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{
"R": {
"Version": "4.5.2",
"Repositories": [
{
"Name": "CRAN",
"URL": "https://cloud.r-project.org"
}
]
},
"Packages": {
"ARTnet": {
"Package": "ARTnet",
"Version": "2.9.0",
"Source": "GitHub",
"Date": "2024-09-06",
"Title": "Epidemic and Network Model Parameterization with the ARTnet Dataset",
"Description": "Epidemic and Network Model Parameterization with the ARTnet Dataset.",
"Maintainer": "Samuel Jenness <samuel.m.jenness@emory.edu>",
"Authors@R": "c(person(\"Samuel\", \"Jenness\", role=c(\"cre\",\"aut\"), email=\"samuel.m.jenness@emory.edu\"))",
"License": "GPL (>= 3)",
"URL": "http://github.com/EpiModel/ARTnet",
"BugReports": "https://github.com/EpiModel/ARTnet/issues",
"Depends": [
"R (>= 4.1)",
"EpiModel (>= 2.5)"
],
"Imports": [
"dplyr"
],
"Suggests": [
"ARTnetData",
"EpiModelHIV",
"knitr",
"rmarkdown",
"testthat (>= 3.0.0)"
],
"VignetteBuilder": "knitr",
"RoxygenNote": "7.3.2",
"Encoding": "UTF-8",
"Roxygen": "list(markdown = TRUE)",
"Config/testthat/edition": "3",
"Author": "Samuel Jenness [cre, aut]",
"RemoteType": "github",
"RemoteHost": "api.github.com",
"RemoteUsername": "EpiModel",
"RemoteRepo": "ARTnet",
"RemoteRef": "main",
"RemoteSha": "b3a2c75ab309711482a0cc054fb72d9ccce46c54",
"Remotes": "github::EpiModel/ARTnetData@main, github::EpiModel/EpiModelHIV-p"
},
"ARTnetData": {
"Package": "ARTnetData",
"Version": "1.1.1",
"Source": "GitHub",
"Date": "2024-07-03",
"Title": "Limited Public Use Dataset for the 2017-2018 ARTnet Study",
"Description": "The limited public use data for the ARTnet study of men who have sex with men (MSM) in the United States. The aims of this study are to characterize the sexual network structure and behavior within networks of MSM across the U.S. for use in descriptive epidemiological research and mathematical modeling studies in this target population.",
"Maintainer": "Samuel Jenness <samuel.m.jenness@emory.edu>",
"Authors@R": "c(person(\"Samuel\", \"Jenness\", role=c(\"cre\",\"aut\"), email=\"samuel.m.jenness@emory.edu\"), person(\"Kevin\", \"Weiss\", role=c(\"ctb\"), email=\"kevin.weiss@emory.edu\"), person(\"Pragati\", \"Prasad\", role=c(\"ctb\"), email=\"pragati.venkata.prasad@emory.edu\"))",
"Depends": [
"R (>= 3.5)"
],
"License": "GPL-3",
"Encoding": "UTF-8",
"LazyData": "true",
"RoxygenNote": "7.0.2",
"Author": "Samuel Jenness [cre, aut], Kevin Weiss [ctb], Pragati Prasad [ctb]",
"RemoteType": "github",
"RemoteHost": "api.github.com",
"RemoteUsername": "EpiModel",
"RemoteRepo": "ARTnetData",
"RemoteRef": "main",
"RemoteSha": "3caad7145ff0031667709a9fcdb4abb27ce5a8c3"
},
"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) <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 <mail@eduardoconceicao.org>",
"Repository": "CRAN",
"Repository/R-Forge/Project": "robustbase",
"Repository/R-Forge/Revision": "1008",
"Repository/R-Forge/DateTimeStamp": "2024-11-23 19:13:45",
"NeedsCompilation": "no"
},
"EpiModel": {
"Package": "EpiModel",
"Version": "2.5.0",
"Source": "Repository",
"Date": "2024-10-10",
"Title": "Mathematical Modeling of Infectious Disease Dynamics",
"Description": "Tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel scientific research aims. Full methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).",
"Maintainer": "Samuel Jenness <samuel.m.jenness@emory.edu>",
"Authors@R": "c(person(\"Samuel\", \"Jenness\", role=c(\"cre\",\"aut\"), email=\"samuel.m.jenness@emory.edu\"), person(\"Steven M.\",\"Goodreau\", role=c(\"aut\"), email=\"goodreau@uw.edu\"), person(\"Martina\", \"Morris\", role=c(\"aut\"), email=\"morrism@uw.edu\"), person(\"Adrien\", \"Le Guillou\", role=c(\"aut\"), email=\"contact@aleguillou.org\"), person(\"Chad\", \"Klumb\", role=c(\"aut\"), email=\"cklumb@gmail.com\"), person(\"Skye\", \"Bender-deMoll\", role=c(\"ctb\"), email=\"skyebend@uw.edu\"))",
"License": "GPL-3",
"URL": "https://www.epimodel.org/, https://epimodel.github.io/EpiModel/",
