suggests": [ + "bslib", + "Cairo", + "curl", + "gganimate", + "ggiraph", + "htmltools", + "jsonlite", + "knitr", + "lattice", + "ragg", + "rmarkdown", + "shiny (>= 1.5.0)", + "showtext", + "stats", + "svglite", + "sysfonts", + "systemfonts", + "testthat", + "vdiffr (>= 1.0.0)", + "withr" + ], + "Config/Needs/check": "shinytest, callr, sf, ggthemes, patchwork, gridExtra, tinytex, devtools, rversions", + "Config/Needs/routine": "ggrepel", + "Config/Needs/website": "GGally, RColorBrewer, patchwork, apreshill/quillt", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'auto.R' 'base.R' 'cache.R' 'gfonts.R' 'ggplot.R' 'globals.R' 'hooks.R' 'knitr.R' 'lattice.R' 'onLoad.R' 'thematic-package.R' 'thematic-save-plot.R' 'thematic.R' 'utils.R' 'view-shinytest.R'", + "NeedsCompilation": "no", + "Author": "Carson Sievert [aut, cre] (), Barret Schloerke [aut] (), Joe Cheng [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, "tibble": { "Package": "tibble", "Version": "3.2.1", @@ -6686,6 +8692,31 @@ "Author": "Thomas Lin Pedersen [aut, cre] ()", "Repository": "CRAN" }, + "twosamples": { + "Package": "twosamples", + "Version": "2.0.1", + "Source": "Repository", + "Type": "Package", + "Title": "Fast Permutation Based Two Sample Tests", + "Authors@R": "person(\"Connor\", \"Dowd\", , \"cd@codowd.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9782-0931\"))", + "Description": "Fast randomization based two sample tests. Testing the hypothesis that two samples come from the same distribution using randomization to create p-values. Included tests are: Kolmogorov-Smirnov, Kuiper, Cramer-von Mises, Anderson-Darling, Wasserstein, and DTS. The default test (two_sample) is based on the DTS test statistic, as it is the most powerful, and thus most useful to most users. The DTS test statistic builds on the Wasserstein distance by using a weighting scheme like that of Anderson-Darling. See the companion paper at or for details of that test statistic, and non-standard uses of the package (parallel for big N, weighted observations, one sample tests, etc). We also include the permutation scheme to make test building simple for others.", + "License": "GPL (>= 2)", + "Encoding": "UTF-8", + "LinkingTo": [ + "cpp11" + ], + "RoxygenNote": "7.2.3", + "URL": "https://twosampletest.com, https://github.com/cdowd/twosamples", + "BugReports": "https://github.com/cdowd/twosamples/issues", + "Suggests": [ + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Connor Dowd [aut, cre] ()", + "Maintainer": "Connor Dowd ", + "Repository": "CRAN" + }, "tzdb": { "Package": "tzdb", "Version": "0.5.0", @@ -6747,6 +8778,24 @@ "Maintainer": "Kirill Müller ", "Repository": "CRAN" }, + "uuid": { + "Package": "uuid", + "Version": "1.2-1", + "Source": "Repository", + "Title": "Tools for Generating and Handling of UUIDs", + "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.org, ), Theodore Ts'o [aut, cph] (libuuid)", + "Maintainer": "Simon Urbanek ", + "Authors@R": "c(person(\"Simon\", \"Urbanek\", role=c(\"aut\",\"cre\",\"cph\"), email=\"Simon.Urbanek@r-project.org\", comment=c(\"https://urbanek.org\", ORCID=\"0000-0003-2297-1732\")), person(\"Theodore\",\"Ts'o\", email=\"tytso@thunk.org\", role=c(\"aut\",\"cph\"), comment=\"libuuid\"))", + "Depends": [ + "R (>= 2.9.0)" + ], + "Description": "Tools for generating and handling of UUIDs (Universally Unique Identifiers).", + "License": "MIT + file LICENSE", + "URL": "https://www.rforge.net/uuid", + "BugReports": "https://github.com/s-u/uuid/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, "vctrs": { "Package": "vctrs", "Version": "0.6.5", @@ -7165,6 +9214,47 @@ "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd]", "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-14", + "Source": "Repository", + "Date": "2025-04-09", + "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", + "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", + "Depends": [ + "R (>= 3.1.0)", + "stats" + ], + "Suggests": [ + "AER", + "coda", + "chron", + "ggplot2 (>= 3.5.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tinyplot", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", + "graphics", + "grDevices", + "lattice (>= 0.20-27)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://zoo.R-Forge.R-project.org/", + "NeedsCompilation": "yes", + "Author": "Achim Zeileis [aut, cre] (), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" } } } diff --git a/inst/apps/FreesearchR/app.R b/inst/apps/FreesearchR/app.R index 993bbae..340380f 100644 --- a/inst/apps/FreesearchR/app.R +++ b/inst/apps/FreesearchR/app.R @@ -1940,7 +1940,7 @@ data_visuals_server <- function(id, rv$plot <- rlang::exec(create_plot, !!!append_list(data(), parameters, "data")) }) - rv$code <- glue::glue("FreesearchR::create_plot(data,{list2str(parameters)})") + rv$code <- glue::glue("FreesearchR::create_plot(df,{list2str(parameters)})") }, # warning = function(warn) { # showNotification(paste0(warn), type = "warning")