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Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".", "Maintainer": "Martin Maechler ", "Authors@R": "c(person(\"Martin\",\"Maechler\", role = c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) ,person(\"Peter\", \"Rousseeuw\", role=\"aut\", email=\"peter.rousseeuw@kuleuven.be\", comment = c(\"Fortran original\", ORCID = \"0000-0002-3807-5353\")) ,person(\"Anja\", \"Struyf\", role=\"aut\", comment= \"S original\") ,person(\"Mia\", \"Hubert\", role=\"aut\", email= \"Mia.Hubert@uia.ua.ac.be\", comment = c(\"S original\", ORCID = \"0000-0001-6398-4850\")) ,person(\"Kurt\", \"Hornik\", role=c(\"trl\", \"ctb\"), email=\"Kurt.Hornik@R-project.org\", comment=c(\"port to R; maintenance(1999-2000)\", ORCID=\"0000-0003-4198-9911\")) ,person(\"Matthias\", \"Studer\", role=\"ctb\") ,person(\"Pierre\", \"Roudier\", role=\"ctb\") ,person(\"Juan\", \"Gonzalez\", role=\"ctb\") ,person(\"Kamil\", \"Kozlowski\", role=\"ctb\") ,person(\"Erich\", \"Schubert\", role=\"ctb\", comment = c(\"fastpam options for pam()\", ORCID = \"0000-0001-9143-4880\")) ,person(\"Keefe\", \"Murphy\", role=\"ctb\", comment = \"volume.ellipsoid({d >= 3})\") #not yet ,person(\"Fischer-Rasmussen\", \"Kasper\", role = \"ctb\", comment = \"Gower distance for CLARA\") )", "Depends": [ "R (>= 3.5.0)" ], "Imports": [ "graphics", "grDevices", "stats", "utils" ], "Suggests": [ "MASS", "Matrix" ], "SuggestsNote": "MASS: two examples using cov.rob() and mvrnorm(); Matrix tools for testing", "Enhances": [ "mvoutlier", "fpc", "ellipse", "sfsmisc" ], "EnhancesNote": "xref-ed in man/*.Rd", "LazyLoad": "yes", "LazyData": "yes", "ByteCompile": "yes", "BuildResaveData": "no", "License": "GPL (>= 2)", "URL": "https://svn.r-project.org/R-packages/trunk/cluster/", "NeedsCompilation": "yes", "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", "Repository": "CRAN" }, "clustree": { "Package": "clustree", "Version": "0.5.1", "Source": "Repository", "Type": "Package", "Title": "Visualise Clusterings at Different Resolutions", "Date": "2023-11-05", "Authors@R": "c(person(\"Luke\", \"Zappia\", role = c(\"aut\", \"cre\"), email = \"luke@lazappi.id.au\", comment = c(ORCID = \"0000-0001-7744-8565\")), person(\"Alicia\", \"Oshlack\", role = c(\"aut\"), email = \"alicia.oshlack@petermac.org\", comment = c(ORCID = \"0000-0001-9788-5690\")), person(\"Andrea\", \"Rau\", role = c(\"ctb\"), email = \"andrea.rau@inra.fr\"), person(\"Paul\", \"Hoffman\", role = c(\"ctb\"), email = \"phoffman@nygenome.org\", comment = c(ORCID = \"0000-0002-7693-8957\")))", "Maintainer": "Luke Zappia ", "Description": "Deciding what resolution to use can be a difficult question when approaching a clustering analysis. 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This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "URL": "https://github.com/lazappi/clustree, https://lazappi.github.io/clustree/", "BugReports": "https://github.com/lazappi/clustree/issues", "VignetteBuilder": "knitr", "Depends": [ "R (>= 3.5)", "ggraph" ], "Imports": [ "checkmate", "igraph", "dplyr", "grid", "ggplot2 (>= 3.4.0)", "viridis", "methods", "rlang", "tidygraph", "ggrepel" ], "Suggests": [ "testthat (>= 2.1.0)", "knitr", "rmarkdown", "SingleCellExperiment", "Seurat (>= 2.3.0)", "covr", "SummarizedExperiment", "pkgdown", "spelling" ], "RoxygenNote": "7.2.3", "Language": "en-GB", "NeedsCompilation": "no", "Author": "Luke Zappia [aut, cre] (), Alicia Oshlack [aut] (), Andrea Rau [ctb], Paul Hoffman [ctb] ()", "Repository": "RSPM" }, "coda": { "Package": "coda", "Version": "0.19-4.1", "Source": "Repository", "Date": "2020-09-30", "Title": "Output Analysis and Diagnostics for MCMC", "Authors@R": "c(person(\"Martyn\", \"Plummer\", role=c(\"aut\",\"cre\",\"trl\"), email=\"martyn.plummer@gmail.com\"), person(\"Nicky\", \"Best\", role=\"aut\"), person(\"Kate\", \"Cowles\", role=\"aut\"), person(\"Karen\", \"Vines\", role=\"aut\"), person(\"Deepayan\", \"Sarkar\", role=\"aut\"), person(\"Douglas\", \"Bates\", role=\"aut\"), person(\"Russell\", \"Almond\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"))", "Depends": [ "R (>= 2.14.0)" ], "Imports": [ "lattice" ], "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.", "License": "GPL (>= 2)", "NeedsCompilation": "no", "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]", "Maintainer": "Martyn Plummer ", "Repository": "RSPM", "Encoding": "UTF-8" }, "codetools": { "Package": "codetools", "Version": "0.2-20", "Source": "Repository", "Priority": "recommended", "Author": "Luke Tierney ", "Description": "Code analysis tools for R.", "Title": "Code Analysis Tools for R", "Depends": [ "R (>= 2.1)" ], "Maintainer": "Luke Tierney ", "URL": "https://gitlab.com/luke-tierney/codetools", "License": "GPL", "NeedsCompilation": "no", "Repository": "CRAN" }, "colorspace": { "Package": "colorspace", "Version": "2.1-1", "Source": "Repository", "Date": "2024-07-26", "Title": "A Toolbox for Manipulating and Assessing Colors and Palettes", "Authors@R": "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"), person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\", comment = c(ORCID = \"0000-0002-3224-8858\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\", comment = c(ORCID = \"0000-0001-9032-8912\")), person(given = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\", comment = c(ORCID = \"0000-0002-3798-5507\")), person(given = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(given = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\", comment = c(ORCID = \"0000-0001-7346-3047\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")))", "Description": "Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. 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(2020, Journal of Statistical Software, ).", "Depends": [ "R (>= 3.0.0)", "methods" ], "Imports": [ "graphics", "grDevices", "stats" ], "Suggests": [ "datasets", "utils", "KernSmooth", "MASS", "kernlab", "mvtnorm", "vcd", "tcltk", "shiny", "shinyjs", "ggplot2", "dplyr", "scales", "grid", "png", "jpeg", "knitr", "rmarkdown", "RColorBrewer", "rcartocolor", "scico", "viridis", "wesanderson" ], "VignetteBuilder": "knitr", "License": "BSD_3_clause + file LICENSE", "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", "LazyData": "yes", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "NeedsCompilation": "yes", "Author": "Ross Ihaka [aut], Paul Murrell [aut] (), Kurt Hornik [aut] (), Jason C. Fisher [aut] (), Reto Stauffer [aut] (), Claus O. Wilke [aut] (), Claire D. McWhite [aut] (), Achim Zeileis [aut, cre] ()", "Maintainer": "Achim Zeileis ", "Repository": "RSPM" }, "commonmark": { "Package": "commonmark", "Version": "2.0.0", "Source": "Repository", "Type": "Package", "Title": "High Performance CommonMark and Github Markdown Rendering in R", "Authors@R": "c( person(\"Jeroen\", \"Ooms\", ,\"jeroenooms@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"John MacFarlane\", role = \"cph\", comment = \"Author of cmark\"))", "Description": "The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. 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It computes the concave polygon(s) for one or several set of points.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "Depends": [ "R (>= 2.10)" ], "Imports": [ "V8", "sf", "magrittr", "jsonlite", "dplyr" ], "RoxygenNote": "7.1.0", "Suggests": [ "testthat" ], "URL": "https://joelgombin.github.io/concaveman/, http://www.github.com/joelgombin/concaveman/", "BugReports": "http://www.github.com/joelgombin/concaveman/issues", "SystemRequirements": "GDAL (>= 2.0.0), GEOS (>= 3.3.0), PROJ.4 (>= 4.8.0)", "NeedsCompilation": "no", "Author": "Joël Gombin [cre, aut], Ramnath Vaidyanathan [aut], Vladimir Agafonkin [aut], Mapbox [cph]", "Maintainer": "Joël Gombin ", "Repository": "RSPM" }, "conflicted": { "Package": "conflicted", "Version": "1.2.0", "Source": "Repository", "Title": "An Alternative Conflict Resolution Strategy", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", "Description": "R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use.", "License": "MIT + file LICENSE", "URL": "https://conflicted.r-lib.org/, https://github.com/r-lib/conflicted", "BugReports": "https://github.com/r-lib/conflicted/issues", "Depends": [ "R (>= 3.2)" ], "Imports": [ "cli (>= 3.4.0)", "memoise", "rlang (>= 1.0.0)" ], "Suggests": [ "callr", "covr", "dplyr", "Matrix", "methods", "pkgload", "testthat (>= 3.0.0)", "withr" ], "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut, cre], RStudio [cph, fnd]", "Maintainer": "Hadley Wickham ", "Repository": "RSPM" }, "cowplot": { "Package": "cowplot", "Version": "1.2.0", "Source": "Repository", "Title": "Streamlined Plot Theme and Plot Annotations for 'ggplot2'", "Authors@R": "person( given = \"Claus O.\", family = \"Wilke\", role = c(\"aut\", \"cre\"), email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\") )", "Description": "Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.", "URL": "https://wilkelab.org/cowplot/", "BugReports": "https://github.com/wilkelab/cowplot/issues", "Depends": [ "R (>= 3.5.0)" ], "Imports": [ "ggplot2 (>= 3.5.2)", "grid", "gtable", "grDevices", "methods", "rlang", "scales" ], "License": "GPL-2", "Suggests": [ "Cairo", "covr", "dplyr", "forcats", "gridGraphics (>= 0.4-0)", "knitr", "lattice", "magick", "maps", "PASWR", "patchwork", "rmarkdown", "ragg", "testthat (>= 1.0.0)", "tidyr", "vdiffr (>= 0.3.0)", "VennDiagram" ], "VignetteBuilder": "knitr", "Collate": "'add_sub.R' 'align_plots.R' 'as_grob.R' 'as_gtable.R' 'axis_canvas.R' 'cowplot.R' 'draw.R' 'get_plot_component.R' 'get_axes.R' 'get_titles.R' 'get_legend.R' 'get_panel.R' 'gtable.R' 'key_glyph.R' 'plot_grid.R' 'save.R' 'set_null_device.R' 'setup.R' 'stamp.R' 'themes.R' 'utils_ggplot2.R'", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "NeedsCompilation": "no", "Author": "Claus O. Wilke [aut, cre] (ORCID: )", "Maintainer": "Claus O. Wilke ", "Repository": "RSPM" }, "cpp11": { "Package": "cpp11", "Version": "0.5.2", "Source": "Repository", "Title": "A C++11 Interface for R's C Interface", "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", "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.", "License": "MIT + file LICENSE", "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", "BugReports": "https://github.com/r-lib/cpp11/issues", "Depends": [ "R (>= 4.0.0)" ], "Suggests": [ "bench", "brio", "callr", "cli", "covr", "decor", "desc", "ggplot2", "glue", "knitr", "lobstr", "mockery", "progress", "rmarkdown", "scales", "Rcpp", "testthat (>= 3.2.0)", "tibble", "utils", "vctrs", "withr" ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", "Maintainer": "Davis Vaughan ", "Repository": "RSPM" }, "crayon": { "Package": "crayon", "Version": "1.5.3", "Source": "Repository", "Title": "Colored Terminal Output", "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", "License": "MIT + file LICENSE", "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", "BugReports": "https://github.com/r-lib/crayon/issues", "Imports": [ "grDevices", "methods", "utils" ], "Suggests": [ "mockery", "rstudioapi", "testthat", "withr" ], "Config/Needs/website": "tidyverse/tidytemplate", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", "NeedsCompilation": "no", "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", "Maintainer": "Gábor Csárdi ", "Repository": "RSPM" }, "credentials": { "Package": "credentials", "Version": "2.0.2", "Source": "Repository", "Type": "Package", "Title": "Tools for Managing SSH and Git Credentials", "Authors@R": "person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\"))", "Description": "Setup and retrieve HTTPS and SSH credentials for use with 'git' and other services. For HTTPS remotes the package interfaces the 'git-credential' utility which 'git' uses to store HTTP usernames and passwords. For SSH remotes we provide convenient functions to find or generate appropriate SSH keys. 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It enables to easily convert standard '%dopar%' loops into fully reproducible loops, independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.", "License": "GPL (>= 2)", "LazyLoad": "yes", "URL": "https://renozao.github.io/doRNG/", "BugReports": "https://github.com/renozao/doRNG/issues", "Depends": [ "R (>= 3.0.0)", "foreach", "rngtools (>= 1.5)" ], "Imports": [ "stats", "utils", "iterators" ], "Suggests": [ "doParallel", "doMPI", "doRedis", "rbenchmark", "devtools", "knitr", "rbibutils (>= 1.3)", "testthat", "covr" ], "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "Author": "Renaud Gaujoux [aut, cre]", "Maintainer": "Renaud Gaujoux ", "Repository": "RSPM" }, "dotCall64": { "Package": "dotCall64", "Version": "1.2", "Source": "Repository", "Type": "Package", "Title": "Enhanced Foreign Function Interface Supporting Long Vectors", "Date": "2024-10-03", "Authors@R": "c(person(\"Kaspar\", \"Moesinger\", role = c(\"aut\"), email = \"kaspar.moesinger@gmail.com\"), person(\"Florian\", \"Gerber\", role = c(\"aut\"), email = \"flora.fauna.gerber@gmail.com\", comment = c(ORCID = \"0000-0001-8545-5263\")), person(\"Reinhard\", \"Furrer\", role = c(\"cre\", \"ctb\"), email = \"reinhard.furrer@uzh.ch\", comment = c(ORCID = \"0000-0002-6319-2332\")))", "Description": "Provides .C64(), which is an enhanced version of .C() and .Fortran() from the foreign function interface. .C64() supports long vectors, arguments of type 64-bit integer, and provides a mechanism to avoid unnecessary copies of read-only and write-only arguments. 