"BugReports": "https://github.com/EpiModel/EpiModel/issues/",
"Depends": [
"R (>= 4.1)",
"deSolve (>= 1.21)",
"networkDynamic (>= 0.11.3)",
"tergm (>= 4.2.1)",
"statnet.common (>= 4.10.0)"
],
"Imports": [
"graphics",
"grDevices",
"stats",
"utils",
"collections",
"doParallel",
"ergm (>= 4.7.1)",
"foreach",
"network (>= 1.18.1)",
"RColorBrewer",
"ape",
"lazyeval",
"ggplot2",
"tibble",
"methods",
"rlang",
"dplyr",
"coda",
"networkLite (>= 1.0.5)"
],
"Suggests": [
"ergm.ego (>= 1.1.0)",
"egor",
"knitr",
"ndtv",
"rmarkdown",
"shiny",
"testthat",
"progressr",
"tidyr"
],
"VignetteBuilder": "knitr",
"LinkingTo": [
"Rcpp",
"ergm"
],
"RoxygenNote": "7.3.2",
"Encoding": "UTF-8",
"NeedsCompilation": "yes",
"Author": "Samuel Jenness [cre, aut], Steven M. Goodreau [aut], Martina Morris [aut], Adrien Le Guillou [aut], Chad Klumb [aut], Skye Bender-deMoll [ctb]",
"Repository": "CRAN"
},
"EpiModelHIV": {
"Package": "EpiModelHIV",
"Version": "3.2.0",
"Source": "GitHub",
"Date": "2025-03-26",
"Type": "Package",
"Title": "Network-Based Epidemic Modeling of HIV/STI Transmission",
"Description": "EpiModelHIV provides extensions to our general EpiModel package to allow for simulating HIV/STI transmission dynamics.",
"Maintainer": "Samuel M. Jenness <samuel.m.jenness@emory.edu>",
"Authors@R": "c( person(\"Samuel M.\", \"Jenness\", role = c(\"cre\", \"aut\"), email = \"samuel.m.jenness@emory.edu\"), person(\"Steven M.\", \"Goodreau\", role = \"aut\", email = \"goodeau@uw.edu\"), person(\"Adrien\", \"Le Guillou\", role=c(\"aut\"), email=\"contact@aleguillou.org\", comment = c(ORCID = \"0000-0002-4791-418X\")))",
"License": "GPL-3",
"Depends": [
"R (>= 4.1.0)",
"EpiModel (>= 2.5.0)"
],
"Imports": [
"ARTnet (>= 2.8.0)",
"tergm",
"ergm (>= 4.3.1)",
"network",
"networkDynamic (>= 0.11.3)",
"statnet.common",
"progressr",
"dplyr",
"rlang",
"networkLite (>= 1.0.1)",
"collections"
],
"Suggests": [
"knitr",
"testthat (>= 3.0.0)",
"withr",
"ARTnetData",
"Rglpk"
],
"VignetteBuilder": "knitr",
"RoxygenNote": "7.3.2",
"Encoding": "UTF-8",
"Config/testthat/edition": "3",
"Roxygen": "list(markdown = TRUE)",
"Author": "Samuel M. Jenness [cre, aut], Steven M. Goodreau [aut], Adrien Le Guillou [aut] (ORCID: <https://orcid.org/0000-0002-4791-418X>)",
"RemoteType": "github",
"RemoteHost": "api.github.com",
"RemoteUsername": "EpiModel",
"RemoteRepo": "EpiModelHIV-p",
"RemoteRef": "offscript",
"RemoteSha": "7d6a96c4e4fb82ccd2ff16429ec0e45738f7cf87",
"Remotes": "github::EpiModel/ARTnet@main, github::EpiModel/ARTnetData@main"
},
"EpiModelHPC": {
"Package": "EpiModelHPC",
"Version": "2.5.0",
"Source": "GitHub",
"Date": "2024-10-18",
"Title": "EpiModel Extensions for High-Performance Computing",
"Description": "Extension package to EpiModel to run large-scale stochastic network models on modern high-performance computing systems. Functionality provided to simulate models in parallel using single-node, multiple-core setups. Check-pointing functions that automatically save and restore simulation work, which may be useful on HPC systems with Portable Batch System (PBS) job scheduling software like OpenPBS, are also included.",
"Maintainer": "Samuel Jenness <samuel.m.jenness@emory.edu>",
"Authors@R": "c(person(\"Samuel\", \"Jenness\", role=c(\"cre\",\"aut\"), email=\"samuel.m.jenness@emory.edu\"))",
"License": "GPL-3",
"URL": "http://epimodel.org/, http://epimodel.github.io/EpiModelHPC/",
"BugReports": "https://github.com/EpiModel/EpiModelHPC/issues",
"Depends": [
"R (>= 4.1)",
"EpiModel (>= 2.5.0)"
],
"Imports": [
"dplyr",
"tidyr",
"doParallel",
"foreach",
"ergm",
"fs",
"future",
"future.apply",
"rlang",
"tidyselect",
"tergm",
"stringr",
"slurmworkflow",
"swfcalib",
"callr"
],
"Suggests": [
"rmarkdown",
"testthat",
"network",
"knitr"
],
"VignetteBuilder": "knitr",
"RoxygenNote": "7.3.2",
"Encoding": "UTF-8",
"Roxygen": "list(markdown = TRUE)",
"Author": "Samuel Jenness [cre, aut]",
"RemoteType": "github",
