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{
"R": {
"Version": "4.4.1",
"Repositories": [
{
"Name": "CRAN",
"URL": "https://cloud.r-project.org"
}
]
},
"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 = \"[email protected]\"), person(\"Martin\", \"Maechler\", role = \"ctb\", email = \"[email protected]\", 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) <doi:10.1109/TEVC.2006.872133> for single-objective optimization and 'NCDE' by Qu et al. (2012) <doi:10.1109/TEVC.2011.2161873> 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] (<https://orcid.org/0000-0002-8685-9910>)",
"Maintainer": "Eduardo L. T. Conceicao <[email protected]>",
"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 = \"[email protected]\", 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] (<https://orcid.org/0000-0002-6255-9059>), Lukas Lohse [ctb], Melina de Souza leite [ctb]",
"Maintainer": "Florian Hartig <[email protected]>",
"Repository": "CRAN"
},
"DT": {
"Package": "DT",
"Version": "0.33",
"Source": "Repository",
"Type": "Package",
"Title": "A Wrapper of the JavaScript Library 'DataTables'",
"Authors@R": "c( person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"Joe\", \"Cheng\", email = \"[email protected]\", role = c(\"aut\", \"cre\")), person(\"Xianying\", \"Tan\", role = \"aut\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Maximilian\", \"Girlich\", role = \"ctb\"), person(\"Greg\", \"Freedman Ellis\", role = \"ctb\"), person(\"Johannes\", \"Rauh\", role = \"ctb\"), person(\"SpryMedia Limited\", role = c(\"ctb\", \"cph\"), comment = \"DataTables in htmlwidgets/lib\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js in htmlwidgets/lib\"), person(\"Leon\", \"Gersen\", role = c(\"ctb\", \"cph\"), comment = \"noUiSlider in htmlwidgets/lib\"), person(\"Bartek\", \"Szopka\", role = c(\"ctb\", \"cph\"), comment = \"jquery.highlight.js in htmlwidgets/lib\"), person(\"Alex\", \"Pickering\", role = c(\"ctb\")), person(\"William\", \"Holmes\", role = c(\"ctb\")), person(\"Mikko\", \"Marttila\", role = c(\"ctb\")), person(\"Andres\", \"Quintero\", role = c(\"ctb\")), person(\"Stéphane\", \"Laurent\", role = c(\"ctb\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
"Description": "Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.",
"URL": "https://github.com/rstudio/DT",
"BugReports": "https://github.com/rstudio/DT/issues",
"License": "GPL-3 | file LICENSE",
"Imports": [
"htmltools (>= 0.3.6)",
"htmlwidgets (>= 1.3)",
"httpuv",
"jsonlite (>= 0.9.16)",
"magrittr",
"crosstalk",
"jquerylib",
"promises"
],
"Suggests": [
"knitr (>= 1.8)",
"rmarkdown",
"shiny (>= 1.6)",
"bslib",
"future",
"testit",
"tibble"
],
"VignetteBuilder": "knitr",
"RoxygenNote": "7.3.1",
"Encoding": "UTF-8",
"NeedsCompilation": "no",
"Author": "Yihui Xie [aut], Joe Cheng [aut, cre], Xianying Tan [aut], JJ Allaire [ctb], Maximilian Girlich [ctb], Greg Freedman Ellis [ctb], Johannes Rauh [ctb], SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib), Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib), Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib), Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib), Alex Pickering [ctb], William Holmes [ctb], Mikko Marttila [ctb], Andres Quintero [ctb], Stéphane Laurent [ctb], Posit Software, PBC [cph, fnd]",
"Maintainer": "Joe Cheng <[email protected]>",
"Repository": "CRAN"
},
"Formula": {
"Package": "Formula",
"Version": "1.2-5",
"Source": "Repository",
"Date": "2023-02-23",
"Title": "Extended Model Formulas",
"Description": "Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side (see <doi:10.18637/jss.v034.i01>).",
"Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Yves\", family = \"Croissant\", role = \"aut\", email = \"[email protected]\"))",
"Depends": [
"R (>= 2.0.0)",
"stats"
],
"License": "GPL-2 | GPL-3",
"NeedsCompilation": "no",
"Author": "Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>), Yves Croissant [aut]",
"Maintainer": "Achim Zeileis <[email protected]>",
"Repository": "CRAN"
},
"GPArotation": {
"Package": "GPArotation",
"Version": "2024.3-1",
"Source": "Repository",
"Title": "Gradient Projection Factor Rotation",
"Authors@R": "c( person(\"Coen\", \"Bernaards\", email = \"[email protected]\", role = c(\"aut\",\"cre\")), person(\"Paul\", \"Gilbert\", email = \"[email protected]\", role = \"aut\"), person(\"Robert\", \"Jennrich\", role = \"aut\") )",
"Depends": [
"R (>= 2.0.0)"
],
"Description": "Gradient Projection Algorithms for Factor Rotation. For details see ?GPArotation. When using this package, please cite: Bernaards and Jennrich (2005) <doi:10.1177/0013164404272507>. \"Gradient Projection Algorithms and Software for Arbitrary Rotation Criteria in Factor Analysis\".",
"LazyData": "yes",
"Imports": [
"stats"
],
"License": "GPL (>= 2)",