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It includes linking of function calls to their documentation on the web, and automatic translation of ANSI escapes in output to the equivalent HTML.", "License": "MIT + file LICENSE", "URL": "https://downlit.r-lib.org/, https://github.com/r-lib/downlit", "BugReports": "https://github.com/r-lib/downlit/issues", "Depends": [ "R (>= 4.0.0)" ], "Imports": [ "brio", "desc", "digest", "evaluate", "fansi", "memoise", "rlang", "vctrs", "withr", "yaml" ], "Suggests": [ "covr", "htmltools", "jsonlite", "MASS", "MassSpecWavelet", "pkgload", "rmarkdown", "testthat (>= 3.0.0)", "xml2" ], "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", "Repository": "RSPM" }, "dplyr": { "Package": "dplyr", "Version": "1.1.4", "Source": "Repository", "Type": "Package", "Title": "A Grammar of Data Manipulation", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Kirill\", \"Müller\", role = \"aut\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", "Description": "A fast, consistent tool for working with data frame like objects, both in memory and out of memory.", "License": "MIT + file LICENSE", "URL": "https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr", "BugReports": "https://github.com/tidyverse/dplyr/issues", "Depends": [ "R (>= 3.5.0)" ], "Imports": [ "cli (>= 3.4.0)", "generics", "glue (>= 1.3.2)", "lifecycle (>= 1.0.3)", "magrittr (>= 1.5)", "methods", "pillar (>= 1.9.0)", "R6", "rlang (>= 1.1.0)", "tibble (>= 3.2.0)", "tidyselect (>= 1.2.0)", "utils", "vctrs (>= 0.6.4)" ], "Suggests": [ "bench", "broom", "callr", "covr", "DBI", "dbplyr (>= 2.2.1)", "ggplot2", "knitr", "Lahman", "lobstr", "microbenchmark", "nycflights13", "purrr", "rmarkdown", "RMySQL", "RPostgreSQL", "RSQLite", "stringi (>= 1.7.6)", "testthat (>= 3.1.5)", "tidyr (>= 1.3.0)", "withr" ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse, shiny, pkgdown, tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.3", "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre] (), Romain François [aut] (), Lionel Henry [aut], Kirill Müller [aut] (), Davis Vaughan [aut] (), Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, "dqrng": { "Package": "dqrng", "Version": "0.4.1", "Source": "Repository", "Type": "Package", "Title": "Fast Pseudo Random Number Generators", "Authors@R": "c( person(\"Ralf\", \"Stubner\", email = \"ralf.stubner@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0009-1908-106X\")), person(\"daqana GmbH\", role = \"cph\"), person(\"David Blackman\", role = \"cph\", comment = \"Xoroshiro / Xoshiro family\"), person(\"Melissa O'Neill\", email = \"oneill@pcg-random.org\", role = \"cph\", comment = \"PCG family\"), person(\"Sebastiano Vigna\", email = \"vigna@acm.org\", role = \"cph\", comment = \"Xoroshiro / Xoshiro family\"), person(\"Aaron\", \"Lun\", role=\"ctb\"), person(\"Kyle\", \"Butts\", role = \"ctb\", email = \"kyle.butts@colorado.edu\"), person(\"Henrik\", \"Sloot\", role = \"ctb\"), person(\"Philippe\", \"Grosjean\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-2694-9471\")) )", "Description": "Several fast random number generators are provided as C++ header only libraries: The PCG family by O'Neill (2014 ) as well as the Xoroshiro / Xoshiro family by Blackman and Vigna (2021 ). In addition fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang (2000, ). The fast sampling methods support unweighted sampling both with and without replacement. These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+/++/** and Xoshiro256+/++/** as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011, ) as provided by the package 'sitmo'.", "License": "AGPL-3", "Depends": [ "R (>= 3.5.0)" ], "Imports": [ "Rcpp (>= 0.12.16)" ], "LinkingTo": [ "Rcpp", "BH (>= 1.64.0-1)", "sitmo (>= 2.0.0)" ], "RoxygenNote": "7.3.1", "Suggests": [ "BH", "testthat", "knitr", "rmarkdown", "mvtnorm (>= 1.2-3)", "bench", "sitmo" ], "VignetteBuilder": "knitr", "URL": "https://daqana.github.io/dqrng/, https://github.com/daqana/dqrng", "BugReports": "https://github.com/daqana/dqrng/issues", "Encoding": "UTF-8", "NeedsCompilation": "yes", "Author": "Ralf Stubner [aut, cre] (), daqana GmbH [cph], David Blackman [cph] (Xoroshiro / Xoshiro family), Melissa O'Neill [cph] (PCG family), Sebastiano Vigna [cph] (Xoroshiro / Xoshiro family), Aaron Lun [ctb], Kyle Butts [ctb], Henrik Sloot [ctb], Philippe Grosjean [ctb] ()", "Maintainer": "Ralf Stubner ", "Repository": "CRAN" }, "drake": { "Package": "drake", "Version": "7.13.11", "Source": "Repository", "Title": "A Pipeline Toolkit for Reproducible Computation at Scale", "Authors@R": "c( person( given = c(\"William\", \"Michael\"), family = \"Landau\", role = c(\"aut\", \"cre\"), email = \"will.landau.oss@gmail.com\", comment = c(ORCID = \"0000-0003-1878-3253\") ), person( given = \"Alex\", family = \"Axthelm\", role = \"ctb\", email = \"aaxthelm@che.IN.gov\" ), person( given = \"Jasper\", family = \"Clarkberg\", role = \"ctb\", email = \"jasper@clarkberg.org\" ), person( given = \"Kirill\", family = \"Müller\", role = \"ctb\", email = \"kirill@cynkra.com\" ), person( given = \"Ben\", family = \"Bond-Lamberty\", role = \"ctb\", email = \"bondlamberty@pnnl.gov\", comment = c(ORCID = \"0000-0001-9525-4633\") ), person( given = \"Tristan\", family = \"Mahr\", role = \"ctb\", email = \"tristan.mahr@wisc.edu\", comment = c(ORCID = \"0000-0002-8890-5116\") ), person( given = \"Miles\", family = \"McBain\", role = \"ctb\", email = \"miles.mcbain@gmail.com\", comment = c(ORCID = \"0000-0003-2865-2548\") ), person( given = \"Noam\", family = \"Ross\", role = \"ctb\", email = \"noam.ross@gmail.com\", comment = c(ORCID = \"0000-0002-2136-0000\") ), person( given = \"Ellis\", family = \"Hughes\", role = \"ctb\", email = \"ellishughes@live.com\" ), person( given = c(\"Matthew\", \"Mark\"), family = \"Strasiotto\", role = \"ctb\", email = c( \"matthew.strasiotto@gmail.com\", \"mstr3336@uni.sydney.edu.au\" ) ), person( given = \"Ben\", family = \"Marwick\", role = \"rev\", email = \"bmarwick@uw.edu\" ), person( given = \"Peter\", family = \"Slaughter\", role = \"rev\", email = \"slaughter@nceas.ucsb.edu\" ), person( family = \"Eli Lilly and Company\", role = \"cph\" ))", "Description": "A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, there is native support for parallel and distributed computing, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website and the online manual .", "License": "GPL-3", "URL": "https://github.com/ropensci/drake, https://docs.ropensci.org/drake/, https://books.ropensci.org/drake/", "BugReports": "https://github.com/ropensci/drake/issues", "Depends": [ "R (>= 3.3.0)" ], "Imports": [ "base64url", "digest (>= 0.6.21)", "igraph (>= 2.0.0)", "methods", "parallel", "rlang (>= 0.2.0)", "storr (>= 1.1.0)", "tidyselect (>= 1.0.0)", "txtq (>= 0.2.3)", "utils", "vctrs (>= 0.2.0)" ], "Suggests": [ "abind", "bindr", "callr", "cli (>= 1.1.0)", "clustermq (>= 0.9.1)", "crayon", "curl (>= 2.7)", "data.table", "datasets", "disk.frame", "downloader", "fst", "future (>= 1.3.0)", "ggplot2", "ggraph", "grDevices", "keras", "knitr", "lubridate", "networkD3", "prettycode", "progress (>= 1.2.2)", "qs (>= 0.20.2)", "Rcpp", "rmarkdown", "rstudioapi", "stats", "styler (>= 1.2.0)", "testthat (>= 2.1.0)", "tibble", "txtplot", "usethis", "visNetwork (>= 2.0.9)", "webshot" ], "Encoding": "UTF-8", "Language": "en-US", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Author": "William Michael Landau [aut, cre] (), Alex Axthelm [ctb], Jasper Clarkberg [ctb], Kirill Müller [ctb], Ben Bond-Lamberty [ctb] (), Tristan Mahr [ctb] (), Miles McBain [ctb] (), Noam Ross [ctb] (), Ellis Hughes [ctb], Matthew Mark Strasiotto [ctb], Ben Marwick [rev], Peter Slaughter [rev], Eli Lilly and Company [cph]", "Maintainer": "William Michael Landau ", "Repository": "RSPM" }, "e1071": { "Package": "e1071", "Version": "1.7-16", "Source": "Repository", "Title": "Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien", "Imports": [ "graphics", "grDevices", "class", "stats", "methods", "utils", "proxy" ], "Suggests": [ "cluster", "mlbench", "nnet", "randomForest", "rpart", "SparseM", "xtable", "Matrix", "MASS", "slam" ], "Authors@R": "c(person(given = \"David\", family = \"Meyer\", role = c(\"aut\", \"cre\"), email = \"David.Meyer@R-project.org\", comment = c(ORCID = \"0000-0002-5196-3048\")), person(given = \"Evgenia\", family = \"Dimitriadou\", role = c(\"aut\",\"cph\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = \"Andreas\", family = \"Weingessel\", role = \"aut\"), person(given = \"Friedrich\", family = \"Leisch\", role = \"aut\"), person(given = \"Chih-Chung\", family = \"Chang\", role = c(\"ctb\",\"cph\"), comment = \"libsvm C++-code\"), person(given = \"Chih-Chen\", family = \"Lin\", role = c(\"ctb\",\"cph\"), comment = \"libsvm C++-code\"))", "Description": "Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, generalized k-nearest neighbour ...", "License": "GPL-2 | GPL-3", "LazyLoad": "yes", "NeedsCompilation": "yes", "Author": "David Meyer [aut, cre] (), Evgenia Dimitriadou [aut, cph], Kurt Hornik [aut] (), Andreas Weingessel [aut], Friedrich Leisch [aut], Chih-Chung Chang [ctb, cph] (libsvm C++-code), Chih-Chen Lin [ctb, cph] (libsvm C++-code)", "Maintainer": "David Meyer ", "Repository": "RSPM", "Encoding": "UTF-8" }, "edgeR": { "Package": "edgeR", "Version": "4.6.3", "Source": "Bioconductor", "Date": "2025-07-05", "Title": "Empirical Analysis of Digital Gene Expression Data in R", "Description": "Differential expression analysis of sequence count data. 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The ellipsis package provides a collection of functions to catch problems and alert the user.", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"RStudio\", role = \"cph\") )", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "URL": "https://ellipsis.r-lib.org, https://github.com/r-lib/ellipsis", "BugReports": "https://github.com/r-lib/ellipsis/issues", "Depends": [ "R (>= 3.2)" ], "Imports": [ "rlang (>= 0.3.0)" ], "Suggests": [ "covr", "testthat" ], "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre], RStudio [cph]", "Maintainer": "Hadley Wickham ", "Repository": "RSPM" }, "emoji": { "Package": "emoji", "Version": "16.0.0", "Source": "Repository", "Title": "Data and Function to Work with Emojis", "Authors@R": "c( person(\"Emil\", \"Hvitfeldt\", , \"emilhhvitfeldt@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0679-1945\")), person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = \"ctb\", comment = \"Data parsing code from hadley/emo\"), person(\"Romain\", \"François\", role = \"ctb\", comment = \"Data parsing code from hadley/emo\") )", "Description": "Contains data about emojis with relevant metadata, and functions to work with emojis when they are in strings.", "License": "MIT + file LICENSE", "URL": "https://emilhvitfeldt.github.io/emoji/, https://github.com/EmilHvitfeldt/emoji", "BugReports": "https://github.com/EmilHvitfeldt/emoji/issues", "Depends": [ "R (>= 3.5)" ], "Imports": [ "glue", "stringr", "tibble" ], "Suggests": [ "covr", "testthat (>= 3.0.0)" ], "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Author": "Emil Hvitfeldt [aut, cre] (), Hadley Wickham [ctb] (Data parsing code from hadley/emo), Romain François [ctb] (Data parsing code from hadley/emo)", "Maintainer": "Emil Hvitfeldt ", "Repository": "RSPM" }, "ensembldb": { "Package": "ensembldb", "Version": "2.32.0", "Source": "Bioconductor", "Type": "Package", "Title": "Utilities to create and use Ensembl-based annotation databases", "Authors@R": "c(person(given = \"Johannes\", family = \"Rainer\", email = \"johannes.rainer@eurac.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6977-7147\")), person(given = \"Tim\", family = \"Triche\", email = \"tim.triche@usc.edu\", role = \"ctb\"), person(given = \"Christian\", family = \"Weichenberger\", email = \"christian.weichenberger@eurac.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2176-0274\")), person(given = \"Sebastian\", family = \"Gibb\", email = \"mail@sebastiangibb.de\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7406-4443\")), person(given = \"Laurent\", family = \"Gatto\", email = \"lg390@cam.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1520-2268\")), person(given = \"Boyu\", family = \"Yu\", email = \"boyu.yu.tim@gmail.com\", role = \"ctb\"))", "Author": "Johannes Rainer with contributions from Tim Triche, Sebastian Gibb, Laurent Gatto Christian Weichenberger and Boyu Yu.", "Maintainer": "Johannes Rainer ", "URL": "https://github.com/jorainer/ensembldb", "BugReports": "https://github.com/jorainer/ensembldb/issues", "Imports": [ "methods", "RSQLite (>= 1.1)", "DBI", "Biobase", "GenomeInfoDb", "AnnotationDbi (>= 1.31.19)", "rtracklayer", "S4Vectors (>= 0.23.10)", "Rsamtools", "IRanges (>= 2.13.24)", "ProtGenerics", "Biostrings (>= 2.47.9)", "curl" ], "Depends": [ "R (>= 3.5.0)", "BiocGenerics (>= 0.15.10)", "GenomicRanges (>= 1.31.18)", "GenomicFeatures (>= 1.49.6)", "AnnotationFilter (>= 1.5.2)" ], "Suggests": [ "BiocStyle", "knitr", "EnsDb.Hsapiens.v86 (>= 0.99.8)", "testthat", "BSgenome.Hsapiens.NCBI.GRCh38", "ggbio (>= 1.24.0)", "Gviz (>= 1.20.0)", "rmarkdown", "AnnotationHub" ], "Enhances": [ "RMariaDB", "shiny" ], "VignetteBuilder": "knitr", "Description": "The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.", "Collate": "'Classes.R' 'Deprecated.R' 'Generics.R' 'Methods-Filter.R' 'Methods.R' 'dbhelpers.R' 'functions-EnsDb.R' 'functions-Filter.R' 'functions-create-EnsDb.R' 'functions-utils.R' 'proteinToX.R' 'transcriptToX.R' 'genomeToX.R' 'select-methods.R' 'seqname-utils.R' 'zzz.R'", "biocViews": "Genetics, AnnotationData, Sequencing, Coverage", "License": "LGPL", "RoxygenNote": "7.3.2", "git_url": "https://git.bioconductor.org/packages/ensembldb", "git_branch": "RELEASE_3_21", "git_last_commit": "28aabc4", "git_last_commit_date": "2025-04-15", "Repository": "Bioconductor 3.21", "NeedsCompilation": "no" }, "escheR": { "Package": "escheR", "Version": "1.8.0", "Source": "Bioconductor", "Title": "Unified multi-dimensional visualizations with Gestalt principles", "Authors@R": "c( person(\"Boyi\", \"Guo\", email = \"boyi.guo.work@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-2950-2349\")), person(c(\"Stephanie\", \"C.\"), \"Hicks\", role = c(\"aut\"), email = \"shicks19@jhu.edu\", comment = c(ORCID = \"0000-0002-7858-0231\")), person(c(\"Erik\", \"D.\"), \"Nelson\", email = \"erik.nelson116@gmail.com\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0001-8477-0982\")) )", "Description": "The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide this open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "biocViews": "Spatial, SingleCell, Transcriptomics, Visualization, Software", "Depends": [ "ggplot2", "R (>= 4.3)" ], "Imports": [ "SpatialExperiment (>= 1.6.1)", "SingleCellExperiment", "rlang", "SummarizedExperiment" ], "BugReports": "https://github.com/boyiguo1/escheR/issues", "URL": "https://github.com/boyiguo1/escheR", "Suggests": [ "STexampleData", "BumpyMatrix", "knitr", "rmarkdown", "BiocStyle", "ggpubr", "scran", "scater", "scuttle", "Seurat", "hexbin" ], "VignetteBuilder": "knitr", "git_url": "https://git.bioconductor.org/packages/escheR", "git_branch": "RELEASE_3_21", "git_last_commit": "8df0b7e", "git_last_commit_date": "2025-04-15", "Repository": "Bioconductor 3.21", "NeedsCompilation": "no", "Author": "Boyi Guo [aut, cre] (ORCID: ), Stephanie C. Hicks [aut] (ORCID: ), Erik D. 