"RemoteUsername": "EpiModel",
"RemoteRepo": "EpiModelHPC",
"RemoteRef": "main",
"RemoteSha": "d2c3143d20468012294601d338386157ef5d4995",
"RemoteHost": "api.github.com",
"Remotes": "github::EpiModel/slurmworkflow, github::EpiModel/swfcalib"
},
"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 = \"Brian.Ripley@R-project.org\"), 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": "<MASS@stats.ox.ac.uk>",
"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 <Brian.Ripley@R-project.org>",
"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": "Matrix-authors@R-project.org",
"Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", 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": [
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"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 <mmaechler+Matrix@gmail.com>",
"Repository": "CRAN"
},
"R6": {
"Package": "R6",
"Version": "2.6.1",
"Source": "Repository",
"Title": "Encapsulated Classes with Reference Semantics",
"Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", 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": [
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],
"Suggests": [
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"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 <winston@posit.co>",
"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 = \"erich.neuwirth@univie.ac.at\"))",
"Author": "Erich Neuwirth [aut, cre]",
"Maintainer": "Erich Neuwirth <erich.neuwirth@univie.ac.at>",
"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"
},
"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 = \"edd@debian.org\", 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": "rcpp-devel@lists.r-forge.r-project.org",
"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 <edd@debian.org>",
"Repository": "CRAN"
},
"RcppRoll": {
"Package": "RcppRoll",
"Version": "0.3.1",
"Source": "Repository",
"Type": "Package",
"Title": "Efficient Rolling / Windowed Operations",
"Author": "Kevin Ushey",
"Maintainer": "Kevin Ushey <kevinushey@gmail.com>",
"Description": "Provides fast and efficient routines for common rolling / windowed operations. Routines for the efficient computation of windowed mean, median, sum, product, minimum, maximum, standard deviation and variance are provided.",
"License": "GPL (>= 2)",
"Depends": [
"R (>= 2.15.1)"
],
"Suggests": [
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"testthat"
],
"Imports": [
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],
"LinkingTo": [
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],
"RoxygenNote": "6.0.1",
"NeedsCompilation": "yes",
"Repository": "CRAN"
},
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"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] (<https://orcid.org/0000-0003-2839-346X>), Duncan Murdoch [ctb]",
"Maintainer": "Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>",
"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] (<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 <Emmanuel.Paradis@ird.fr>",
"Repository": "CRAN"
},
"base64enc": {
"Package": "base64enc",
"Version": "0.1-3",
"Source": "Repository",
"Title": "Tools for base64 encoding",
"Author": "Simon Urbanek <Simon.Urbanek@r-project.org>",
"Maintainer": "Simon Urbanek <Simon.Urbanek@r-project.org>",
"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"
},
"bit": {
"Package": "bit",
"Version": "4.6.0",
"Source": "Repository",
"Title": "Classes and Methods for Fast Memory-Efficient Boolean Selections",
"Authors@R": "c( person(\"Michael\", \"Chirico\", email = \"MichaelChirico4@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Jens\", \"Oehlschlägel\", role = \"aut\"), person(\"Brian\", \"Ripley\", role = \"ctb\") )",
"Depends": [
"R (>= 3.4.0)"
],
"Suggests": [
"testthat (>= 3.0.0)",
"roxygen2",
"knitr",
"markdown",
"rmarkdown",
"microbenchmark",
"bit64 (>= 4.0.0)",
"ff (>= 4.0.0)"
],