"URL": "https://optimizer.r-forge.r-project.org/GPArotation_www/",
"NeedsCompilation": "no",
"Author": "Coen Bernaards [aut, cre], Paul Gilbert [aut], Robert Jennrich [aut]",
"Maintainer": "Coen Bernaards <[email protected]>",
"Repository": "CRAN"
},
"GenSA": {
"Package": "GenSA",
"Version": "1.1.14.1",
"Source": "Repository",
"Type": "Package",
"Title": "R Functions for Generalized Simulated Annealing",
"Date": "2024-01-22",
"Author": "Sylvain Gubian, Yang Xiang, Brian Suomela, Julia Hoeng, PMP SA.",
"Maintainer": "Sylvain Gubian <[email protected]>",
"Depends": [
"R (>= 2.12.0)"
],
"Description": "Performs search for global minimum of a very complex non-linear objective function with a very large number of optima.",
"License": "GPL-2",
"LazyLoad": "yes",
"NeedsCompilation": "yes",
"Repository": "CRAN",
"RoxygenNote": "7.2.3"
},
"Hmisc": {
"Package": "Hmisc",
"Version": "5.2-3",
"Source": "Repository",
"Date": "2025-03-16",
"Title": "Harrell Miscellaneous",
"Authors@R": "c(person(given = \"Frank E\", family = \"Harrell Jr\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0002-8271-5493\")), person(given = \"Charles\", family = \"Dupont\", role = \"ctb\", email = \"[email protected]\", comment = \"contributed several functions and maintains latex functions\"))",
"Maintainer": "Frank E Harrell Jr <[email protected]>",
"Depends": [
"R (>= 4.2.0)"
],
"Imports": [
"methods",
"ggplot2",
"cluster",
"rpart",
"nnet",
"foreign",
"gtable",
"grid",
"gridExtra",
"data.table",
"htmlTable (>= 1.11.0)",
"viridis",
"htmltools",
"base64enc",
"colorspace",
"rmarkdown",
"knitr",
"Formula"
],
"Suggests": [
"survival",
"qreport",
"acepack",
"chron",
"rms",
"mice",
"rstudioapi",
"tables",
"plotly (>= 4.5.6)",
"rlang",
"plyr",
"VGAM",
"leaps",
"pcaPP",
"digest",
"parallel",
"polspline",
"abind",
"kableExtra",
"rio",
"lattice",
"latticeExtra",
"gt",
"sparkline",
"jsonlite",
"htmlwidgets",
"qs",
"getPass",
"keyring",
"safer",
"htm2txt"
],
"Description": "Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.",
"License": "GPL (>= 2)",
"LazyLoad": "Yes",
"URL": "https://hbiostat.org/R/Hmisc/",
"Encoding": "UTF-8",
"RoxygenNote": "7.3.2",
"NeedsCompilation": "yes",
"Author": "Frank E Harrell Jr [aut, cre] (<https://orcid.org/0000-0002-8271-5493>), Charles Dupont [ctb] (contributed several functions and maintains latex functions)",
"Repository": "CRAN"
},
"IDEAFilter": {
"Package": "IDEAFilter",
"Version": "0.2.0",
"Source": "Repository",
"Type": "Package",
"Title": "Agnostic, Idiomatic Data Filter Module for Shiny",
"Description": "When added to an existing shiny app, users may subset any developer-chosen R data.frame on the fly. That is, users are empowered to slice & dice data by applying multiple (order specific) filters using the AND (&) operator between each, and getting real-time updates on the number of rows effected/available along the way. Thus, any downstream processes that leverage this data source (like tables, plots, or statistical procedures) will re-render after new filters are applied. The shiny module’s user interface has a 'minimalist' aesthetic so that the focus can be on the data & other visuals. In addition to returning a reactive (filtered) data.frame, 'IDEAFilter' as also returns 'dplyr' filter statements used to actually slice the data.",
"Authors@R": "c( person( given = \"Aaron\", family = \"Clark\", email = \"[email protected]\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0123-0970\")), person( given = \"Jeff\", family = \"Thompson\", email = \"[email protected]\", role = \"aut\"), person( given = \"Doug\", family = \"Kelkhoff\", email = \"[email protected]\", role = c(\"ctb\", \"cph\"), comment = \"Author of shinyDataFilter\"), person( given = \"Maya\", family = \"Gans\", email = \"[email protected]\", role = \"ctb\"), person(family = \"SortableJS contributors\", role = \"ctb\", comment = \"SortableJS library\"), person(given = \"Biogen\", role = \"cph\"))",
"License": "MIT + file LICENSE",
"URL": "https://biogen-inc.github.io/IDEAFilter/, https://github.com/Biogen-Inc/IDEAFilter",
"BugReports": "https://github.com/Biogen-Inc/IDEAFilter/issues",
"Encoding": "UTF-8",
"RoxygenNote": "7.3.1",
"Imports": [
"crayon",
"ggplot2",
"pillar (>= 1.5.0)",
"purrr",
"RColorBrewer",
"shiny",
"shinyTime"
],
"Suggests": [
"dplyr",
"knitr",
"rmarkdown",
"shinytest",
"shinytest2",
"spelling",
"testthat"
],
"Language": "en-US",
"VignetteBuilder": "knitr",
"Depends": [
"R (>= 2.10)"
],
"NeedsCompilation": "no",
"Author": "Aaron Clark [aut, cre] (<https://orcid.org/0000-0002-0123-0970>), Jeff Thompson [aut], Doug Kelkhoff [ctb, cph] (Author of shinyDataFilter), Maya Gans [ctb], SortableJS contributors [ctb] (SortableJS library), Biogen [cph]",
"Maintainer": "Aaron Clark <[email protected]>",
"Repository": "CRAN"