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As different colour spaces have different uses, efficient conversion between these representations are important. The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.", "License": "MIT + file LICENSE", "URL": "https://farver.data-imaginist.com, https://github.com/thomasp85/farver", "BugReports": "https://github.com/thomasp85/farver/issues", "Suggests": [ "covr", "testthat (>= 3.0.0)" ], "Config/testthat/edition": "3", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]", "Maintainer": "Thomas Lin Pedersen ", "Repository": "CRAN" }, "fastDummies": { "Package": "fastDummies", "Version": "1.7.5", "Source": "Repository", "Type": "Package", "Title": "Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables", "Authors@R": "c( person(\"Jacob\", \"Kaplan\", email = \"jkkaplan6@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0601-0387\")), person(\"Benjamin\", \"Schlegel\", email = \"kontakt@benjaminschlegl.ch\", role = \"ctb\"))", "Description": "Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through model.matrix().", "Depends": [ "R (>= 2.10)" ], "Imports": [ "data.table", "tibble", "stringr" ], "License": "MIT + file LICENSE", "Encoding": "UTF-8", "URL": "https://github.com/jacobkap/fastDummies, https://jacobkap.github.io/fastDummies/", "BugReports": "https://github.com/jacobkap/fastDummies/issues", "RoxygenNote": "7.3.2", "Suggests": [ "testthat (>= 2.1.0)", "knitr", "rmarkdown", "covr", "spelling" ], "VignetteBuilder": "knitr", "Language": "en-US", "NeedsCompilation": "no", "Author": "Jacob Kaplan [aut, cre] (), Benjamin Schlegel [ctb]", "Maintainer": "Jacob Kaplan ", "Repository": "RSPM" }, "fastmap": { "Package": "fastmap", "Version": "1.2.0", "Source": "Repository", "Title": "Fast Data Structures", "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Tessil\", role = \"cph\", comment = \"hopscotch_map library\") )", "Description": "Fast implementation of data structures, including a key-value store, stack, and queue. Environments are commonly used as key-value stores in R, but every time a new key is used, it is added to R's global symbol table, causing a small amount of memory leakage. This can be problematic in cases where many different keys are used. 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The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding the source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI . Development of this package was supported in part by the National Science Foundation Grant 1417857, the National Center for Atmospheric Research, and Colorado School of Mines. 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Source code of other languages is supported via Andre Simon's highlight package ().", "Depends": [ "R (>= 3.3.0)" ], "Imports": [ "xfun (>= 0.18)" ], "Suggests": [ "knitr", "markdown", "testit" ], "License": "GPL", "URL": "https://github.com/yihui/highr", "BugReports": "https://github.com/yihui/highr/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "NeedsCompilation": "no", "Author": "Yihui Xie [aut, cre] (), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]", "Maintainer": "Yihui Xie ", "Repository": "RSPM" }, "hms": { "Package": "hms", "Version": "1.1.3", "Source": "Repository", "Title": "Pretty Time of Day", "Date": "2023-03-21", "Authors@R": "c( person(\"Kirill\", \"Müller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\"), person(\"RStudio\", role = \"fnd\") )", "Description": "Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.", "Imports": [ "lifecycle", "methods", "pkgconfig", "rlang (>= 1.0.2)", "vctrs (>= 0.3.8)" ], "Suggests": [ "crayon", "lubridate", "pillar (>= 1.1.0)", "testthat (>= 3.0.0)" ], "License": "MIT + file LICENSE", "Encoding": "UTF-8", "URL": "https://hms.tidyverse.org/, https://github.com/tidyverse/hms", "BugReports": "https://github.com/tidyverse/hms/issues", "RoxygenNote": "7.2.3", "Config/testthat/edition": "3", "Config/autostyle/scope": "line_breaks", "Config/autostyle/strict": "false", "Config/Needs/website": "tidyverse/tidytemplate", "NeedsCompilation": "no", "Author": "Kirill Müller [aut, cre] (), R Consortium [fnd], RStudio [fnd]", "Maintainer": "Kirill Müller ", "Repository": "CRAN" }, "htmltools": { "Package": "htmltools", "Version": "0.5.8.1", "Source": "Repository", "Type": "Package", "Title": "Tools for HTML", "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Yihui\", \"Xie\", , \"yihui@posit.co\", role = \"aut\"), person(\"Jeff\", \"Allen\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", "Description": "Tools for HTML generation and output.", "License": "GPL (>= 2)", "URL": "https://github.com/rstudio/htmltools, https://rstudio.github.io/htmltools/", "BugReports": "https://github.com/rstudio/htmltools/issues", "Depends": [ "R (>= 2.14.1)" ], "Imports": [ "base64enc", "digest", "fastmap (>= 1.1.0)", "grDevices", "rlang (>= 1.0.0)", "utils" ], "Suggests": [ "Cairo", "markdown", "ragg", "shiny", "testthat", "withr" ], "Enhances": [ "knitr" ], "Config/Needs/check": "knitr", "Config/Needs/website": "rstudio/quillt, bench", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "Collate": "'colors.R' 'fill.R' 'html_dependency.R' 'html_escape.R' 'html_print.R' 'htmltools-package.R' 'images.R' 'known_tags.R' 'selector.R' 'staticimports.R' 'tag_query.R' 'utils.R' 'tags.R' 'template.R'", "NeedsCompilation": "yes", "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (), Barret Schloerke [aut] (), Winston Chang [aut] (), Yihui Xie [aut], Jeff Allen [aut], Posit Software, PBC [cph, fnd]", "Maintainer": "Carson Sievert ", "Repository": "RSPM" }, "htmlwidgets": { "Package": "htmlwidgets", "Version": "1.6.4", "Source": "Repository", "Type": "Package", "Title": "HTML Widgets for R", "Authors@R": "c( person(\"Ramnath\", \"Vaidyanathan\", role = c(\"aut\", \"cph\")), person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"JJ\", \"Allaire\", role = \"aut\"), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Kenton\", \"Russell\", role = c(\"aut\", \"cph\")), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", "Description": "A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.", "License": "MIT + file LICENSE", "URL": "https://github.com/ramnathv/htmlwidgets", "BugReports": "https://github.com/ramnathv/htmlwidgets/issues", "Imports": [ "grDevices", "htmltools (>= 0.5.7)", "jsonlite (>= 0.9.16)", "knitr (>= 1.8)", "rmarkdown", "yaml" ], "Suggests": [ "testthat" ], "Enhances": [ "shiny (>= 1.1)" ], "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "Author": "Ramnath Vaidyanathan [aut, cph], Yihui Xie [aut], JJ Allaire [aut], Joe Cheng [aut], Carson Sievert [aut, cre] (), Kenton Russell [aut, cph], Ellis Hughes [ctb], Posit Software, PBC [cph, fnd]", "Maintainer": "Carson Sievert ", "Repository": "RSPM" }, "httpuv": { "Package": "httpuv", "Version": "1.6.16", "Source": "Repository", "Type": "Package", "Title": "HTTP and WebSocket Server Library", "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit, PBC\", \"fnd\", role = \"cph\"), person(\"Hector\", \"Corrada Bravo\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Andrzej\", \"Krzemienski\", role = \"cph\", comment = \"optional.hpp\"), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library, see src/libuv/AUTHORS file\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file\"), person(\"Niels\", \"Provos\", role = \"cph\", comment = \"libuv subcomponent: tree.h\"), person(\"Internet Systems Consortium, Inc.\", role = \"cph\", comment = \"libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c\"), person(\"Alexander\", \"Chemeris\", role = \"cph\", comment = \"libuv subcomponent: stdint-msvc2008.h (from msinttypes)\"), person(\"Google, Inc.\", role = \"cph\", comment = \"libuv subcomponent: pthread-fixes.c\"), person(\"Sony Mobile Communcations AB\", role = \"cph\", comment = \"libuv subcomponent: pthread-fixes.c\"), person(\"Berkeley Software Design Inc.\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Kenneth\", \"MacKay\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016)\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Steve\", \"Reid\", role = \"aut\", comment = \"SHA-1 implementation\"), person(\"James\", \"Brown\", role = \"aut\", comment = \"SHA-1 implementation\"), person(\"Bob\", \"Trower\", role = \"aut\", comment = \"base64 implementation\"), person(\"Alexander\", \"Peslyak\", role = \"aut\", comment = \"MD5 implementation\"), person(\"Trantor Standard Systems\", role = \"cph\", comment = \"base64 implementation\"), person(\"Igor\", \"Sysoev\", role = \"cph\", comment = \"http-parser\") )", "Description": "Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. 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[cph] (libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c), Alexander Chemeris [cph] (libuv subcomponent: stdint-msvc2008.h (from msinttypes)), Google, Inc. [cph] (libuv subcomponent: pthread-fixes.c), Sony Mobile Communcations AB [cph] (libuv subcomponent: pthread-fixes.c), Berkeley Software Design Inc. [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Kenneth MacKay [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016) [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Steve Reid [aut] (SHA-1 implementation), James Brown [aut] (SHA-1 implementation), Bob Trower [aut] (base64 implementation), Alexander Peslyak [aut] (MD5 implementation), Trantor Standard Systems [cph] (base64 implementation), Igor Sysoev [cph] (http-parser)", "Maintainer": "Winston Chang ", "Repository": "RSPM" }, "httr": { "Package": "httr", "Version": "1.4.7", "Source": "Repository", "Title": "Tools for Working with URLs and HTTP", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", "Description": "Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).", "License": "MIT + file LICENSE", "URL": "https://httr.r-lib.org/, https://github.com/r-lib/httr", "BugReports": "https://github.com/r-lib/httr/issues", "Depends": [ "R (>= 3.5)" ], "Imports": [ "curl (>= 5.0.2)", "jsonlite", "mime", "openssl (>= 0.8)", "R6" ], "Suggests": [ "covr", "httpuv", "jpeg", "knitr", "png", "readr", "rmarkdown", "testthat (>= 0.8.0)", "xml2" ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut, cre], Posit, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, "httr2": { "Package": "httr2", "Version": "1.2.1", "Source": "Repository", "Title": "Perform HTTP Requests and Process the Responses", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Maximilian\", \"Girlich\", role = \"ctb\") )", "Description": "Tools for creating and modifying HTTP requests, then performing them and processing the results. 'httr2' is a modern re-imagining of 'httr' that uses a pipe-based interface and solves more of the problems that API wrapping packages face.", "License": "MIT + file LICENSE", "URL": "https://httr2.r-lib.org, https://github.com/r-lib/httr2", "BugReports": "https://github.com/r-lib/httr2/issues", "Depends": [ "R (>= 4.1)" ], "Imports": [ "cli (>= 3.0.0)", "curl (>= 6.4.0)", "glue", "lifecycle", "magrittr", "openssl", "R6", "rappdirs", "rlang (>= 1.1.0)", "vctrs (>= 0.6.3)", "withr" ], "Suggests": [ "askpass", "bench", "clipr", "covr", "docopt", "httpuv", "jose", "jsonlite", "knitr", "later (>= 1.4.0)", "nanonext", "paws.common", "promises", "rmarkdown", "testthat (>= 3.1.8)", "tibble", "webfakes (>= 1.4.0)", "xml2" ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Config/testthat/start-first": "resp-stream, req-perform", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd], Maximilian Girlich [ctb]", "Maintainer": "Hadley Wickham ", "Repository": "RSPM" }, "ica": { "Package": "ica", "Version": "1.0-3", "Source": "Repository", "Type": "Package", "Title": "Independent Component Analysis", "Date": "2022-07-08", "Author": "Nathaniel E. Helwig ", "Maintainer": "Nathaniel E. Helwig ", "Description": "Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).", "License": "GPL (>= 2)", "NeedsCompilation": "no", "Repository": "RSPM", "Encoding": "UTF-8" }, "igraph": { "Package": "igraph", "Version": "2.1.4", "Source": "Repository", "Title": "Network Analysis and Visualization", "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-7098-9676\")), person(\"Tamás\", \"Nepusz\", , \"ntamas@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-1451-338X\")), person(\"Vincent\", \"Traag\", role = \"aut\", comment = c(ORCID = \"0000-0003-3170-3879\")), person(\"Szabolcs\", \"Horvát\", , \"szhorvat@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-3100-523X\")), person(\"Fabio\", \"Zanini\", , \"fabio.zanini@unsw.edu.au\", role = \"aut\", comment = c(ORCID = \"0000-0001-7097-8539\")), person(\"Daniel\", \"Noom\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Maëlle\", \"Salmon\", role = \"ctb\"), person(\"Michael\", \"Antonov\", role = \"ctb\"), person(\"Chan Zuckerberg Initiative\", role = \"fnd\") )", "Description": "Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.", "License": "GPL (>= 2)", "URL": "https://r.igraph.org/, https://igraph.org/, https://igraph.discourse.group/", "BugReports": "https://github.com/igraph/rigraph/issues", "Depends": [ "methods", "R (>= 3.5.0)" ], "Imports": [ "cli", "graphics", "grDevices", "lifecycle", "magrittr", "Matrix", "pkgconfig (>= 2.0.0)", "rlang", "stats", "utils", "vctrs" ], "Suggests": [ "ape (>= 5.7-0.1)", "callr", "decor", "digest", "igraphdata", "knitr", "rgl (>= 1.3.14)", "rmarkdown", "scales", "stats4", "tcltk", "testthat", "vdiffr", "withr" ], "Enhances": [ "graph" ], "LinkingTo": [ "cpp11 (>= 0.5.0)" ], "VignetteBuilder": "knitr", "Config/Needs/build": "roxygen2, devtools, irlba, pkgconfig, igraph/igraph.r2cdocs, moodymudskipper/devtag", "Config/Needs/coverage": "covr", "Config/Needs/website": "readr", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Config/testthat/start-first": "vs-es, scan, vs-operators, weakref, watts.strogatz.game", "Encoding": "UTF-8", "RoxygenNote": "7.3.2.9000", "SystemRequirements": "libxml2 (optional), glpk (>= 4.57, optional)", "NeedsCompilation": "yes", "Author": "Gábor Csárdi [aut] (), Tamás Nepusz [aut] (), Vincent Traag [aut] (), Szabolcs Horvát [aut] (), Fabio Zanini [aut] (), Daniel Noom [aut], Kirill Müller [aut, cre] (), Maëlle Salmon [ctb], Michael Antonov [ctb], Chan Zuckerberg Initiative [fnd]", "Maintainer": "Kirill Müller ", "Repository": "CRAN" }, "ini": { "Package": "ini", "Version": "0.3.1", "Source": "Repository", "Type": "Package", "Title": "Read and Write '.ini' Files", "Date": "2018-05-19", "Author": "David Valentim Dias", "Maintainer": "David Valentim Dias ", "Description": "Parse simple '.ini' configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications.", "License": "GPL-3", "URL": "https://github.com/dvdscripter/ini", "BugReports": "https://github.com/dvdscripter/ini/issues", "LazyData": "FALSE", "RoxygenNote": "6.0.1", "Suggests": [ "testthat" ], "NeedsCompilation": "no", "Repository": "RSPM", "Encoding": "UTF-8" }, "irlba": { "Package": "irlba", "Version": "2.3.5.1", "Source": "Repository", "Type": "Package", "Title": "Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices", "Date": "2021-12-05", "Authors@R": "c( person(\"Jim\", \"Baglama\", role=c(\"aut\", \"cph\"), email=\"jbaglama@uri.edu\"), person(\"Lothar\", \"Reichel\", role=c(\"aut\", \"cph\"), email=\"reichel@math.kent.edu\"), person(\"B. W.