"Description": "Provided are classes for boolean and skewed boolean vectors, fast boolean methods, fast unique and non-unique integer sorting, fast set operations on sorted and unsorted sets of integers, and foundations for ff (range index, compression, chunked processing).",
"License": "GPL-2 | GPL-3",
"LazyLoad": "yes",
"ByteCompile": "yes",
"Encoding": "UTF-8",
"URL": "https://github.com/r-lib/bit",
"VignetteBuilder": "knitr, rmarkdown",
"RoxygenNote": "7.3.2",
"Config/testthat/edition": "3",
"NeedsCompilation": "yes",
"Author": "Michael Chirico [aut, cre], Jens Oehlschlägel [aut], Brian Ripley [ctb]",
"Maintainer": "Michael Chirico <MichaelChirico4@gmail.com>",
"Repository": "CRAN"
},
"bit64": {
"Package": "bit64",
"Version": "4.6.0-1",
"Source": "Repository",
"Title": "A S3 Class for Vectors of 64bit Integers",
"Authors@R": "c( person(\"Michael\", \"Chirico\", email = \"michaelchirico4@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Jens\", \"Oehlschlägel\", role = \"aut\"), person(\"Leonardo\", \"Silvestri\", role = \"ctb\"), person(\"Ofek\", \"Shilon\", role = \"ctb\") )",
"Depends": [
"R (>= 3.4.0)",
"bit (>= 4.0.0)"
],
"Description": "Package 'bit64' provides serializable S3 atomic 64bit (signed) integers. These are useful for handling database keys and exact counting in +-2^63. WARNING: do not use them as replacement for 32bit integers, integer64 are not supported for subscripting by R-core and they have different semantics when combined with double, e.g. integer64 + double => integer64. Class integer64 can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support inter- active data exploration and manipulation and optionally leverage caching.",
"License": "GPL-2 | GPL-3",
"LazyLoad": "yes",
"ByteCompile": "yes",
"URL": "https://github.com/r-lib/bit64",
"Encoding": "UTF-8",
"Imports": [
"graphics",
"methods",
"stats",
"utils"
],
"Suggests": [
"testthat (>= 3.0.3)",
"withr"
],
"Config/testthat/edition": "3",
"Config/needs/development": "testthat",
"RoxygenNote": "7.3.2",
"NeedsCompilation": "yes",
"Author": "Michael Chirico [aut, cre], Jens Oehlschlägel [aut], Leonardo Silvestri [ctb], Ofek Shilon [ctb]",
"Maintainer": "Michael Chirico <michaelchirico4@gmail.com>",
"Repository": "CRAN"
},
"bslib": {
"Package": "bslib",
"Version": "0.9.0",
"Source": "Repository",
"Title": "Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'",
"Authors@R": "c( person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Garrick\", \"Aden-Buie\", , \"garrick@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Javi\", \"Aguilar\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap colorpicker library\"), person(\"Thomas\", \"Park\", role = c(\"ctb\", \"cph\"), comment = \"Bootswatch library\"), person(, \"PayPal\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap accessibility plugin\") )",
"Description": "Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as well as their various 'Bootswatch' themes. An interactive widget is also provided for previewing themes in real time.",
"License": "MIT + file LICENSE",
"URL": "https://rstudio.github.io/bslib/, https://github.com/rstudio/bslib",
"BugReports": "https://github.com/rstudio/bslib/issues",
"Depends": [
"R (>= 2.10)"
],
"Imports": [
"base64enc",
"cachem",
"fastmap (>= 1.1.1)",
"grDevices",
"htmltools (>= 0.5.8)",
"jquerylib (>= 0.1.3)",
"jsonlite",
"lifecycle",
"memoise (>= 2.0.1)",
"mime",
"rlang",
"sass (>= 0.4.9)"
],
"Suggests": [
"bsicons",
"curl",
"fontawesome",
"future",
"ggplot2",
"knitr",
"magrittr",
"rappdirs",
"rmarkdown (>= 2.7)",
"shiny (> 1.8.1)",
"testthat",
"thematic",
"tools",
"utils",
"withr",
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"URL": "https://cli.r-lib.org, https://github.com/r-lib/cli",
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],
"Description": "Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.",