},
"KernSmooth": {
"Package": "KernSmooth",
"Version": "2.23-26",
"Source": "Repository",
"Priority": "recommended",
"Date": "2024-12-10",
"Title": "Functions for Kernel Smoothing Supporting Wand & Jones (1995)",
"Authors@R": "c(person(\"Matt\", \"Wand\", role = \"aut\", email = \"[email protected]\"), person(\"Cleve\", \"Moler\", role = \"ctb\", comment = \"LINPACK routines in src/d*\"), person(\"Brian\", \"Ripley\", role = c(\"trl\", \"cre\", \"ctb\"), email = \"[email protected]\", comment = \"R port and updates\"))",
"Note": "Maintainers are not available to give advice on using a package they did not author.",
"Depends": [
"R (>= 2.5.0)",
"stats"
],
"Suggests": [
"MASS",
"carData"
],
"Description": "Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) \"Kernel Smoothing\".",
"License": "Unlimited",
"ByteCompile": "yes",
"NeedsCompilation": "yes",
"Author": "Matt Wand [aut], Cleve Moler [ctb] (LINPACK routines in src/d*), Brian Ripley [trl, cre, ctb] (R port and updates)",
"Maintainer": "Brian Ripley <[email protected]>",
"Repository": "CRAN"
},
"MASS": {
"Package": "MASS",
"Version": "7.3-65",
"Source": "Repository",
"Priority": "recommended",
"Date": "2025-02-19",
"Revision": "$Rev: 3681 $",
"Depends": [
"R (>= 4.4.0)",
"grDevices",
"graphics",
"stats",
"utils"
],
"Imports": [
"methods"
],
"Suggests": [
"lattice",
"nlme",
"nnet",
"survival"
],
"Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"[email protected]\"), person(\"Bill\", \"Venables\", role = c(\"aut\", \"cph\")), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\", comment = \"support functions for polr\"))",
"Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).",
"Title": "Support Functions and Datasets for Venables and Ripley's MASS",
"LazyData": "yes",
"ByteCompile": "yes",
"License": "GPL-2 | GPL-3",
"URL": "http://www.stats.ox.ac.uk/pub/MASS4/",
"Contact": "<[email protected]>",
"NeedsCompilation": "yes",
"Author": "Brian Ripley [aut, cre, cph], Bill Venables [aut, cph], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb] (support functions for polr)",
"Maintainer": "Brian Ripley <[email protected]>",
"Repository": "CRAN"
},
"Matrix": {
"Package": "Matrix",
"Version": "1.7-3",
"Source": "Repository",
"VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h",
"Date": "2025-03-05",
"Priority": "recommended",
"Title": "Sparse and Dense Matrix Classes and Methods",
"Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.",
"License": "GPL (>= 2) | file LICENCE",
"URL": "https://Matrix.R-forge.R-project.org",
"BugReports": "https://R-forge.R-project.org/tracker/?atid=294&group_id=61",
"Contact": "[email protected]",
"Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Timothy A.\", \"Davis\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7614-6899\", \"SuiteSparse libraries\", \"collaborators listed in dir(system.file(\\\"doc\\\", \\\"SuiteSparse\\\", package=\\\"Matrix\\\"), pattern=\\\"License\\\", full.names=TRUE, recursive=TRUE)\")), person(\"George\", \"Karypis\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2753-1437\", \"METIS library\", \"Copyright: Regents of the University of Minnesota\")), person(\"Jason\", \"Riedy\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4345-4200\", \"GNU Octave's condest() and onenormest()\", \"Copyright: Regents of the University of California\")), person(\"Jens\", \"Oehlschlägel\", role = \"ctb\", comment = \"initial nearPD()\"), person(\"R Core Team\", role = \"ctb\", comment = c(ROR = \"02zz1nj61\", \"base R's matrix implementation\")))",
"Depends": [
"R (>= 4.4)",
"methods"
],
"Imports": [
"grDevices",
"graphics",
"grid",
"lattice",
"stats",
"utils"
],
"Suggests": [
"MASS",
"datasets",
"sfsmisc",
"tools"
],
"Enhances": [
"SparseM",
"graph"
],
"LazyData": "no",
"LazyDataNote": "not possible, since we use data/*.R and our S4 classes",
"BuildResaveData": "no",
"Encoding": "UTF-8",
"NeedsCompilation": "yes",
"Author": "Douglas Bates [aut] (<https://orcid.org/0000-0001-8316-9503>), Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>), Mikael Jagan [aut] (<https://orcid.org/0000-0002-3542-2938>), Timothy A. Davis [ctb] (<https://orcid.org/0000-0001-7614-6899>, SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (<https://orcid.org/0000-0003-2753-1437>, METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (<https://orcid.org/0000-0002-4345-4200>, GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (02zz1nj61, base R's matrix implementation)",
"Maintainer": "Martin Maechler <[email protected]>",
"Repository": "CRAN"
},
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"Version": "1.8.2",
"Source": "Repository",
"Depends": [
"R (>= 2.13.0)"
],
"Imports": [
"utils"
],
"Suggests": [
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],
"Title": "S3 Methods Simplified",
"Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email = \"[email protected]\"))",
"Author": "Henrik Bengtsson [aut, cre, cph]",
"Maintainer": "Henrik Bengtsson <[email protected]>",
"Description": "Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods.",
"License": "LGPL (>= 2.1)",
"LazyLoad": "TRUE",
"URL": "https://github.com/HenrikBengtsson/R.methodsS3",
"BugReports": "https://github.com/HenrikBengtsson/R.methodsS3/issues",
"NeedsCompilation": "no",
"Repository": "CRAN"
},
"R.oo": {
"Package": "R.oo",
"Version": "1.27.0",
"Source": "Repository",
"Depends": [
"R (>= 2.13.0)",
"R.methodsS3 (>= 1.8.2)"
],
"Imports": [
"methods",
"utils"
],
"Suggests": [
"tools"
],
"Title": "R Object-Oriented Programming with or without References",
"Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email = \"[email protected]\"))",
"Author": "Henrik Bengtsson [aut, cre, cph]",
"Maintainer": "Henrik Bengtsson <[email protected]>",
"Description": "Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.",
"License": "LGPL (>= 2.1)",
"LazyLoad": "TRUE",
"URL": "https://github.com/HenrikBengtsson/R.oo",
"BugReports": "https://github.com/HenrikBengtsson/R.oo/issues",
"NeedsCompilation": "no",
"Repository": "CRAN"
},
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"Package": "R.utils",
"Version": "2.13.0",
"Source": "Repository",
"Depends": [
"R (>= 2.14.0)",
"R.oo"
],
"Imports": [
"methods",
"utils",
"tools",
"R.methodsS3"
],
"Suggests": [
"datasets",
"digest (>= 0.6.10)"
],
"Title": "Various Programming Utilities",
"Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email = \"[email protected]\"))",
"Author": "Henrik Bengtsson [aut, cre, cph]",
"Maintainer": "Henrik Bengtsson <[email protected]>",
"Description": "Utility functions useful when programming and developing R packages.",
"License": "LGPL (>= 2.1)",
"LazyLoad": "TRUE",
"URL": "https://henrikbengtsson.github.io/R.utils/, https://github.com/HenrikBengtsson/R.utils",
"BugReports": "https://github.com/HenrikBengtsson/R.utils/issues",
"NeedsCompilation": "no",
"Repository": "CRAN"
},
"R6": {
"Package": "R6",
"Version": "2.6.1",
"Source": "Repository",
"Title": "Encapsulated Classes with Reference Semantics",
"Authors@R": "c( person(\"Winston\", \"Chang\", , \"[email protected]\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
"Description": "Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.",
"License": "MIT + file LICENSE",
"URL": "https://r6.r-lib.org, https://github.com/r-lib/R6",
"BugReports": "https://github.com/r-lib/R6/issues",
"Depends": [
"R (>= 3.6)"
],
"Suggests": [
"lobstr",
"testthat (>= 3.0.0)"
],
"Config/Needs/website": "tidyverse/tidytemplate, ggplot2, microbenchmark, scales",
"Config/testthat/edition": "3",
"Encoding": "UTF-8",
"RoxygenNote": "7.3.2",
"NeedsCompilation": "no",
"Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd]",
"Maintainer": "Winston Chang <[email protected]>",
"Repository": "CRAN"
},
"RColorBrewer": {
"Package": "RColorBrewer",
"Version": "1.1-3",
"Source": "Repository",
"Date": "2022-04-03",
"Title": "ColorBrewer Palettes",
"Authors@R": "c(person(given = \"Erich\", family = \"Neuwirth\", role = c(\"aut\", \"cre\"), email = \"[email protected]\"))",
"Author": "Erich Neuwirth [aut, cre]",
"Maintainer": "Erich Neuwirth <[email protected]>",
"Depends": [
"R (>= 2.0.0)"
],
"Description": "Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org.",
"License": "Apache License 2.0",
"NeedsCompilation": "no",
"Repository": "CRAN"
},
"REDCapCAST": {
"Package": "REDCapCAST",
"Version": "25.3.2",
"Source": "Repository",
"Title": "REDCap Metadata Casting and Castellated Data Handling",
"Authors@R": "c( person(\"Andreas Gammelgaard\", \"Damsbo\", email = \"[email protected]\", role = c(\"aut\", \"cre\"),comment = c(ORCID = \"0000-0002-7559-1154\")), person(\"Paul\", \"Egeler\", email = \"[email protected]\", role = c(\"aut\"), comment = c(ORCID = \"0000-0001-6948-9498\")))",
"Description": "Casting metadata for REDCap database creation and handling of castellated data using repeated instruments and longitudinal projects in 'REDCap'. Keeps a focused data export approach, by allowing to only export required data from the database. Also for casting new REDCap databases based on datasets from other sources. Originally forked from the R part of 'REDCapRITS' by Paul Egeler. See <https://github.com/pegeler/REDCapRITS>. 'REDCap' (Research Electronic Data Capture) is a secure, web-based software platform designed to support data capture for research studies, providing 1) an intuitive interface for validated data capture; 2) audit trails for tracking data manipulation and export procedures; 3) automated export procedures for seamless data downloads to common statistical packages; and 4) procedures for data integration and interoperability with external sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>; Harris et al (2019) <doi:10.1016/j.jbi.2019.103208>).",