\", \"Lewis\", role=c(\"aut\",\"cre\",\"cph\"), email=\"blewis@illposed.net\"))", "Description": "Fast and memory efficient methods for truncated singular value decomposition and principal components analysis of large sparse and dense matrices.", "Depends": [ "R (>= 3.6.2)", "Matrix" ], "LinkingTo": [ "Matrix" ], "Imports": [ "stats", "methods" ], "License": "GPL-3", "BugReports": "https://github.com/bwlewis/irlba/issues", "RoxygenNote": "5.0.1", "NeedsCompilation": "yes", "Author": "Jim Baglama [aut, cph], Lothar Reichel [aut, cph], B. W. Lewis [aut, cre, cph]", "Maintainer": "B. W. Lewis ", "Repository": "RSPM", "Encoding": "UTF-8" }, "isoband": { "Package": "isoband", "Version": "0.2.7", "Source": "Repository", "Title": "Generate Isolines and Isobands from Regularly Spaced Elevation Grids", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Claus O.\", \"Wilke\", , \"wilke@austin.utexas.edu\", role = \"aut\", comment = c(\"Original author\", ORCID = \"0000-0002-7470-9261\")), person(\"Thomas Lin\", \"Pedersen\", , \"thomasp85@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-5147-4711\")) )", "Description": "A fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.", "License": "MIT + file LICENSE", "URL": "https://isoband.r-lib.org", "BugReports": "https://github.com/r-lib/isoband/issues", "Imports": [ "grid", "utils" ], "Suggests": [ "covr", "ggplot2", "knitr", "magick", "microbenchmark", "rmarkdown", "sf", "testthat", "xml2" ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "SystemRequirements": "C++11", "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre] (), Claus O. Wilke [aut] (Original author, ), Thomas Lin Pedersen [aut] ()", "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, "iterators": { "Package": "iterators", "Version": "1.0.14", "Source": "Repository", "Type": "Package", "Title": "Provides Iterator Construct", "Authors@R": "c(person(\"Folashade\", \"Daniel\", role=\"cre\", email=\"fdaniel@microsoft.com\"), person(\"Revolution\", \"Analytics\", role=c(\"aut\", \"cph\")), person(\"Steve\", \"Weston\", role=\"aut\"))", "Description": "Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.", "URL": "https://github.com/RevolutionAnalytics/iterators", "Depends": [ "R (>= 2.5.0)", "utils" ], "Suggests": [ "RUnit", "foreach" ], "License": "Apache License (== 2.0)", "NeedsCompilation": "no", "Author": "Folashade Daniel [cre], Revolution Analytics [aut, cph], Steve Weston [aut]", "Maintainer": "Folashade Daniel ", "Repository": "RSPM", "Encoding": "UTF-8" }, "janitor": { "Package": "janitor", "Version": "2.2.1", "Source": "Repository", "Title": "Simple Tools for Examining and Cleaning Dirty Data", "Authors@R": "c(person(\"Sam\", \"Firke\", email = \"samuel.firke@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Bill\", \"Denney\", email = \"wdenney@humanpredictions.com\", role = \"ctb\"), person(\"Chris\", \"Haid\", email = \"chrishaid@gmail.com\", role = \"ctb\"), person(\"Ryan\", \"Knight\", email = \"ryangknight@gmail.com\", role = \"ctb\"), person(\"Malte\", \"Grosser\", email = \"malte.grosser@gmail.com\", role = \"ctb\"), person(\"Jonathan\", \"Zadra\", email = \"jonathan.zadra@sorensonimpact.com\", role = \"ctb\"))", "Description": "The main janitor functions can: perfectly format data.frame column names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and explore duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Microsoft Excel. 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Minka [aut] (Enhancements), Alex Deckmyn [aut, cre] (ORCID: )", "Maintainer": "Alex Deckmyn ", "Encoding": "UTF-8" }, "matrixStats": { "Package": "matrixStats", "Version": "1.5.0", "Source": "Repository", "Depends": [ "R (>= 3.4.0)" ], "Suggests": [ "utils", "base64enc", "ggplot2", "knitr", "markdown", "microbenchmark", "R.devices", "R.rsp" ], "VignetteBuilder": "R.rsp", "Title": "Functions that Apply to Rows and Columns of Matrices (and to Vectors)", "Authors@R": "c( person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email=\"henrikb@braju.com\"), person(\"Constantin\", \"Ahlmann-Eltze\", role = \"ctb\"), person(\"Hector\", \"Corrada Bravo\", role=\"ctb\"), person(\"Robert\", \"Gentleman\", role=\"ctb\"), person(\"Jan\", \"Gleixner\", role=\"ctb\"), person(\"Peter\", \"Hickey\", role=\"ctb\"), person(\"Ola\", \"Hossjer\", role=\"ctb\"), person(\"Harris\", \"Jaffee\", role=\"ctb\"), person(\"Dongcan\", \"Jiang\", role=\"ctb\"), person(\"Peter\", \"Langfelder\", role=\"ctb\"), person(\"Brian\", \"Montgomery\", role=\"ctb\"), person(\"Angelina\", \"Panagopoulou\", role=\"ctb\"), person(\"Hugh\", \"Parsonage\", role=\"ctb\"), person(\"Jakob Peder\", \"Pettersen\", role=\"ctb\"))", "Author": "Henrik Bengtsson [aut, cre, cph], Constantin Ahlmann-Eltze [ctb], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Jan Gleixner [ctb], Peter Hickey [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb], Brian Montgomery [ctb], Angelina Panagopoulou [ctb], Hugh Parsonage [ctb], Jakob Peder Pettersen [ctb]", "Maintainer": "Henrik Bengtsson ", "Description": "High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). 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Users specify the distribution by an R function that evaluates the log unnormalized density. Algorithms are random walk Metropolis algorithm (function metrop), simulated tempering (function temper), and morphometric random walk Metropolis (Johnson and Geyer, 2012, , function morph.metrop), which achieves geometric ergodicity by change of variable.", "License": "MIT + file LICENSE", "URL": "http://www.stat.umn.edu/geyer/mcmc/, https://github.com/cjgeyer/mcmc", "NeedsCompilation": "yes", "Repository": "RSPM", "Encoding": "UTF-8" }, "memoise": { "Package": "memoise", "Version": "2.0.1", "Source": "Repository", "Title": "'Memoisation' of Functions", "Authors@R": "c(person(given = \"Hadley\", family = \"Wickham\", role = \"aut\", email = \"hadley@rstudio.com\"), person(given = \"Jim\", family = \"Hester\", role = \"aut\"), person(given = \"Winston\", family = \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@rstudio.com\"), person(given = \"Kirill\", family = \"Müller\", role = \"aut\", email = \"krlmlr+r@mailbox.org\"), person(given = \"Daniel\", family = \"Cook\", role = \"aut\", email = \"danielecook@gmail.com\"), person(given = \"Mark\", family = \"Edmondson\", role = \"ctb\", email = \"r@sunholo.com\"))", "Description": "Cache the results of a function so that when you call it again with the same arguments it returns the previously computed value.", "License": "MIT + file LICENSE", "URL": "https://memoise.r-lib.org, https://github.com/r-lib/memoise", "BugReports": "https://github.com/r-lib/memoise/issues", "Imports": [ "rlang (>= 0.4.10)", "cachem" ], "Suggests": [ "digest", "aws.s3", "covr", "googleAuthR", "googleCloudStorageR", "httr", "testthat" ], "Encoding": "UTF-8", "RoxygenNote": "7.1.2", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut], Jim Hester [aut], Winston Chang [aut, cre], Kirill Müller [aut], Daniel Cook [aut], Mark Edmondson [ctb]", "Maintainer": "Winston Chang ", "Repository": "RSPM" }, "metapod": { "Package": "metapod", "Version": "1.16.0", "Source": "Bioconductor", "Date": "2023-12-22", "Title": "Meta-Analyses on P-Values of Differential Analyses", "Authors@R": "person(\"Aaron\", \"Lun\", role=c(\"aut\", \"cre\"), email = \"infinite.monkeys.with.keyboards@gmail.com\")", "Imports": [ "Rcpp" ], "Suggests": [ "testthat", "knitr", "BiocStyle", "rmarkdown" ], "LinkingTo": [ "Rcpp" ], "biocViews": "MultipleComparison, DifferentialPeakCalling", "Description": "Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. 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Support is provided for handling log-transformed input p-values, missing values and weighting where appropriate.", "License": "GPL-3", "NeedsCompilation": "yes", "SystemRequirements": "C++11", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.1", "git_url": "https://git.bioconductor.org/packages/metapod", "git_branch": "RELEASE_3_21", "git_last_commit": "4223c40", "git_last_commit_date": "2025-04-15", "Repository": "Bioconductor 3.21", "Author": "Aaron Lun [aut, cre]", "Maintainer": "Aaron Lun " }, "mgcv": { "Package": "mgcv", "Version": "1.9-3", "Source": "Repository", "Authors@R": "person(given = \"Simon\", family = \"Wood\", role = c(\"aut\", \"cre\"), email = \"simon.wood@r-project.org\")", "Title": "Mixed GAM Computation Vehicle with Automatic Smoothness Estimation", "Description": "Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. 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Log-likelihoods for multivariate Gaussian models and Gaussian copulae parameterised by Cholesky factors of covariance or precision matrices are implemented for interval-censored and exact data, or a mix thereof. Score functions for these log-likelihoods are available. A class representing multiple lower triangular matrices and corresponding methods are part of this package.", "Imports": [ "stats" ], "Depends": [ "R(>= 3.5.0)" ], "Suggests": [ "qrng", "numDeriv" ], "License": "GPL-2", "URL": "http://mvtnorm.R-forge.R-project.org", "NeedsCompilation": "yes", "Author": "Alan Genz [aut], Frank Bretz [aut], Tetsuhisa Miwa [aut], Xuefei Mi [aut], Friedrich Leisch [ctb], Fabian Scheipl [ctb], Bjoern Bornkamp [ctb] (), Martin Maechler [ctb] (), Torsten Hothorn [aut, cre] ()", "Maintainer": "Torsten Hothorn ", "Repository": "RSPM", "Encoding": "UTF-8" }, "nlme": { "Package": "nlme", "Version": "3.1-168", "Source": "Repository", "Date": "2025-03-31", "Priority": "recommended", "Title": "Linear and Nonlinear Mixed Effects Models", "Authors@R": "c(person(\"José\", \"Pinheiro\", role = \"aut\", comment = \"S version\"), person(\"Douglas\", \"Bates\", role = \"aut\", comment = \"up to 2007\"), person(\"Saikat\", \"DebRoy\", role = \"ctb\", comment = \"up to 2002\"), person(\"Deepayan\", \"Sarkar\", role = \"ctb\", comment = \"up to 2005\"), person(\"EISPACK authors\", role = \"ctb\", comment = \"src/rs.f\"), person(\"Siem\", \"Heisterkamp\", role = \"ctb\", comment = \"Author fixed sigma\"), person(\"Bert\", \"Van Willigen\",role = \"ctb\", comment = \"Programmer fixed sigma\"), person(\"Johannes\", \"Ranke\", role = \"ctb\", comment = \"varConstProp()\"), person(\"R Core Team\", email = \"R-core@R-project.org\", role = c(\"aut\", \"cre\"), comment = c(ROR = \"02zz1nj61\")))", "Contact": "see 'MailingList'", "Description": "Fit and compare Gaussian linear and nonlinear mixed-effects models.", "Depends": [ "R (>= 3.6.0)" ], "Imports": [ "graphics", "stats", "utils", "lattice" ], "Suggests": [ "MASS", "SASmixed" ], "LazyData": "yes", "Encoding": "UTF-8", "License": "GPL (>= 2)", "BugReports": "https://bugs.r-project.org", "MailingList": "R-help@r-project.org", "URL": "https://svn.r-project.org/R-packages/trunk/nlme/", "NeedsCompilation": "yes", "Author": "José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R Core Team [aut, cre] (02zz1nj61)", "Maintainer": "R Core Team ", "Repository": "CRAN" }, "nnSVG": { "Package": "nnSVG", "Version": "1.12.0", "Source": "Bioconductor", "Title": "Scalable identification of spatially variable genes in spatially-resolved transcriptomics data", "Description": "Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.", "Authors@R": "c( person(\"Lukas M.\", \"Weber\", email = \"lmweb012@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-3282-1730\")), person(\"Stephanie C.\", \"Hicks\", email = \"shicks19@jhu.edu\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-7858-0231\")))", "URL": "https://github.com/lmweber/nnSVG", "BugReports": "https://github.com/lmweber/nnSVG/issues", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "biocViews": "Spatial, SingleCell, Transcriptomics, GeneExpression, Preprocessing", "Depends": [ "R (>= 4.2)" ], "Imports": [ "SpatialExperiment", "SingleCellExperiment", "SummarizedExperiment", "BRISC", "BiocParallel", "Matrix", "matrixStats", "stats", "methods" ], "VignetteBuilder": "knitr", "Suggests": [ "BiocStyle", "knitr", "rmarkdown", "STexampleData", "WeberDivechaLCdata", "scran", "ggplot2", "testthat" ], "RoxygenNote": "7.2.3", "git_url": "https://git.bioconductor.org/packages/nnSVG", "git_branch": "RELEASE_3_21", "git_last_commit": "b308132", "git_last_commit_date": "2025-04-15", "Repository": "Bioconductor 3.21", "NeedsCompilation": "no", "Author": "Lukas M. Weber [aut, cre] (ORCID: ), Stephanie C. Hicks [aut] (ORCID: )", "Maintainer": "Lukas M. Weber " }, "nnls": { "Package": "nnls", "Version": "1.6", "Source": "Repository", "Type": "Package", "Title": "The Lawson-Hanson Algorithm for Non-Negative Least Squares (NNLS)", "Authors@R": "c(person(given = c(\"Katharine\", \"M.\"), family = \"Mullen\", role = \"aut\"), person(given = c(\"Ivo\", \"H.\", \"M.\"), family = \"van Stokkum\", role = \"aut\"), person(given = \"Katharine\", family = \"Mullen\", role = \"cre\", email = \"mullenkate@gmail.com\"))", "Maintainer": "Katharine Mullen ", "Suggests": [ "bvls", "quadprog" ], "Description": "An R interface to the Lawson-Hanson implementation of an algorithm for non-negative least squares (NNLS). Also allows the combination of non-negative and non-positive constraints.", "License": "GPL (>= 2)", "NeedsCompilation": "yes", "Author": "Katharine M. Mullen [aut], Ivo H. 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Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.", "License": "MIT + file LICENSE", "URL": "https://jeroen.r-universe.dev/openssl", "BugReports": "https://github.com/jeroen/openssl/issues", "SystemRequirements": "OpenSSL >= 1.0.2", "VignetteBuilder": "knitr", "Imports": [ "askpass" ], "Suggests": [ "curl", "testthat (>= 2.1.0)", "digest", "knitr", "rmarkdown", "jsonlite", "jose", "sodium" ], "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "NeedsCompilation": "yes", "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Oliver Keyes [ctb]", "Maintainer": "Jeroen Ooms ", "Repository": "RSPM" }, "pals": { "Package": "pals", "Version": "1.10", "Source": "Repository", "Title": "Color Palettes, Colormaps, and Tools to Evaluate Them", "Authors@R": "person(\"Kevin\", \"Wright\", , \"kw.stat@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0002-0617-8673\"))", "Description": "A comprehensive collection of color palettes, colormaps, and tools to evaluate them. See Kovesi (2015) .", "License": "MIT + file LICENSE", "URL": "https://kwstat.github.io/pals/", "BugReports": "https://github.com/kwstat/pals/issues", "Depends": [ "R (>= 4.1.0)" ], "Imports": [ "colorspace", "dichromat", "graphics", "grDevices", "mapproj", "maps", "methods", "stats" ], "Suggests": [ "classInt", "ggplot2", "knitr", "latticeExtra", "reshape2", "rgl", "rmarkdown", "testthat" ], "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Language": "en-US", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Author": "Kevin Wright [aut, cre, cph] ()", "Maintainer": "Kevin Wright ", "Repository": "RSPM" }, "parallelly": { "Package": "parallelly", "Version": "1.45.1", "Source": "Repository", "Title": "Enhancing the 'parallel' Package", "Imports": [ "parallel", "tools", "utils" ], "Suggests": [ "commonmark", "base64enc" ], "VignetteBuilder": "parallelly", "Authors@R": "c( person(\"Henrik\", \"Bengtsson\", role = c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Mike\", \"Cheng\", role = c(\"ctb\"), email = \"mikefc@coolbutuseless.com\") )", "Description": "Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. 