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"Author": "Martyn Plummer [aut, cre, trl], Nicky Best [aut], Kate Cowles [aut], Karen Vines [aut], Deepayan Sarkar [aut], Douglas Bates [aut], Russell Almond [aut], Arni Magnusson [aut]",
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"Maintainer": "Luke Tierney <luke-tierney@uiowa.edu>",
"URL": "https://gitlab.com/luke-tierney/codetools",
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"Description": "Provides high performance container data types such as queues, stacks, deques, dicts and ordered dicts. Benchmarks <https://randy3k.github.io/collections/articles/benchmark.html> have shown that these containers are asymptotically more efficient than those offered by other packages.",
"License": "MIT + file LICENSE",
"URL": "https://github.com/randy3k/collections/",
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"Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.",
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"URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11",
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"License": "MIT + file LICENSE",
"URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon",
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"NeedsCompilation": "no",
"Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]",
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"Repository": "CRAN"
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"Title": "Solvers for Initial Value Problems of Differential Equations ('ODE', 'DAE', 'DDE')",
"Authors@R": "c(person(\"Karline\",\"Soetaert\", role = c(\"aut\"), email = \"karline.soetaert@nioz.nl\", comment = c(ORCID = \"0000-0003-4603-7100\")), person(\"Thomas\",\"Petzoldt\", role = c(\"aut\", \"cre\"), email = \"thomas.petzoldt@tu-dresden.de\", comment = c(ORCID = \"0000-0002-4951-6468\")), person(\"R. Woodrow\",\"Setzer\", role = c(\"aut\"), email = \"setzer.woodrow@epa.gov\", comment = c(ORCID = \"0000-0002-6709-9186\")), person(\"Peter N.\",\"Brown\", role = \"ctb\", comment = \"files ddaspk.f, dvode.f, zvode.f\"), person(\"George D.\",\"Byrne\", role = \"ctb\", comment = \"files dvode.f, zvode.f\"), person(\"Ernst\",\"Hairer\", role = \"ctb\", comment = \"files radau5.f, radau5a\"), person(\"Alan C.\",\"Hindmarsh\", role = \"ctb\", comment = \"files ddaspk.f, dlsode.f, dvode.f, zvode.f, opdkmain.f, opdka1.f\"), person(\"Cleve\",\"Moler\", role = \"ctb\", comment = \"file dlinpck.f\"), person(\"Linda R.\",\"Petzold\", role = \"ctb\", comment = \"files ddaspk.f, dlsoda.f\"), person(\"Youcef\", \"Saad\", role = \"ctb\", comment = \"file dsparsk.f\"), person(\"Clement W.\",\"Ulrich\", role = \"ctb\", comment = \"file ddaspk.f\") )",
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"Maintainer": "Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>",
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"Description": "Functions that solve initial value problems of a system of first-order ordinary differential equations ('ODE'), of partial differential equations ('PDE'), of differential algebraic equations ('DAE'), and of delay differential equations. The functions provide an interface to the FORTRAN functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK' collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk' and a C-implementation of solvers of the 'Runge-Kutta' family with fixed or variable time steps. The package contains routines designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D partial differential equations ('PDE') that have been converted to 'ODEs' by numerical differencing.",
"License": "GPL (>= 2)",
"URL": "http://desolve.r-forge.r-project.org/",
"LazyData": "yes",
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"desc": {
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"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 <csardi.gabor@gmail.com>",
"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",
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