"Depends": [
"R (>= 4.1.0)"
],
"Suggests": [
"httr",
"jsonlite",
"testthat",
"Hmisc",
"knitr",
"rmarkdown",
"styler",
"devtools",
"roxygen2",
"spelling",
"rhub",
"rsconnect",
"pkgconfig"
],
"License": "GPL (>= 3)",
"Encoding": "UTF-8",
"LazyData": "true",
"RoxygenNote": "7.3.2",
"URL": "https://github.com/agdamsbo/REDCapCAST, https://agdamsbo.github.io/REDCapCAST/",
"BugReports": "https://github.com/agdamsbo/REDCapCAST/issues",
"Imports": [
"dplyr",
"REDCapR",
"tidyr",
"tidyselect",
"keyring",
"purrr",
"readr",
"stats",
"zip",
"assertthat",
"forcats",
"vctrs",
"gt",
"bslib",
"here",
"glue",
"gtsummary",
"shiny",
"haven",
"openxlsx2",
"readODS"
],
"Language": "en-US",
"VignetteBuilder": "knitr",
"Collate": "'REDCapCAST-package.R' 'utils.r' 'process_user_input.r' 'REDCap_split.r' 'as_factor.R' 'as_logical.R' 'doc2dd.R' 'ds2dd_detailed.R' 'easy_redcap.R' 'export_redcap_instrument.R' 'fct_drop.R' 'html_styling.R' 'mtcars_redcap.R' 'read_redcap_instrument.R' 'read_redcap_tables.R' 'redcap_wider.R' 'redcapcast_data.R' 'redcapcast_meta.R' 'shiny_cast.R'",
"NeedsCompilation": "no",
"Author": "Andreas Gammelgaard Damsbo [aut, cre] (<https://orcid.org/0000-0002-7559-1154>), Paul Egeler [aut] (<https://orcid.org/0000-0001-6948-9498>)",
"Maintainer": "Andreas Gammelgaard Damsbo <[email protected]>",
"Repository": "CRAN"
},
"REDCapR": {
"Package": "REDCapR",
"Version": "1.4.0",
"Source": "Repository",
"Title": "Interaction Between R and REDCap",
"Description": "Encapsulates functions to streamline calls from R to the REDCap API. REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.",
"Authors@R": "c(person(\"Will\", \"Beasley\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0002-5613-5006\")), person(\"David\", \"Bard\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3922-8489\")), person(\"Thomas\", \"Wilson\", role = \"ctb\"), person(given=\"John J\", family=\"Aponte\", role = \"ctb\", email=\"[email protected]\"), person(\"Rollie\", \"Parrish\", role = \"ctb\", email = \"[email protected]\", comment = c(ORCID = \"0000-0001-8858-6381\")), person(\"Benjamin\", \"Nutter\", role = \"ctb\"), person(\"Andrew\", \"Peters\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2487-1268\")), person(\"Hao\", \"Zhu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3386-6076\")), person(\"Janosch\", \"Linkersdörfer\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1577-1233\")), person(\"Jonathan\", \"Mang\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0518-4710\")), person(\"Felix\", \"Torres\", role = \"ctb\", email = \"[email protected]\"), person(\"Philip\", \"Chase\", role = \"ctb\", email = \"[email protected]\", comment = c(ORCID = \"0000-0002-5318-9420\")), person(\"Victor\", \"Castro\", role = \"ctb\", email = \"[email protected]\", comment = c(ORCID = \"0000-0001-7390-6354\")), person(\"Greg\", \"Botwin\", role = \"ctb\"), person(\"Stephan\", \"Kadauke\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2996-8034\")), person(\"Ezra\", \"Porter\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4690-8343\")), person(\"Matthew\", \"Schuelke\", role = \"ctb\", email=\"[email protected]\", comment = c(ORCID = \"0000-0001-5755-1725\")))",
"URL": "https://ouhscbbmc.github.io/REDCapR/, https://github.com/OuhscBbmc/REDCapR, https://www.ouhsc.edu/bbmc/, https://projectredcap.org",
"BugReports": "https://github.com/OuhscBbmc/REDCapR/issues",
"Depends": [
"R(>= 3.5.0)"
],
"Imports": [
"checkmate (>= 2.0)",
"dplyr (>= 1.0)",
"httr (>= 1.4.0)",
"jsonlite",
"magrittr (>= 1.5)",
"methods",
"readr (>= 2.0)",
"rlang (>= 0.4)",
"tibble (>= 2.0)",
"tidyr (>= 1.0)"
],
"Suggests": [
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"covr (>= 3.4)",
"DBI (>= 1.1)",
"kableExtra (>= 1.0)",
"knitr",
"odbc (>= 1.1.1)",
"purrr (>= 0.3.4)",
"rmarkdown",
"sessioninfo (>= 1.1.1)",
"testthat (>= 3.0)",
"tidyselect",
"yaml"
],
"License": "MIT + file LICENSE",
"VignetteBuilder": "knitr",
"Encoding": "UTF-8",
"RoxygenNote": "7.3.2",
"Config/testthat/edition": "3",
"Language": "en-US",
"NeedsCompilation": "no",
"Author": "Will Beasley [aut, cre] (<https://orcid.org/0000-0002-5613-5006>), David Bard [ctb] (<https://orcid.org/0000-0002-3922-8489>), Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb] (<https://orcid.org/0000-0001-8858-6381>), Benjamin Nutter [ctb], Andrew Peters [ctb] (<https://orcid.org/0000-0003-2487-1268>), Hao Zhu [ctb] (<https://orcid.org/0000-0002-3386-6076>), Janosch Linkersdörfer [ctb] (<https://orcid.org/0000-0002-1577-1233>), Jonathan Mang [ctb] (<https://orcid.org/0000-0003-0518-4710>), Felix Torres [ctb], Philip Chase [ctb] (<https://orcid.org/0000-0002-5318-9420>), Victor Castro [ctb] (<https://orcid.org/0000-0001-7390-6354>), Greg Botwin [ctb], Stephan Kadauke [ctb] (<https://orcid.org/0000-0003-2996-8034>), Ezra Porter [ctb] (<https://orcid.org/0000-0002-4690-8343>), Matthew Schuelke [ctb] (<https://orcid.org/0000-0001-5755-1725>)",