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'patchwork' is a package that expands the API to allow for arbitrarily complex composition of plots by, among others, providing mathematical operators for combining multiple plots. 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This is a key part of the 'devtools' package as it allows you to rapidly iterate while developing a package.", "License": "GPL-3", "URL": "https://github.com/r-lib/pkgload, https://pkgload.r-lib.org", "BugReports": "https://github.com/r-lib/pkgload/issues", "Depends": [ "R (>= 3.4.0)" ], "Imports": [ "cli (>= 3.3.0)", "desc", "fs", "glue", "lifecycle", "methods", "pkgbuild", "processx", "rlang (>= 1.1.1)", "rprojroot", "utils", "withr (>= 2.4.3)" ], "Suggests": [ "bitops", "jsonlite", "mathjaxr", "pak", "Rcpp", "remotes", "rstudioapi", "testthat (>= 3.2.1.1)", "usethis" ], "Config/Needs/website": "tidyverse/tidytemplate, ggplot2", "Config/testthat/edition": "3", "Config/testthat/parallel": "TRUE", "Config/testthat/start-first": "dll", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut], Winston Chang [aut], Jim Hester [aut], Lionel Henry [aut, cre], Posit Software, PBC [cph, fnd], R Core team [ctb] (Some namespace and vignette code extracted from base R)", "Maintainer": "Lionel Henry ", "Repository": "RSPM" }, "plogr": { "Package": "plogr", "Version": "0.2.0", "Source": "Repository", "Title": "The 'plog' C++ Logging Library", "Date": "2018-03-24", "Authors@R": "c( person(\"Kirill\", \"Müller\", role = c(\"aut\", \"cre\"), email = \"krlmlr+r@mailbox.org\"), person(\"Sergey\", \"Podobry\", role = \"cph\", comment = \"Author of the bundled plog library\"))", "Description": "A simple header-only logging library for C++. 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[cph]", "Maintainer": "Carson Sievert ", "Repository": "RSPM" }, "plyr": { "Package": "plyr", "Version": "1.8.9", "Source": "Repository", "Title": "Tools for Splitting, Applying and Combining Data", "Authors@R": "person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\"))", "Description": "A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. 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Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. Computes Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.", "License": "BSL", "URL": "https://www.angusj.com, https://sourceforge.net/projects/polyclipping, https://github.com/baddstats/polyclip", "BugReports": "https://github.com/baddstats/polyclip/issues", "ByteCompile": "true", "Note": "built from Clipper C++ version 6.4.0", "NeedsCompilation": "yes", "Author": "Angus Johnson [aut] (C++ original, http://www.angusj.com/delphi/clipper.php), Adrian Baddeley [aut, trl, cre], Kurt Hornik [ctb], Brian D. 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Time intervals: '1337000' -> '15d 11h 23m 20s'. Vague time intervals: '2674000' -> 'about a month ago'. Bytes: '1337' -> '1.34 kB'. Rounding: '99' with 3 significant digits -> '99.0' p-values: '0.00001' -> '<0.0001'. Colors: '#FF0000' -> 'red'. 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Automatic \"reactive\" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.", "License": "GPL-3 | file LICENSE", "Depends": [ "R (>= 3.0.2)", "methods" ], "Imports": [ "utils", "grDevices", "httpuv (>= 1.5.2)", "mime (>= 0.3)", "jsonlite (>= 0.9.16)", "xtable", "fontawesome (>= 0.4.0)", "htmltools (>= 0.5.4)", "R6 (>= 2.0)", "sourcetools", "later (>= 1.0.0)", "promises (>= 1.3.2)", "tools", "cli", "rlang (>= 0.4.10)", "fastmap (>= 1.1.1)", "withr", "commonmark (>= 1.7)", "glue (>= 1.3.2)", "bslib (>= 0.6.0)", "cachem (>= 1.1.0)", "lifecycle (>= 0.2.0)" ], "Suggests": [ "coro (>= 1.1.0)", "datasets", "DT", "Cairo (>= 1.5-5)", "testthat (>= 3.2.1)", "knitr (>= 1.6)", "markdown", "rmarkdown", "ggplot2", "reactlog (>= 1.0.0)", "magrittr", "yaml", "mirai", "future", "dygraphs", "ragg", "showtext", "sass", "watcher" ], "URL": "https://shiny.posit.co/, https://github.com/rstudio/shiny", "BugReports": "https://github.com/rstudio/shiny/issues", "Collate": "'globals.R' 'app-state.R' 'app_template.R' 'bind-cache.R' 'bind-event.R' 'bookmark-state-local.R' 'bookmark-state.R' 'bootstrap-deprecated.R' 'bootstrap-layout.R' 'conditions.R' 'map.R' 'utils.R' 'bootstrap.R' 'busy-indicators-spinners.R' 'busy-indicators.R' 'cache-utils.R' 'deprecated.R' 'devmode.R' 'diagnose.R' 'extended-task.R' 'fileupload.R' 'graph.R' 'reactives.R' 'reactive-domains.R' 'history.R' 'hooks.R' 'html-deps.R' 'image-interact-opts.R' 'image-interact.R' 'imageutils.R' 'input-action.R' 'input-checkbox.R' 'input-checkboxgroup.R' 'input-date.R' 'input-daterange.R' 'input-file.R' 'input-numeric.R' 'input-password.R' 'input-radiobuttons.R' 'input-select.R' 'input-slider.R' 'input-submit.R' 'input-text.R' 'input-textarea.R' 'input-utils.R' 'insert-tab.R' 'insert-ui.R' 'jqueryui.R' 'knitr.R' 'middleware-shiny.R' 'middleware.R' 'timer.R' 'shiny.R' 'mock-session.R' 'modal.R' 'modules.R' 'notifications.R' 'priorityqueue.R' 'progress.R' 'react.R' 'reexports.R' 'render-cached-plot.R' 'render-plot.R' 'render-table.R' 'run-url.R' 'runapp.R' 'serializers.R' 'server-input-handlers.R' 'server-resource-paths.R' 'server.R' 'shiny-options.R' 'shiny-package.R' 'shinyapp.R' 'shinyui.R' 'shinywrappers.R' 'showcase.R' 'snapshot.R' 'staticimports.R' 'tar.R' 'test-export.R' 'test-server.R' 'test.R' 'update-input.R' 'utils-lang.R' 'version_bs_date_picker.R' 'version_ion_range_slider.R' 'version_jquery.R' 'version_jqueryui.R' 'version_selectize.R' 'version_strftime.R' 'viewer.R'", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Config/testthat/edition": "3", "Config/Needs/check": "shinytest2", "NeedsCompilation": "no", "Author": "Winston Chang [aut, cre] (ORCID: ), Joe Cheng [aut], JJ Allaire [aut], Carson Sievert [aut] (ORCID: ), Barret Schloerke [aut] (ORCID: ), Yihui Xie [aut], Jeff Allen [aut], Jonathan McPherson [aut], Alan Dipert [aut], Barbara Borges [aut], Posit Software, PBC [cph, fnd], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Prem Nawaz Khan [ctb] (Bootstrap accessibility plugin), Victor Tsaran [ctb] (Bootstrap accessibility plugin), Dennis Lembree [ctb] (Bootstrap accessibility plugin), Srinivasu Chakravarthula [ctb] (Bootstrap accessibility plugin), Cathy O'Connor [ctb] (Bootstrap accessibility plugin), PayPal, Inc [cph] (Bootstrap accessibility plugin), Stefan Petre [ctb, cph] (Bootstrap-datepicker library), Andrew Rowls [ctb, cph] (Bootstrap-datepicker library), Brian Reavis [ctb, cph] (selectize.js library), Salmen Bejaoui [ctb, cph] (selectize-plugin-a11y library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library), SpryMedia Limited [ctb, cph] (DataTables library), John Fraser [ctb, cph] (showdown.js library), John Gruber [ctb, cph] (showdown.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), R Core Team [ctb, cph] (tar implementation from R)", "Maintainer": "Winston Chang ", "Repository": "RSPM" }, "sitmo": { "Package": "sitmo", "Version": "2.0.2", "Source": "Repository", "Title": "Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files", "Authors@R": "c(person(\"James\", \"Balamuta\", email = \"balamut2@illinois.edu\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0003-2826-8458\")), person(\"Thijs\",\"van den Berg\", email = \"thijs@sitmo.com\", role = c(\"aut\", \"cph\")), person(\"Ralf\", \"Stubner\", email = \"ralf.stubner@daqana.com\", role = c(\"ctb\")))", "Description": "Provided within are two high quality and fast PPRNGs that may be used in an 'OpenMP' parallel environment. In addition, there is a generator for one dimensional low-discrepancy sequence. The objective of this library to consolidate the distribution of the 'sitmo' (C++98 & C++11), 'threefry' and 'vandercorput' (C++11-only) engines on CRAN by enabling others to link to the header files inside of 'sitmo' instead of including a copy of each engine within their individual package. Lastly, the package contains example implementations using the 'sitmo' package and three accompanying vignette that provide additional information.", "Depends": [ "R (>= 3.2.0)" ], "URL": "https://github.com/coatless/sitmo, http://thecoatlessprofessor.com/projects/sitmo/, https://github.com/stdfin/random/", "BugReports": "https://github.com/coatless/sitmo/issues", "License": "MIT + file LICENSE", "LinkingTo": [ "Rcpp" ], "Imports": [ "Rcpp (>= 0.12.13)" ], "RoxygenNote": "7.1.1", "Suggests": [ "knitr", "rmarkdown", "ggplot2" ], "VignetteBuilder": "knitr", "Encoding": "UTF-8", "NeedsCompilation": "yes", "Author": "James Balamuta [aut, cre, cph] (), Thijs van den Berg [aut, cph], Ralf Stubner [ctb]", "Maintainer": "James Balamuta ", "Repository": "CRAN" }, "snakecase": { "Package": "snakecase", "Version": "0.11.1", "Source": "Repository", "Date": "2023-08-27", "Title": "Convert Strings into any Case", "Description": "A consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others.", "Authors@R": "c( person(\"Malte\", \"Grosser\", , \"malte.grosser@gmail.com\", role = c(\"aut\", \"cre\")))", "Maintainer": "Malte Grosser ", "Depends": [ "R (>= 3.2)" ], "Imports": [ "stringr", "stringi" ], "Suggests": [ "testthat", "covr", "tibble", "purrrlyr", "knitr", "rmarkdown", "magrittr" ], "URL": "https://github.com/Tazinho/snakecase", "BugReports": "https://github.com/Tazinho/snakecase/issues", "Encoding": "UTF-8", "License": "GPL-3", "RoxygenNote": "6.1.1", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Author": "Malte Grosser [aut, cre]", "Repository": "RSPM" }, "snow": { "Package": "snow", "Version": "0.4-4", "Source": "Repository", "Title": "Simple Network of Workstations", "Author": "Luke Tierney, A. J. Rossini, Na Li, H. Sevcikova", "Description": "Support for simple parallel computing in R.", "Maintainer": "Luke Tierney ", "Suggests": [ "rlecuyer" ], "Enhances": [ "Rmpi" ], "License": "GPL", "Depends": [ "R (>= 2.13.1)", "utils" ], "NeedsCompilation": "no", "Repository": "RSPM", "Encoding": "UTF-8" }, "sourcetools": { "Package": "sourcetools", "Version": "0.1.7-1", "Source": "Repository", "Type": "Package", "Title": "Tools for Reading, Tokenizing and Parsing R Code", "Author": "Kevin Ushey", "Maintainer": "Kevin Ushey ", "Description": "Tools for the reading and tokenization of R code. The 'sourcetools' package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.", "License": "MIT + file LICENSE", "Depends": [ "R (>= 3.0.2)" ], "Suggests": [ "testthat" ], "RoxygenNote": "5.0.1", "BugReports": "https://github.com/kevinushey/sourcetools/issues", "Encoding": "UTF-8", "NeedsCompilation": "yes", "Repository": "RSPM" }, "sp": { "Package": "sp", "Version": "2.2-0", "Source": "Repository", "Title": "Classes and Methods for Spatial Data", "Authors@R": "c(person(\"Edzer\", \"Pebesma\", role = c(\"aut\", \"cre\"), email = \"edzer.pebesma@uni-muenster.de\"), person(\"Roger\", \"Bivand\", role = \"aut\", email = \"Roger.Bivand@nhh.no\"), person(\"Barry\", \"Rowlingson\", role = \"ctb\"), person(\"Virgilio\", \"Gomez-Rubio\", role = \"ctb\"), person(\"Robert\", \"Hijmans\", role = \"ctb\"), person(\"Michael\", \"Sumner\", role = \"ctb\"), person(\"Don\", \"MacQueen\", role = \"ctb\"), person(\"Jim\", \"Lemon\", role = \"ctb\"), person(\"Finn\", \"Lindgren\", role = \"ctb\"), person(\"Josh\", \"O'Brien\", role = \"ctb\"), person(\"Joseph\", \"O'Rourke\", role = \"ctb\"), person(\"Patrick\", \"Hausmann\", role = \"ctb\"))", "Depends": [ "R (>= 3.5.0)", "methods" ], "Imports": [ "utils", "stats", "graphics", "grDevices", "lattice", "grid" ], "Suggests": [ "RColorBrewer", "gstat", "deldir", "knitr", "maps", "mapview", "rmarkdown", "sf", "terra", "raster" ], "Description": "Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc. From this version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all, see for details.", "License": "GPL (>= 2)", "URL": "https://github.com/edzer/sp/ https://edzer.github.io/sp/", "BugReports": "https://github.com/edzer/sp/issues", "Collate": "bpy.colors.R AAA.R Class-CRS.R CRS-methods.R Class-Spatial.R Spatial-methods.R projected.R Class-SpatialPoints.R SpatialPoints-methods.R Class-SpatialPointsDataFrame.R SpatialPointsDataFrame-methods.R Class-SpatialMultiPoints.R SpatialMultiPoints-methods.R Class-SpatialMultiPointsDataFrame.R SpatialMultiPointsDataFrame-methods.R Class-GridTopology.R Class-SpatialGrid.R Class-SpatialGridDataFrame.R Class-SpatialLines.R SpatialLines-methods.R Class-SpatialLinesDataFrame.R SpatialLinesDataFrame-methods.R Class-SpatialPolygons.R Class-SpatialPolygonsDataFrame.R SpatialPolygons-methods.R SpatialPolygonsDataFrame-methods.R GridTopology-methods.R SpatialGrid-methods.R SpatialGridDataFrame-methods.R SpatialPolygons-internals.R point.in.polygon.R SpatialPolygons-displayMethods.R zerodist.R image.R stack.R bubble.R mapasp.R select.spatial.R gridded.R asciigrid.R spplot.R over.R spsample.R recenter.R dms.R gridlines.R spdists.R rbind.R flipSGDF.R chfids.R loadmeuse.R compassRose.R surfaceArea.R spOptions.R subset.R disaggregate.R sp_spat1.R merge.R aggregate.R elide.R sp2Mondrian.R", "VignetteBuilder": "knitr", "NeedsCompilation": "yes", "Author": "Edzer Pebesma [aut, cre], Roger Bivand [aut], Barry Rowlingson [ctb], Virgilio Gomez-Rubio [ctb], Robert Hijmans [ctb], Michael Sumner [ctb], Don MacQueen [ctb], Jim Lemon [ctb], Finn Lindgren [ctb], Josh O'Brien [ctb], Joseph O'Rourke [ctb], Patrick Hausmann [ctb]", "Maintainer": "Edzer Pebesma ", "Repository": "RSPM", "Encoding": "UTF-8" }, "spacexr": { "Package": "spacexr", "Version": "1.0.0", "Source": "Bioconductor", "Type": "Package", "Title": "SpatialeXpressionR: Cell Type Identification in Spatial Transcriptomics", "Authors@R": "c( person(\"Dylan\", \"Cable\", email = \"dmcable@umich.edu\", role = \"aut\"), person( \"Gabriel\", \"Grajeda\", email = \"gabriel.grajeda@gmail.com\", role = \"cre\", comment=c(ORCID=\"0009-0003-7242-7476\") ), person(\"Fannie and John Hertz Foundation\", role = \"fnd\") )", "Description": "Spatial-eXpression-R (spacexr) is a package for analyzing cell types in spatial transcriptomics data. This implementation is a fork of the spacexr GitHub repo (https://github.com/dmcable/spacexr), adapted to work with Bioconductor objects. The original package implements two statistical methods: RCTD for learning cell types and CSIDE for inferring cell type-specific differential expression. Currently, this fork only implements RCTD, which learns cell type profiles from annotated RNA sequencing (RNA-seq) reference data and uses these profiles to identify cell types in spatial transcriptomic pixels while accounting for platform-specific effects. Future releases will include an implementation of CSIDE.", "URL": "https://github.com/ggrajeda/spacexr", "BugReports": "https://github.com/ggrajeda/spacexr/issues", "Depends": [ "R (>= 4.5.0)" ], "License": "GPL (>= 3)", "Encoding": "UTF-8", "Imports": [ "ggplot2", "Matrix", "parallel", "quadprog", "httr", "methods", "memoise", "BiocParallel", "BiocFileCache", "SummarizedExperiment", "scatterpie", "SpatialExperiment" ], "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Suggests": [ "BiocStyle", "knitr", "rmarkdown", "testthat" ], "Config/testthat/edition": "3", "biocViews": "GeneExpression, DifferentialExpression, SingleCell, RNASeq, Software, Spatial, Transcriptomics", "git_url": "https://git.bioconductor.org/packages/spacexr", "git_branch": "RELEASE_3_21", "git_last_commit": "a8a9650", "git_last_commit_date": "2025-04-15", "Repository": "Bioconductor 3.21", "NeedsCompilation": "no", "Author": "Dylan Cable [aut], Gabriel Grajeda [cre] (ORCID: ), Fannie and John Hertz Foundation [fnd]", "Maintainer": "Gabriel Grajeda " }, "spam": { "Package": "spam", "Version": "2.11-1", "Source": "Repository", "Type": "Package", "Title": "SPArse Matrix", "Date": "2025-01-20", "Authors@R": "c(person(\"Reinhard\", \"Furrer\", role = c(\"aut\", \"cre\"), email = \"reinhard.furrer@math.uzh.ch\", comment = c(ORCID = \"0000-0002-6319-2332\")), person(\"Florian\", \"Gerber\", role = c(\"aut\"), email = \"florian.gerber@math.uzh.ch\", comment = c(ORCID = \"0000-0001-8545-5263\")), person(\"Roman\", \"Flury\", role = c(\"aut\"), email = \"roman.flury@math.uzh.ch\", comment = c(ORCID = \"0000-0002-0349-8698\")), person(\"Daniel\", \"Gerber\", role = \"ctb\", email = \"daniel_gerber_2222@hotmail.com\"), person(\"Kaspar\", \"Moesinger\", role = \"ctb\", email = \"kaspar.moesinger@gmail.com\"), person(\"Annina\", \"Cincera\", email = \"annina.cincera@math.uzh.ch\", role = \"ctb\"), person(\"Youcef\", \"Saad\", role = \"ctb\", comment = \"SPARSEKIT http://www-users.cs.umn.edu/~saad/software/SPARSKIT/\"), person(c(\"Esmond\", \"G.\"), \"Ng\", role = \"ctb\", comment = \"Fortran Cholesky routines\"), person(c(\"Barry\", \"W.\"), \"Peyton\", role = \"ctb\", comment = \"Fortran Cholesky routines\"), person(c(\"Joseph\", \"W.H.\"), \"Liu\", role = \"ctb\", comment = \"Fortran Cholesky routines\"), person(c(\"Alan\", \"D.\"), \"George\", role = \"ctb\", comment = \"Fortran Cholesky routines\"), person(c(\"Lehoucq\", \"B.\"), \"Rich\", role = \"ctb\", comment = \"ARPACK\"), person(c(\"Maschhoff\"), \"Kristi\", role = \"ctb\", comment = \"ARPACK\"), person(c(\"Sorensen\", \"C.\"), \"Danny\", role = \"ctb\", comment = \"ARPACK\"), person(c(\"Yang\"), \"Chao\", role = \"ctb\", comment = \"ARPACK\"))", "Depends": [ "R (>= 4.0)" ], "Imports": [ "dotCall64", "grid", "methods", "Rcpp (>= 1.0.8.3)" ], "LinkingTo": [ "Rcpp" ], "Suggests": [ "spam64", "fields", "Matrix", "testthat", "R.rsp", "truncdist", "knitr", "rmarkdown" ], "VignetteBuilder": "R.rsp, knitr", "Description": "Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within G(M)RF. (4) and it is fast and scalable (with the extension package spam64). Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) ; see 'citation(\"spam\")' for details.", "LazyData": "true", "License": "LGPL-2 | BSD_3_clause + file LICENSE", "URL": "https://www.math.uzh.ch/pages/spam/", "BugReports": "https://git.math.uzh.ch/reinhard.furrer/spam/-/issues", "NeedsCompilation": "yes", "Author": "Reinhard Furrer [aut, cre] (), Florian Gerber [aut] (), Roman Flury [aut] (), Daniel Gerber [ctb], Kaspar Moesinger [ctb], Annina Cincera [ctb], Youcef Saad [ctb] (SPARSEKIT http://www-users.cs.umn.edu/~saad/software/SPARSKIT/), Esmond G. Ng [ctb] (Fortran Cholesky routines), Barry W. Peyton [ctb] (Fortran Cholesky routines), Joseph W.H. Liu [ctb] (Fortran Cholesky routines), Alan D. George [ctb] (Fortran Cholesky routines), Lehoucq B. Rich [ctb] (ARPACK), Maschhoff Kristi [ctb] (ARPACK), Sorensen C. Danny [ctb] (ARPACK), Yang Chao [ctb] (ARPACK)", "Maintainer": "Reinhard Furrer ", "Repository": "RSPM", "Encoding": "UTF-8" }, "sparseMatrixStats": { "Package": "sparseMatrixStats", "Version": "1.20.0", "Source": "Bioconductor", "Type": "Package", "Title": "Summary Statistics for Rows and Columns of Sparse Matrices", "Authors@R": "person(\"Constantin\", \"Ahlmann-Eltze\", email = \"artjom31415@googlemail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-3762-068X\"))", "Description": "High performance functions for row and column operations on sparse matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently, the optimizations are limited to data in the column sparse format. This package is inspired by the matrixStats package by Henrik Bengtsson.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "LinkingTo": [ "Rcpp" ], "Imports": [ "Rcpp", "Matrix", "matrixStats (>= 0.60.0)", "methods" ], "Depends": [ "MatrixGenerics (>= 1.5.3)" ], "Suggests": [ "testthat (>= 2.1.0)", "knitr", "bench", "rmarkdown", "BiocStyle" ], "SystemRequirements": "C++11", "VignetteBuilder": "knitr", "URL": "https://github.com/const-ae/sparseMatrixStats", "BugReports": "https://github.com/const-ae/sparseMatrixStats/issues", "biocViews": "Infrastructure, Software, DataRepresentation", "git_url": "https://git.bioconductor.org/packages/sparseMatrixStats", "git_branch": "RELEASE_3_21", "git_last_commit": "b3b8af1", "git_last_commit_date": "2025-04-15", "Repository": "Bioconductor 3.21", "NeedsCompilation": "yes", "Author": "Constantin Ahlmann-Eltze [aut, cre] (ORCID: )", "Maintainer": "Constantin Ahlmann-Eltze " }, "spatialEco": { "Package": "spatialEco", "Version": "2.0-2", "Source": "Repository", "Type": "Package", "Title": "Spatial Analysis and Modelling Utilities", "Date": "2023-11-17", "Authors@R": "c( person(family=\"Evans\", given=\"Jeffrey S.\", email = \"jeffrey_evans@tnc.org\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5533-7044\")), person(family=\"Murphy\", given=\"Melanie A.\", role = \"ctb\"),\t\t\t person(family=\"Ram\", given=\"Karthik\", role = \"ctb\") )", "Description": "Utilities to support spatial data manipulation, query, sampling and modelling in ecological applications. Functions include models for species population density, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and analysis, auto-logistic modeling, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.", "Depends": [ "R (>= 4.2)" ], "Imports": [ "sf", "terra" ], "Suggests": [ "spatstat.geom (>= 3.0-3)", "spatstat.explore", "spdep", "ks", "cluster", "readr", "RCurl", "RANN", "rms", "yaImpute", "mgcv", "zyp", "SpatialPack (>= 0.3)", "MASS", "caret", "dplyr", "earth", "Matrix", "gstat", "spatstat.data", "methods", "units", "sp", "stringr", "lwgeom", "geodata" ], "Maintainer": "Jeffrey S. Evans ", "License": "GPL-3", "URL": "https://github.com/jeffreyevans/spatialEco, https://jeffreyevans.github.io/spatialEco/", "BugReports": "https://github.com/jeffreyevans/spatialEco/issues", "NeedsCompilation": "no", "Repository": "CRAN", "LazyData": "true", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "Author": "Jeffrey S. Evans [aut, cre] (), Melanie A. Murphy [ctb], Karthik Ram [ctb]" }, "spatstat.data": { "Package": "spatstat.data", "Version": "3.1-6", "Source": "Repository", "Date": "2025-03-17", "Title": "Datasets for 'spatstat' Family", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = \"aut\", email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = \"aut\", email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"W\", \"Aherne\", role=\"ctb\"), person(\"Freda\", \"Alexander\", role=\"ctb\"), person(\"Qi Wei\", \"Ang\", role=\"ctb\"), person(\"Sourav\", \"Banerjee\", role=\"ctb\"), person(\"Mark\", \"Berman\", role=\"ctb\"), person(\"R\", \"Bernhardt\", role=\"ctb\"), person(\"Thomas\", \"Berndtsen\", role=\"ctb\"), person(\"Andrew\", \"Bevan\", role=\"ctb\"), person(\"Jeffrey\", \"Betts\", role=\"ctb\"), person(\"Ray\", \"Cartwright\", role=\"ctb\"), person(\"Lucia\", \"Cobo Sanchez\", role=\"ctb\"), person(\"Richard\", \"Condit\", role=\"ctb\"), person(\"Francis\", \"Crick\", role=\"ctb\"), person(\"Marcelino\", \"de la Cruz Rot\", role=\"ctb\"), person(\"Jack\", \"Cuzick\", role=\"ctb\"), person(\"Tilman\", \"Davies\", role=\"ctb\"), person(\"Peter\", \"Diggle\", role=\"ctb\"), person(\"Michael\", \"Drinkwater\", role=\"ctb\"), person(\"Stephen\", \"Eglen\", role=\"ctb\"), person(\"Robert\", \"Edwards\", role=\"ctb\"), person(\"Johannes\", \"Elias\", role=\"ctb\"), person(\"AE\", \"Esler\", role=\"ctb\"), person(\"Gregory\", \"Evans\", role=\"ctb\"), person(\"Bernard\", \"Fingleton\", role=\"ctb\"), person(\"Olivier\", \"Flores\", role=\"ctb\"), person(\"David\", \"Ford\", role=\"ctb\"), person(\"Robin\", \"Foster\", role=\"ctb\"), person(\"Janet\", \"Franklin\", role=\"ctb\"), person(\"Neba\", \"Funwi-Gabga\", role=\"ctb\"), person(\"DJ\", \"Gerrard\", role=\"ctb\"), person(\"Andy\", \"Green\", role=\"ctb\"), person(\"Tim\", \"Griffin\", role=\"ctb\"), person(\"Ute\", \"Hahn\", role=\"ctb\"), person(\"RD\", \"Harkness\", role=\"ctb\"), person(\"Arthur\", \"Hickman\", role=\"ctb\"), person(\"Stephen\", \"Hubbell\", role=\"ctb\"), person(\"Austin\", \"Hughes\", role=\"ctb\"), person(\"Jonathan\", \"Huntington\", role=\"ctb\"), person(\"MJ\", \"Hutchings\", role=\"ctb\"), person(\"Jackie\", \"Inwald\", role=\"ctb\"), person(\"Valerie\", \"Isham\", role=\"ctb\"), person(\"Aruna\", \"Jammalamadaka\", role=\"ctb\"), person(\"Carl\", \"Knox-Robinson\", role=\"ctb\"), person(\"Mahdieh\", \"Khanmohammadi\", role=\"ctb\"), person(\"Tero\", \"Kokkila\", role=\"ctb\"), person(\"Bas\", \"Kooijman\", role=\"ctb\"), person(\"Kenneth\", \"Kosik\", role=\"ctb\"), person(\"Peter\", \"Kovesi\", role=\"ctb\"), person(\"Lily\", \"Kozmian-Ledward\", role=\"ctb\"), person(\"Robert\", \"Lamb\", role=\"ctb\"), person(\"NA\", \"Laskurain\", role=\"ctb\"), person(\"George\", \"Leser\", role=\"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role=\"ctb\"), person(\"AF\", \"Mark\", role=\"ctb\"), person(\"Sebastian\", \"Meyer\", role=\"ctb\"), person(\"Jorge\", \"Mateu\", role=\"ctb\"), person(\"Annikki\", \"Makela\", role=\"ctb\"), person(\"Enrique\", \"Miranda\", role=\"ctb\"), person(\"Nicoletta\", \"Nava\", role=\"ctb\"), person(\"M\", \"Numata\", role=\"ctb\"), person(\"Matti\", \"Nummelin\", role=\"ctb\"), person(\"Jens Randel\", \"Nyengaard\", role=\"ctb\"), person(\"Yosihiko\", \"Ogata\", role=\"ctb\"), person(\"Si\", \"Palmer\", role=\"ctb\"), person(\"Antti\", \"Penttinen\", role=\"ctb\"), person(\"Sandra\", \"Pereira\", role=\"ctb\"), person(\"Nicolas\", \"Picard\", role=\"ctb\"), person(\"William\", \"Platt\", role=\"ctb\"), person(\"Stephen\", \"Rathbun\", role=\"ctb\"), person(\"Brian\", \"Ripley\", role=\"ctb\"), person(\"Roger\", \"Sainsbury\", role=\"ctb\"), person(\"Dietrich\", \"Stoyan\", role=\"ctb\"), person(\"David\", \"Strauss\", role=\"ctb\"), person(\"L\", \"Strand\", role=\"ctb\"), person(\"Masaharu\", \"Tanemura\", role=\"ctb\"), person(\"Graham\", \"Upton\", role=\"ctb\"), person(\"Bill\", \"Venables\", role=\"ctb\"), person(\"Ulrich\", \"Vogel\", role=\"ctb\"), person(\"Sasha\", \"Voss\", role=\"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role=\"ctb\"), person(\"Keith\", \"Watkins\", role=\"ctb\"), person(\"H\", \"Wendrock\", role=\"ctb\") )", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)" ], "Imports": [ "spatstat.utils (>= 3.1-2)", "Matrix" ], "Suggests": [ "spatstat.geom", "spatstat.random", "spatstat.explore", "spatstat.model", "spatstat.linnet" ], "Description": "Contains all the datasets for the 'spatstat' family of packages.", "License": "GPL (>= 2)", "URL": "http://spatstat.org/", "LazyData": "true", "NeedsCompilation": "no", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.data/issues", "Author": "Adrian Baddeley [aut, cre] (), Rolf Turner [aut] (), Ege Rubak [aut] (), W Aherne [ctb], Freda Alexander [ctb], Qi Wei Ang [ctb], Sourav Banerjee [ctb], Mark Berman [ctb], R Bernhardt [ctb], Thomas Berndtsen [ctb], Andrew Bevan [ctb], Jeffrey Betts [ctb], Ray Cartwright [ctb], Lucia Cobo Sanchez [ctb], Richard Condit [ctb], Francis Crick [ctb], Marcelino de la Cruz Rot [ctb], Jack Cuzick [ctb], Tilman Davies [ctb], Peter Diggle [ctb], Michael Drinkwater [ctb], Stephen Eglen [ctb], Robert Edwards [ctb], Johannes Elias [ctb], AE Esler [ctb], Gregory Evans [ctb], Bernard Fingleton [ctb], Olivier Flores [ctb], David Ford [ctb], Robin Foster [ctb], Janet Franklin [ctb], Neba Funwi-Gabga [ctb], DJ Gerrard [ctb], Andy Green [ctb], Tim Griffin [ctb], Ute Hahn [ctb], RD Harkness [ctb], Arthur Hickman [ctb], Stephen Hubbell [ctb], Austin Hughes [ctb], Jonathan Huntington [ctb], MJ Hutchings [ctb], Jackie Inwald [ctb], Valerie Isham [ctb], Aruna Jammalamadaka [ctb], Carl Knox-Robinson [ctb], Mahdieh Khanmohammadi [ctb], Tero Kokkila [ctb], Bas Kooijman [ctb], Kenneth Kosik [ctb], Peter Kovesi [ctb], Lily Kozmian-Ledward [ctb], Robert Lamb [ctb], NA Laskurain [ctb], George Leser [ctb], Marie-Colette van Lieshout [ctb], AF Mark [ctb], Sebastian Meyer [ctb], Jorge Mateu [ctb], Annikki Makela [ctb], Enrique Miranda [ctb], Nicoletta Nava [ctb], M Numata [ctb], Matti Nummelin [ctb], Jens Randel Nyengaard [ctb], Yosihiko Ogata [ctb], Si Palmer [ctb], Antti Penttinen [ctb], Sandra Pereira [ctb], Nicolas Picard [ctb], William Platt [ctb], Stephen Rathbun [ctb], Brian Ripley [ctb], Roger Sainsbury [ctb], Dietrich Stoyan [ctb], David Strauss [ctb], L Strand [ctb], Masaharu Tanemura [ctb], Graham Upton [ctb], Bill Venables [ctb], Ulrich Vogel [ctb], Sasha Voss [ctb], Rasmus Waagepetersen [ctb], Keith Watkins [ctb], H Wendrock [ctb]", "Repository": "RSPM", "Encoding": "UTF-8" }, "spatstat.explore": { "Package": "spatstat.explore", "Version": "3.5-2", "Source": "Repository", "Date": "2025-07-22", "Title": "Exploratory Data Analysis for the 