"Maintainer": "Will Beasley <[email protected]>",
"Repository": "CRAN"
},
"Rcpp": {
"Package": "Rcpp",
"Version": "1.0.14",
"Source": "Repository",
"Title": "Seamless R and C++ Integration",
"Date": "2025-01-11",
"Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))",
"Description": "The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013, <doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018, <doi:10.1080/00031305.2017.1375990>); see 'citation(\"Rcpp\")' for details.",
"Imports": [
"methods",
"utils"
],
"Suggests": [
"tinytest",
"inline",
"rbenchmark",
"pkgKitten (>= 0.1.2)"
],
"URL": "https://www.rcpp.org, https://dirk.eddelbuettel.com/code/rcpp.html, https://github.com/RcppCore/Rcpp",
"License": "GPL (>= 2)",
"BugReports": "https://github.com/RcppCore/Rcpp/issues",
"MailingList": "[email protected]",
"RoxygenNote": "6.1.1",
"Encoding": "UTF-8",
"NeedsCompilation": "yes",
"Author": "Dirk Eddelbuettel [aut, cre] (<https://orcid.org/0000-0001-6419-907X>), Romain Francois [aut] (<https://orcid.org/0000-0002-2444-4226>), JJ Allaire [aut] (<https://orcid.org/0000-0003-0174-9868>), Kevin Ushey [aut] (<https://orcid.org/0000-0003-2880-7407>), Qiang Kou [aut] (<https://orcid.org/0000-0001-6786-5453>), Nathan Russell [aut], Iñaki Ucar [aut] (<https://orcid.org/0000-0001-6403-5550>), Doug Bates [aut] (<https://orcid.org/0000-0001-8316-9503>), John Chambers [aut]",
"Maintainer": "Dirk Eddelbuettel <[email protected]>",
"Repository": "CRAN"
},
"RcppArmadillo": {
"Package": "RcppArmadillo",
"Version": "14.4.0-1",
"Source": "Repository",
"Type": "Package",
"Title": "'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library",
"Date": "2025-02-17",
"Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Binxiang\", \"Ni\", role = \"aut\"), person(\"Conrad\", \"Sanderson\", role = \"aut\", comment = c(ORCID = \"0000-0002-0049-4501\")))",
"Description": "'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.",
"License": "GPL (>= 2)",
"LazyLoad": "yes",
"Depends": [
"R (>= 3.3.0)"
],
"LinkingTo": [
"Rcpp"
],
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"stats",
"utils",
"methods"
],
"Suggests": [
"tinytest",
"Matrix (>= 1.3.0)",
"pkgKitten",
"reticulate",
"slam"
],
"URL": "https://github.com/RcppCore/RcppArmadillo, https://dirk.eddelbuettel.com/code/rcpp.armadillo.html",
"BugReports": "https://github.com/RcppCore/RcppArmadillo/issues",
"RoxygenNote": "6.0.1",
"NeedsCompilation": "yes",
"Author": "Dirk Eddelbuettel [aut, cre] (<https://orcid.org/0000-0001-6419-907X>), Romain Francois [aut] (<https://orcid.org/0000-0002-2444-4226>), Doug Bates [aut] (<https://orcid.org/0000-0001-8316-9503>), Binxiang Ni [aut], Conrad Sanderson [aut] (<https://orcid.org/0000-0002-0049-4501>)",
"Maintainer": "Dirk Eddelbuettel <[email protected]>",
"Repository": "CRAN"
},
"RcppEigen": {
"Package": "RcppEigen",
"Version": "0.3.4.0.2",
"Source": "Repository",
"Type": "Package",
"Title": "'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library",
"Date": "2024-08-23",
"Authors@R": "c(person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Yixuan\", \"Qiu\", role = \"aut\", comment = c(ORCID = \"0000-0003-0109-6692\")), person(\"Authors of\", \"Eigen\", role = \"cph\", comment = \"Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS\"))",
"Copyright": "See the file COPYRIGHTS for various Eigen copyright details",
"Description": "R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library. Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.",
"License": "GPL (>= 2) | file LICENSE",
"LazyLoad": "yes",
"Depends": [
"R (>= 3.6.0)"
],
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],
"Imports": [
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"stats",
"utils"
],
"Suggests": [
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"inline",
"tinytest",
"pkgKitten",
"microbenchmark"
],
"URL": "https://github.com/RcppCore/RcppEigen, https://dirk.eddelbuettel.com/code/rcpp.eigen.html",
"BugReports": "https://github.com/RcppCore/RcppEigen/issues",
"NeedsCompilation": "yes",
"Author": "Doug Bates [aut] (<https://orcid.org/0000-0001-8316-9503>), Dirk Eddelbuettel [aut, cre] (<https://orcid.org/0000-0001-6419-907X>), Romain Francois [aut] (<https://orcid.org/0000-0002-2444-4226>), Yixuan Qiu [aut] (<https://orcid.org/0000-0003-0109-6692>), Authors of Eigen [cph] (Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS)",
"Maintainer": "Dirk Eddelbuettel <[email protected]>",
"Repository": "CRAN"
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"Version": "2.6.3",
"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 = \"[email protected]\", comment = c(ORCID = \"0000-0003-2839-346X\")), person(given = \"Duncan\", family = \"Murdoch\", role = \"ctb\", email = \"[email protected]\") )",
"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": [
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"testthat",
"rstudioapi",
"rprojroot",
"gbRd"
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"Author": "Georgi N. Boshnakov [aut, cre] (<https://orcid.org/0000-0003-2839-346X>), Duncan Murdoch [ctb]",
"Maintainer": "Georgi N. Boshnakov <[email protected]>",
"Repository": "CRAN"
},
"V8": {
"Package": "V8",
"Version": "6.0.2",
"Source": "Repository",
"Type": "Package",
"Title": "Embedded JavaScript and WebAssembly Engine for R",
"Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Jan Marvin\", \"Garbuszus\", role = \"ctb\"))",
"Description": "An R interface to V8 <https://v8.dev>: Google's open source JavaScript and WebAssembly engine. This package can be compiled either with V8 version 6 and up or NodeJS when built as a shared library.",
"License": "MIT + file LICENSE",
"URL": "https://jeroen.r-universe.dev/V8",
"BugReports": "https://github.com/jeroen/v8/issues",
"SystemRequirements": "V8 engine version 6+ is needed for ES6 and WASM support. On Linux you can build against libv8-dev (Debian) or v8-devel (Fedora). We also provide static libv8 binaries for most platforms, see the README for details.",
"NeedsCompilation": "yes",
"VignetteBuilder": "knitr",
"Imports": [
"Rcpp (>= 0.12.12)",
"jsonlite (>= 1.0)",
"curl (>= 1.0)",
"utils"
],
"LinkingTo": [
"Rcpp"
],
"Suggests": [
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"rmarkdown"
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"RoxygenNote": "7.3.1",
"Language": "en-US",
"Encoding": "UTF-8",
"Biarch": "true",
"Author": "Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Jan Marvin Garbuszus [ctb]",
"Maintainer": "Jeroen Ooms <[email protected]>",
"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 = \"[email protected]\", 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": [
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],
"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] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Federico Marotta [aut, cph], Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)",
"Maintainer": "Emmanuel Paradis <[email protected]>",
"Repository": "CRAN"
},
"apexcharter": {
"Package": "apexcharter",
"Version": "0.4.4",
"Source": "Repository",
"Title": "Create Interactive Chart with the JavaScript 'ApexCharts' Library",
"Description": "Provides an 'htmlwidgets' interface to 'apexcharts.js'. 'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API. 'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.",
"Authors@R": "c( person(\"Victor\", \"Perrier\", email = \"[email protected]\", role = c(\"aut\", \"cre\")), person(\"Fanny\", \"Meyer\", role = \"aut\"), person(\"Juned\", \"Chhipa\", role = \"cph\", comment = \"apexcharts.js library\"), person(\"Mike\", \"Bostock\", role = \"cph\", comment = \"d3.format library\"))",
"License": "MIT + file LICENSE",
"Encoding": "UTF-8",
"LazyData": "true",
"ByteCompile": "true",
"Depends": [
"R (>= 2.10)"
],
"Imports": [
"htmltools",
"htmlwidgets (>= 1.5.3)",
"magrittr",
"rlang",
"ggplot2",
"jsonlite",
"shiny (>= 1.1.0)"
],
"Suggests": [
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"knitr",
"scales",
"rmarkdown",
"covr"
],
"RoxygenNote": "7.3.2",
"URL": "https://github.com/dreamRs/apexcharter, https://dreamrs.github.io/apexcharter/",
"BugReports": "https://github.com/dreamRs/apexcharter/issues",
"VignetteBuilder": "knitr",
"NeedsCompilation": "no",
"Author": "Victor Perrier [aut, cre], Fanny Meyer [aut], Juned Chhipa [cph] (apexcharts.js library), Mike Bostock [cph] (d3.format library)",
"Maintainer": "Victor Perrier <[email protected]>",
"Repository": "CRAN"
},
"askpass": {
"Package": "askpass",
"Version": "1.2.1",
"Source": "Repository",
"Type": "Package",
"Title": "Password Entry Utilities for R, Git, and SSH",
"Authors@R": "person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0002-4035-0289\"))",
"Description": "Cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key. Includes native programs for MacOS and Windows, hence no 'tcltk' is required. Password entry can be invoked in two different ways: directly from R via the askpass() function, or indirectly as password-entry back-end for 'ssh-agent' or 'git-credential' via the SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can be prompted for credentials or a passphrase if needed when R calls out to git or ssh.",
"License": "MIT + file LICENSE",
"URL": "https://r-lib.r-universe.dev/askpass",
"BugReports": "https://github.com/r-lib/askpass/issues",