'spatstat' Family", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = \"ctb\"), person(\"Warick\", \"Brown\", role = \"cph\"), person(\"Achmad\", \"Choiruddin\", role = \"ctb\"), person(\"Ya-Mei\", \"Chang\", role = \"ctb\"), person(\"Jean-Francois\", \"Coeurjolly\", role = \"ctb\"), person(\"Ottmar\", \"Cronie\", role = \"ctb\"), person(\"Tilman\", \"Davies\", role = c(\"ctb\", \"cph\")), person(\"Julian\", \"Gilbey\", role = \"ctb\"), person(\"Jonatan\", \"Gonzalez\", role = \"ctb\"), person(\"Yongtao\", \"Guan\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Martin\", \"Hazelton\", role = \"ctb\"), person(\"Kassel\", \"Hingee\", role = c(\"ctb\", \"cph\")), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Frederic\", \"Lavancier\", role = \"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role = c(\"ctb\", \"cph\")), person(\"Greg\", \"McSwiggan\", role = \"ctb\"), person(\"Robin K\", \"Milne\", role = \"cph\"), person(\"Tuomas\", \"Rajala\", role = \"ctb\"), person(\"Suman\", \"Rakshit\", role = c(\"ctb\", \"cph\")), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Plenge Waagepetersen\", role = \"ctb\"), person(\"Hangsheng\", \"Wang\", role = \"ctb\"), person(\"Tingting\", \"Zhan\", role=\"ctb\"))", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)", "spatstat.data (>= 3.1-2)", "spatstat.univar (>= 3.1-4)", "spatstat.geom (>= 3.5-0)", "spatstat.random (>= 3.4)", "stats", "graphics", "grDevices", "utils", "methods", "nlme" ], "Imports": [ "spatstat.utils (>= 3.1-5)", "spatstat.sparse (>= 3.1-0)", "goftest (>= 1.2-2)", "Matrix", "abind" ], "Suggests": [ "sm", "gsl", "locfit", "spatial", "fftwtools (>= 0.9-8)", "spatstat.linnet (>= 3.2-1)", "spatstat.model (>= 3.3-1)", "spatstat (>= 3.3)" ], "Description": "Functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.", "License": "GPL (>= 2)", "URL": "http://spatstat.org/", "NeedsCompilation": "yes", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.explore/issues", "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Kasper Klitgaard Berthelsen [ctb], Warick Brown [cph], Achmad Choiruddin [ctb], Ya-Mei Chang [ctb], Jean-Francois Coeurjolly [ctb], Ottmar Cronie [ctb], Tilman Davies [ctb, cph], Julian Gilbey [ctb], Jonatan Gonzalez [ctb], Yongtao Guan [ctb], Ute Hahn [ctb], Martin Hazelton [ctb], Kassel Hingee [ctb, cph], Abdollah Jalilian [ctb], Frederic Lavancier [ctb], Marie-Colette van Lieshout [ctb, cph], Greg McSwiggan [ctb], Robin K Milne [cph], Tuomas Rajala [ctb], Suman Rakshit [ctb, cph], Dominic Schuhmacher [ctb], Rasmus Plenge Waagepetersen [ctb], Hangsheng Wang [ctb], Tingting Zhan [ctb]", "Repository": "RSPM", "Encoding": "UTF-8" }, "spatstat.geom": { "Package": "spatstat.geom", "Version": "3.5-0", "Source": "Repository", "Date": "2025-07-20", "Title": "Geometrical Functionality of the 'spatstat' Family", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Warick\", \"Brown\" , role = \"ctb\"), person(\"Tilman\", \"Davies\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Martin\", \"Hazelton\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Greg\", \"McSwiggan\", role = c(\"ctb\", \"cph\")), person(\"Sebastian\", \"Meyer\", role = c(\"ctb\", \"cph\")), person(\"Jens\", \"Oehlschlaegel\", role = c(\"ctb\", \"cph\")), person(\"Suman\", \"Rakshit\", role = \"ctb\"), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role = \"ctb\"))", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)", "spatstat.data (>= 3.1)", "spatstat.univar (>= 3.1-4)", "stats", "graphics", "grDevices", "utils", "methods" ], "Imports": [ "spatstat.utils (>= 3.1-5)", "deldir (>= 1.0-2)", "polyclip (>= 1.10)" ], "Suggests": [ "spatstat.random (>= 3.4)", "spatstat.explore (>= 3.4)", "spatstat.model (>= 3.3)", "spatstat.linnet (>= 3.2)", "spatial", "fftwtools (>= 0.9-8)", "spatstat (>= 3.3)" ], "Description": "Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)", "License": "GPL (>= 2)", "URL": "http://spatstat.org/", "NeedsCompilation": "yes", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.geom/issues", "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Warick Brown [ctb], Tilman Davies [ctb], Ute Hahn [ctb], Martin Hazelton [ctb], Abdollah Jalilian [ctb], Greg McSwiggan [ctb, cph], Sebastian Meyer [ctb, cph], Jens Oehlschlaegel [ctb, cph], Suman Rakshit [ctb], Dominic Schuhmacher [ctb], Rasmus Waagepetersen [ctb]", "Repository": "RSPM", "Encoding": "UTF-8" }, "spatstat.random": { "Package": "spatstat.random", "Version": "3.4-1", "Source": "Repository", "Date": "2025-05-20", "Title": "Random Generation Functionality for the 'spatstat' Family", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Tilman\", \"Davies\", role = c(\"aut\", \"cph\"), comment=c(ORCID=\"0000-0003-0565-1825\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = c(\"ctb\", \"cph\")), person(\"David\", \"Bryant\", role = c(\"ctb\", \"cph\")), person(\"Ya-Mei\", \"Chang\", role = c(\"ctb\", \"cph\"), email = \"yamei628@gmail.com\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Dominic\", \"Schuhmacher\", role = c(\"ctb\", \"cph\")), person(\"Rasmus\", \"Plenge Waagepetersen\", role = c(\"ctb\", \"cph\")))", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)", "spatstat.data (>= 3.1)", "spatstat.univar (>= 3.1)", "spatstat.geom (>= 3.3-6)", "stats", "utils", "methods", "grDevices" ], "Imports": [ "spatstat.utils (>= 3.1-4)" ], "Suggests": [ "spatial", "spatstat.linnet (>= 3.2)", "spatstat.explore", "spatstat.model", "spatstat (>= 3.3)", "gsl" ], "Description": "Functionality for random generation of spatial data in the 'spatstat' family of packages. Generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes including simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes (using direct, Brix-Kendall, or hybrid algorithms), log-Gaussian Cox processes, product shot noise cluster processes and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler, or coupling-from-the-past perfect simulation). Also generates random spatial patterns of line segments, random tessellations, and random images (random noise, random mosaics). Excludes random generation on a linear network, which is covered by the separate package 'spatstat.linnet'.", "License": "GPL (>= 2)", "URL": "http://spatstat.org/", "NeedsCompilation": "yes", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.random/issues", "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Tilman Davies [aut, cph] (ORCID: ), Kasper Klitgaard Berthelsen [ctb, cph], David Bryant [ctb, cph], Ya-Mei Chang [ctb, cph], Ute Hahn [ctb], Abdollah Jalilian [ctb], Dominic Schuhmacher [ctb, cph], Rasmus Plenge Waagepetersen [ctb, cph]", "Repository": "RSPM", "Encoding": "UTF-8" }, "spatstat.sparse": { "Package": "spatstat.sparse", "Version": "3.1-0", "Source": "Repository", "Date": "2024-06-21", "Title": "Sparse Three-Dimensional Arrays and Linear Algebra Utilities", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")))", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)", "stats", "utils", "methods", "Matrix", "abind", "tensor" ], "Imports": [ "spatstat.utils (>= 3.0-5)" ], "Description": "Defines sparse three-dimensional arrays and supports standard operations on them. The package also includes utility functions for matrix calculations that are common in statistics, such as quadratic forms.", "License": "GPL (>= 2)", "URL": "http://spatstat.org/", "NeedsCompilation": "yes", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.sparse/issues", "Author": "Adrian Baddeley [aut, cre, cph] (), Rolf Turner [aut, cph] (), Ege Rubak [aut, cph] ()", "Repository": "RSPM", "Encoding": "UTF-8" }, "spatstat.univar": { "Package": "spatstat.univar", "Version": "3.1-4", "Source": "Repository", "Date": "2025-07-13", "Title": "One-Dimensional Probability Distribution Support for the 'spatstat' Family", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(c(\"Tilman\", \"M.\"), \"Davies\", role = c(\"aut\", \"ctb\", \"cph\"), email = \"Tilman.Davies@otago.ac.nz\", comment = c(ORCID=\"0000-0003-0565-1825\")), person(c(\"Martin\", \"L.\"), \"Hazelton\", role = c(\"aut\", \"ctb\", \"cph\"), email = \"Martin.Hazelton@otago.ac.nz\", comment = c(ORCID=\"0000-0001-7831-725X\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Greg\", \"McSwiggan\", role = c(\"ctb\", \"cph\")))", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)", "stats" ], "Imports": [ "spatstat.utils (>= 3.1-2)", "graphics" ], "Description": "Estimation of one-dimensional probability distributions including kernel density estimation, weighted empirical cumulative distribution functions, Kaplan-Meier and reduced-sample estimators for right-censored data, heat kernels, kernel properties, quantiles and integration.", "License": "GPL (>= 2)", "URL": "http://spatstat.org/", "NeedsCompilation": "yes", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.univar/issues", "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Tilman M. Davies [aut, ctb, cph] (ORCID: ), Martin L. Hazelton [aut, ctb, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Greg McSwiggan [ctb, cph]", "Repository": "RSPM", "Encoding": "UTF-8" }, "spatstat.utils": { "Package": "spatstat.utils", "Version": "3.1-5", "Source": "Repository", "Date": "2025-07-17", "Title": "Utility Functions for 'spatstat'", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = \"aut\", email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = \"aut\", email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")))", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)", "stats", "graphics", "grDevices", "utils", "methods" ], "Suggests": [ "spatstat.model" ], "Description": "Contains utility functions for the 'spatstat' family of packages which may also be useful for other purposes.", "License": "GPL (>= 2)", "URL": "http://spatstat.org/", "NeedsCompilation": "yes", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.utils/issues", "Author": "Adrian Baddeley [aut, cre] (ORCID: ), Rolf Turner [aut] (ORCID: ), Ege Rubak [aut] (ORCID: )", "Repository": "RSPM", "Encoding": "UTF-8" }, "statmod": { "Package": "statmod", "Version": "1.5.0", "Source": "Repository", "Date": "2022-12-28", "Title": "Statistical Modeling", "Author": "Gordon Smyth [cre, aut], Lizhong Chen [aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]", "Maintainer": "Gordon Smyth ", "Depends": [ "R (>= 3.0.0)" ], "Imports": [ "stats", "graphics" ], "Suggests": [ "MASS", "tweedie" ], "Description": "A collection of algorithms and functions to aid statistical modeling. Includes limiting dilution analysis (aka ELDA), growth curve comparisons, mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Also includes advanced generalized linear model functions including Tweedie and Digamma distributional families, secure convergence and exact distributional calculations for unit deviances.", "License": "GPL-2 | GPL-3", "NeedsCompilation": "yes", "Repository": "RSPM", "Encoding": "UTF-8" }, "storr": { "Package": "storr", "Version": "1.2.6", "Source": "Repository", "Title": "Simple Key Value Stores", "Description": "Creates and manages simple key-value stores. These can use a variety of approaches for storing the data. This package implements the base methods and support for file system, in-memory and DBI-based database stores.", "Depends": [ "R (>= 3.3.0)" ], "License": "MIT + file LICENSE", "Authors@R": "c(person(\"Rich\", \"FitzJohn\", role = c(\"aut\", \"cre\"), email = \"rich.fitzjohn@gmail.com\"), person(c(\"William\", \"Michael\"), \"Landau\", email = \"will.landau@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\") ))", "URL": "https://richfitz.github.io/storr/, https://github.com/richfitz/storr", "BugReports": "https://github.com/richfitz/storr/issues", "Imports": [ "R6 (>= 2.1.0)", "digest" ], "Suggests": [ "DBI (>= 0.6)", "RSQLite (>= 1.1-2)", "RPostgres", "knitr", "mockr", "parallel", "progress", "rbenchmark", "rmarkdown", "testthat (>= 3.0.0)" ], "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Language": "en-GB", "NeedsCompilation": "yes", "Author": "Rich FitzJohn [aut, cre], William Michael Landau [ctb] ()", "Maintainer": "Rich FitzJohn ", "Repository": "RSPM" }, "stringi": { "Package": "stringi", "Version": "1.8.7", "Source": "Repository", "Date": "2025-03-27", "Title": "Fast and Portable Character String Processing Facilities", "Description": "A collection of character string/text/natural language processing tools for pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date-time formatting and parsing, and many more. They are fast, consistent, convenient, and - thanks to 'ICU' (International Components for Unicode) - portable across all locales and platforms. Documentation about 'stringi' is provided via its website at and the paper by Gagolewski (2022, ).", "URL": "https://stringi.gagolewski.com/, https://github.com/gagolews/stringi, https://icu.unicode.org/", "BugReports": "https://github.com/gagolews/stringi/issues", "SystemRequirements": "ICU4C (>= 61, optional)", "Type": "Package", "Depends": [ "R (>= 3.4)" ], "Imports": [ "tools", "utils", "stats" ], "Biarch": "TRUE", "License": "file LICENSE", "Authors@R": "c(person(given = \"Marek\", family = \"Gagolewski\", role = c(\"aut\", \"cre\", \"cph\"), email = \"marek@gagolewski.com\", comment = c(ORCID = \"0000-0003-0637-6028\")), person(given = \"Bartek\", family = \"Tartanus\", role = \"ctb\"), person(\"Unicode, Inc. and others\", role=\"ctb\", comment = \"ICU4C source code, Unicode Character Database\") )", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "NeedsCompilation": "yes", "Author": "Marek Gagolewski [aut, cre, cph] (), Bartek Tartanus [ctb], Unicode, Inc. and others [ctb] (ICU4C source code, Unicode Character Database)", "Maintainer": "Marek Gagolewski ", "License_is_FOSS": "yes", "Repository": "RSPM" }, "stringr": { "Package": "stringr", "Version": "1.5.1", "Source": "Repository", "Title": "Simple, Consistent Wrappers for Common String Operations", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", "Description": "A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with \"NA\"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.", "License": "MIT + file LICENSE", "URL": "https://stringr.tidyverse.org, https://github.com/tidyverse/stringr", "BugReports": "https://github.com/tidyverse/stringr/issues", "Depends": [ "R (>= 3.6)" ], "Imports": [ "cli", "glue (>= 1.6.1)", "lifecycle (>= 1.0.3)", "magrittr", "rlang (>= 1.0.0)", "stringi (>= 1.5.3)", "vctrs (>= 0.4.0)" ], "Suggests": [ "covr", "dplyr", "gt", "htmltools", "htmlwidgets", "knitr", "rmarkdown", "testthat (>= 3.0.0)", "tibble" ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut, cre, cph], Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", "Repository": "RSPM" }, "survival": { "Package": "survival", "Version": "3.8-3", "Source": "Repository", "Title": "Survival Analysis", "Priority": "recommended", "Date": "2024-12-17", "Depends": [ "R (>= 3.5.0)" ], "Imports": [ "graphics", "Matrix", "methods", "splines", "stats", "utils" ], "LazyData": "Yes", "LazyDataCompression": "xz", "ByteCompile": "Yes", "Authors@R": "c(person(c(\"Terry\", \"M\"), \"Therneau\", email=\"therneau.terry@mayo.edu\", role=c(\"aut\", \"cre\")), person(\"Thomas\", \"Lumley\", role=c(\"ctb\", \"trl\"), comment=\"original S->R port and R maintainer until 2009\"), person(\"Atkinson\", \"Elizabeth\", role=\"ctb\"), person(\"Crowson\", \"Cynthia\", role=\"ctb\"))", "Description": "Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.", "License": "LGPL (>= 2)", "URL": "https://github.com/therneau/survival", "NeedsCompilation": "yes", "Author": "Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and R maintainer until 2009), Atkinson Elizabeth [ctb], Crowson Cynthia [ctb]", "Maintainer": "Terry M Therneau ", "Repository": "CRAN" }, "svglite": { "Package": "svglite", "Version": "2.2.1", "Source": "Repository", "Title": "An 'SVG' Graphics Device", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"T Jake\", \"Luciani\", , \"jake@apache.org\", role = \"aut\"), person(\"Matthieu\", \"Decorde\", , \"matthieu.decorde@ens-lyon.fr\", role = \"aut\"), person(\"Vaudor\", \"Lise\", , \"lise.vaudor@ens-lyon.fr\", role = \"aut\"), person(\"Tony\", \"Plate\", role = \"ctb\", comment = \"Early line dashing code\"), person(\"David\", \"Gohel\", role = \"ctb\", comment = \"Line dashing code and early raster code\"), person(\"Yixuan\", \"Qiu\", role = \"ctb\", comment = \"Improved styles; polypath implementation\"), person(\"Håkon\", \"Malmedal\", role = \"ctb\", comment = \"Opacity code\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "A graphics device for R that produces 'Scalable Vector Graphics'. 