"Encoding": "UTF-8",
"Imports": [
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],
"RoxygenNote": "7.2.3",
"Suggests": [
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],
"Language": "en-US",
"NeedsCompilation": "yes",
"Author": "Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)",
"Maintainer": "Jeroen Ooms <[email protected]>",
"Repository": "CRAN"
},
"assertthat": {
"Package": "assertthat",
"Version": "0.2.1",
"Source": "Repository",
"Title": "Easy Pre and Post Assertions",
"Authors@R": "person(\"Hadley\", \"Wickham\", , \"[email protected]\", c(\"aut\", \"cre\"))",
"Description": "An extension to stopifnot() that makes it easy to declare the pre and post conditions that you code should satisfy, while also producing friendly error messages so that your users know what's gone wrong.",
"License": "GPL-3",
"Imports": [
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],
"Suggests": [
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"RoxygenNote": "6.0.1",
"Collate": "'assert-that.r' 'on-failure.r' 'assertions-file.r' 'assertions-scalar.R' 'assertions.r' 'base.r' 'base-comparison.r' 'base-is.r' 'base-logical.r' 'base-misc.r' 'utils.r' 'validate-that.R'",
"NeedsCompilation": "no",
"Author": "Hadley Wickham [aut, cre]",
"Maintainer": "Hadley Wickham <[email protected]>",
"Repository": "CRAN"
},
"backports": {
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"Version": "1.5.0",
"Source": "Repository",
"Type": "Package",
"Title": "Reimplementations of Functions Introduced Since R-3.0.0",
"Authors@R": "c( person(\"Michel\", \"Lang\", NULL, \"[email protected]\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Duncan\", \"Murdoch\", NULL, \"[email protected]\", role = c(\"aut\")), person(\"R Core Team\", role = \"aut\"))",
"Maintainer": "Michel Lang <[email protected]>",
"Description": "Functions introduced or changed since R v3.0.0 are re-implemented in this package. The backports are conditionally exported in order to let R resolve the function name to either the implemented backport, or the respective base version, if available. Package developers can make use of new functions or arguments by selectively importing specific backports to support older installations.",
"URL": "https://github.com/r-lib/backports",
"BugReports": "https://github.com/r-lib/backports/issues",
"License": "GPL-2 | GPL-3",
"NeedsCompilation": "yes",
"ByteCompile": "yes",
"Depends": [
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],
"Encoding": "UTF-8",
"RoxygenNote": "7.3.1",
"Author": "Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Duncan Murdoch [aut], R Core Team [aut]",
"Repository": "CRAN"
},
"base64enc": {
"Package": "base64enc",
"Version": "0.1-3",
"Source": "Repository",
"Title": "Tools for base64 encoding",
"Author": "Simon Urbanek <[email protected]>",
"Maintainer": "Simon Urbanek <[email protected]>",
"Depends": [
"R (>= 2.9.0)"
],
"Enhances": [
"png"
],
"Description": "This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.",
"License": "GPL-2 | GPL-3",
"URL": "http://www.rforge.net/base64enc",
"NeedsCompilation": "yes",
"Repository": "CRAN"
},
"bayestestR": {
"Package": "bayestestR",
"Version": "0.15.2",
"Source": "Repository",
"Type": "Package",
"Title": "Understand and Describe Bayesian Models and Posterior Distributions",
"Authors@R": "c(person(given = \"Dominique\", family = \"Makowski\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Daniel\", family = \"Lüdecke\", role = \"aut\", email = \"[email protected]\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = \"aut\", email = \"[email protected]\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"[email protected]\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Micah K.\", family = \"Wilson\", role = \"aut\", email = \"[email protected]\", comment = c(ORCID = \"0000-0003-4143-7308\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"aut\", email = \"[email protected]\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Paul-Christian\", family = \"Bürkner\", role = \"rev\", email = \"[email protected]\"), person(given = \"Tristan\", family = \"Mahr\", role = \"rev\", email = \"[email protected]\", comment = c(ORCID = \"0000-0002-8890-5116\")), person(given = \"Henrik\", family = \"Singmann\", role = \"ctb\", email = \"[email protected]\", comment = c(ORCID = \"0000-0002-4842-3657\")), person(given = \"Quentin F.\", family = \"Gronau\", role = \"ctb\", comment = c(ORCID = \"0000-0001-5510-6943\")), person(given = \"Sam\", family = \"Crawley\", role = \"ctb\", email = \"[email protected]\", comment = c(ORCID = \"0000-0002-7847-0411\")))",
"Maintainer": "Dominique Makowski <[email protected]>",
"Description": "Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.",
"Depends": [
"R (>= 3.6)"
],