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Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. Arguments on Windows automatically get encoded and quoted to work on different locales.", "License": "MIT + file LICENSE", "URL": "https://jeroen.r-universe.dev/sys", "BugReports": "https://github.com/jeroen/sys/issues", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "Suggests": [ "unix (>= 1.4)", "spelling", "testthat" ], "Language": "en-US", "NeedsCompilation": "yes", "Author": "Jeroen Ooms [aut, cre] (), Gábor Csárdi [ctb]", "Maintainer": "Jeroen Ooms ", "Repository": "RSPM" }, "systemfonts": { "Package": "systemfonts", "Version": "1.2.3", "Source": "Repository", "Type": "Package", "Title": "System Native Font Finding", "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Jeroen\", \"Ooms\", , \"jeroen@berkeley.edu\", role = \"aut\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Devon\", \"Govett\", role = \"aut\", comment = \"Author of font-manager\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts' package provides bindings to the native libraries on Windows, macOS and Linux for finding font files that can then be used further by e.g. graphic devices. The main use is intended to be from compiled code but 'systemfonts' also provides access from R.", "License": "MIT + file LICENSE", "URL": "https://github.com/r-lib/systemfonts, https://systemfonts.r-lib.org", "BugReports": "https://github.com/r-lib/systemfonts/issues", "Depends": [ "R (>= 3.2.0)" ], "Imports": [ "base64enc", "grid", "jsonlite", "lifecycle", "tools", "utils" ], "Suggests": [ "covr", "farver", "graphics", "knitr", "rmarkdown", "testthat (>= 2.1.0)" ], "LinkingTo": [ "cpp11 (>= 0.2.1)" ], "VignetteBuilder": "knitr", "Config/build/compilation-database": "true", "Config/Needs/website": "tidyverse/tidytemplate", "Config/usethis/last-upkeep": "2025-04-23", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "SystemRequirements": "fontconfig, freetype2", "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [aut, cre] (ORCID: ), Jeroen Ooms [aut] (ORCID: ), Devon Govett [aut] (Author of font-manager), Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Thomas Lin Pedersen ", "Repository": "RSPM" }, "tensor": { "Package": "tensor", "Version": "1.5.1", "Source": "Repository", "Title": "Tensor Product of Arrays", "Authors@R": "person(given = \"Jonathan\", family = \"Rougier\", role = c(\"aut\", \"cre\"), email = \"j.c.rougier@bristol.ac.uk\")", "Description": "The tensor product of two arrays is notionally an outer product of the arrays collapsed in specific extents by summing along the appropriate diagonals.", "License": "GPL (>= 2)", "Repository": "RSPM", "NeedsCompilation": "no", "Author": "Jonathan Rougier [aut, cre]", "Maintainer": "Jonathan Rougier ", "Encoding": "UTF-8" }, "terra": { "Package": "terra", "Version": "1.8-60", "Source": "Repository", "Type": "Package", "Title": "Spatial Data Analysis", "Date": "2025-07-18", "Depends": [ "R (>= 3.5.0)" ], "Suggests": [ "parallel", "tinytest", "ncdf4", "sf (>= 0.9-8)", "deldir", "XML", "leaflet (>= 2.2.1)", "htmlwidgets" ], "LinkingTo": [ "Rcpp" ], "Imports": [ "methods", "Rcpp (>= 1.0-10)" ], "SystemRequirements": "C++17, GDAL (>= 2.2.3), GEOS (>= 3.4.0), PROJ (>= 4.9.3), TBB, sqlite3", "Encoding": "UTF-8", "Language": "en-US", "Maintainer": "Robert J. Hijmans ", "Description": "Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).", "License": "GPL (>= 3)", "URL": "https://rspatial.org/, https://rspatial.github.io/terra/", "BugReports": "https://github.com/rspatial/terra/issues/", "LazyLoad": "yes", "Authors@R": "c( person(\"Robert J.\", \"Hijmans\", role=c(\"cre\", \"aut\"), email=\"r.hijmans@gmail.com\", comment=c(ORCID=\"0000-0001-5872-2872\")),\t\t\t person(\"Márcia\", \"Barbosa\", role=\"ctb\", comment=c(ORCID=\"0000-0001-8972-7713\")), person(\"Roger\", \"Bivand\", role=\"ctb\", comment=c(ORCID=\"0000-0003-2392-6140\")), person(\"Andrew\", \"Brown\", role=\"ctb\", comment=c(ORCID=\"0000-0002-4565-533X\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment=c(ORCID=\"0000-0003-0787-087X\")), person(\"Emanuele\", \"Cordano\", role=\"ctb\",comment=c(ORCID=\"0000-0002-3508-5898\")), person(\"Krzysztof\", \"Dyba\", role=\"ctb\", comment=c(ORCID=\"0000-0002-8614-3816\")), person(\"Edzer\", \"Pebesma\", role=\"ctb\", comment=c(ORCID=\"0000-0001-8049-7069\")), person(\"Barry\", \"Rowlingson\", role=\"ctb\", comment=c(ORCID=\"0000-0002-8586-6625\")), person(\"Michael D.\", \"Sumner\", role=\"ctb\", comment=c(ORCID=\"0000-0002-2471-7511\")))", "NeedsCompilation": "yes", "Author": "Robert J. Hijmans [cre, aut] (ORCID: ), Márcia Barbosa [ctb] (ORCID: ), Roger Bivand [ctb] (ORCID: ), Andrew Brown [ctb] (ORCID: ), Michael Chirico [ctb] (ORCID: ), Emanuele Cordano [ctb] (ORCID: ), Krzysztof Dyba [ctb] (ORCID: ), Edzer Pebesma [ctb] (ORCID: ), Barry Rowlingson [ctb] (ORCID: ), Michael D. Sumner [ctb] (ORCID: )", "Repository": "RSPM" }, "testthat": { "Package": "testthat", "Version": "3.2.3", "Source": "Repository", "Title": "Unit Testing for R", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"R Core team\", role = \"ctb\", comment = \"Implementation of utils::recover()\") )", "Description": "Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy to learn and use, and integrates with your existing 'workflow'.", "License": "MIT + file LICENSE", "URL": "https://testthat.r-lib.org, https://github.com/r-lib/testthat", "BugReports": "https://github.com/r-lib/testthat/issues", "Depends": [ "R (>= 3.6.0)" ], "Imports": [ "brio (>= 1.1.3)", "callr (>= 3.7.3)", "cli (>= 3.6.1)", "desc (>= 1.4.2)", "digest (>= 0.6.33)", "evaluate (>= 1.0.1)", "jsonlite (>= 1.8.7)", "lifecycle (>= 1.0.3)", "magrittr (>= 2.0.3)", "methods", "pkgload (>= 1.3.2.1)", "praise (>= 1.0.0)", "processx (>= 3.8.2)", "ps (>= 1.7.5)", "R6 (>= 2.5.1)", "rlang (>= 1.1.1)", "utils", "waldo (>= 0.6.0)", "withr (>= 3.0.2)" ], "Suggests": [ "covr", "curl (>= 0.9.5)", "diffviewer (>= 0.1.0)", "knitr", "rmarkdown", "rstudioapi", "S7", "shiny", "usethis", "vctrs (>= 0.1.0)", "xml2" ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Config/testthat/start-first": "watcher, parallel*", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd], R Core team [ctb] (Implementation of utils::recover())", "Maintainer": "Hadley Wickham ", "Repository": "RSPM" }, "textshaping": { "Package": "textshaping", "Version": "1.0.1", "Source": "Repository", "Title": "Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text Shaping", "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Provides access to the text shaping functionality in the 'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi' library. 'textshaping' is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the 'systemfonts' package.", "License": "MIT + file LICENSE", "URL": "https://github.com/r-lib/textshaping", "BugReports": "https://github.com/r-lib/textshaping/issues", "Depends": [ "R (>= 3.2.0)" ], "Imports": [ "lifecycle", "stats", "stringi", "systemfonts (>= 1.1.0)", "utils" ], "Suggests": [ "covr", "grDevices", "grid", "knitr", "rmarkdown", "testthat (>= 3.0.0)" ], "LinkingTo": [ "cpp11 (>= 0.2.1)", "systemfonts (>= 1.0.0)" ], "VignetteBuilder": "knitr", "Config/build/compilation-database": "true", "Config/testthat/edition": "3", "Config/usethis/last-upkeep": "2025-04-23", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "SystemRequirements": "freetype2, harfbuzz, fribidi", "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Thomas Lin Pedersen ", "Repository": "RSPM" }, "tibble": { "Package": "tibble", "Version": "3.3.0", "Source": "Repository", "Title": "Simple Data Frames", "Authors@R": "c(person(given = \"Kirill\", family = \"M\\u00fcller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Hadley\", family = \"Wickham\", role = \"aut\", email = \"hadley@rstudio.com\"), person(given = \"Romain\", family = \"Francois\", role = \"ctb\", email = \"romain@r-enthusiasts.com\"), person(given = \"Jennifer\", family = \"Bryan\", role = \"ctb\", email = \"jenny@rstudio.com\"), person(given = \"RStudio\", role = c(\"cph\", \"fnd\")))", "Description": "Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the traditional data frame.", "License": "MIT + file LICENSE", "URL": "https://tibble.tidyverse.org/, https://github.com/tidyverse/tibble", "BugReports": "https://github.com/tidyverse/tibble/issues", "Depends": [ "R (>= 3.4.0)" ], "Imports": [ "cli", "lifecycle (>= 1.0.0)", "magrittr", "methods", "pillar (>= 1.8.1)", "pkgconfig", "rlang (>= 1.0.2)", "utils", "vctrs (>= 0.5.0)" ], "Suggests": [ "bench", "bit64", "blob", "brio", "callr", "DiagrammeR", "dplyr", "evaluate", "formattable", "ggplot2", "here", "hms", "htmltools", "knitr", "lubridate", "nycflights13", "pkgload", "purrr", "rmarkdown", "stringi", "testthat (>= 3.0.2)", "tidyr", "withr" ], "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.3.2.9000", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Config/testthat/start-first": "vignette-formats, as_tibble, add, invariants", "Config/autostyle/scope": "line_breaks", "Config/autostyle/strict": "true", "Config/autostyle/rmd": "false", "Config/Needs/website": "tidyverse/tidytemplate", "NeedsCompilation": "yes", "Author": "Kirill Müller [aut, cre] (ORCID: ), Hadley Wickham [aut], Romain Francois [ctb], Jennifer Bryan [ctb], RStudio [cph, fnd]", "Maintainer": "Kirill Müller ", "Repository": "RSPM" }, "tidygraph": { "Package": "tidygraph", "Version": "1.3.1", "Source": "Repository", "Type": "Package", "Title": "A Tidy API for Graph Manipulation", "Authors@R": "person(\"Thomas Lin\", \"Pedersen\", , \"thomasp85@gmail.com\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\"))", "Maintainer": "Thomas Lin Pedersen ", "Description": "A graph, while not \"tidy\" in itself, can be thought of as two tidy data frames describing node and edge data respectively. 'tidygraph' provides an approach to manipulate these two virtual data frames using the API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.", "License": "MIT + file LICENSE", "URL": "https://tidygraph.data-imaginist.com, https://github.com/thomasp85/tidygraph", "BugReports": "https://github.com/thomasp85/tidygraph/issues", "Imports": [ "cli", "dplyr (>= 0.8.5)", "igraph (>= 2.0.0)", "lifecycle", "magrittr", "pillar", "R6", "rlang", "stats", "tibble", "tidyr", "tools", "utils" ], "Suggests": [ "ape", "covr", "data.tree", "graph", "influenceR", "methods", "netrankr", "NetSwan", "network", "seriation", "testthat (>= 3.0.0)" ], "LinkingTo": [ "cpp11" ], "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "Config/testthat/edition": "3", "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [cre, aut] ()", "Repository": "RSPM" }, "tidyr": { "Package": "tidyr", "Version": "1.3.1", "Source": "Repository", "Title": "Tidy Messy Data", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\"), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevin@posit.co\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", "Description": "Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).", "License": "MIT + file LICENSE", "URL": "https://tidyr.tidyverse.org, https://github.com/tidyverse/tidyr", "BugReports": "https://github.com/tidyverse/tidyr/issues", "Depends": [ "R (>= 3.6)" ], "Imports": [ "cli (>= 3.4.1)", "dplyr (>= 1.0.10)", "glue", "lifecycle (>= 1.0.3)", "magrittr", "purrr (>= 1.0.1)", "rlang (>= 1.1.1)", "stringr (>= 1.5.0)", "tibble (>= 2.1.1)", "tidyselect (>= 1.2.0)", "utils", "vctrs (>= 0.5.2)" ], "Suggests": [ "covr", "data.table", "knitr", "readr", "repurrrsive (>= 1.1.0)", "rmarkdown", "testthat (>= 3.0.0)" ], "LinkingTo": [ "cpp11 (>= 0.4.0)" ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.0", "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre], Davis Vaughan [aut], Maximilian Girlich [aut], Kevin Ushey [ctb], Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, "tidyselect": { "Package": "tidyselect", "Version": "1.2.1", "Source": "Repository", "Title": "Select from a Set of Strings", "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", "Description": "A backend for the selecting functions of the 'tidyverse'. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.", "License": "MIT + file LICENSE", "URL": "https://tidyselect.r-lib.org, https://github.com/r-lib/tidyselect", "BugReports": "https://github.com/r-lib/tidyselect/issues", "Depends": [ "R (>= 3.4)" ], "Imports": [ "cli (>= 3.3.0)", "glue (>= 1.3.0)", "lifecycle (>= 1.0.3)", "rlang (>= 1.0.4)", "vctrs (>= 0.5.2)", "withr" ], "Suggests": [ "covr", "crayon", "dplyr", "knitr", "magrittr", "rmarkdown", "stringr", "testthat (>= 3.1.1)", "tibble (>= 2.1.3)" ], "VignetteBuilder": "knitr", "ByteCompile": "true", "Config/testthat/edition": "3", "Config/Needs/website": "tidyverse/tidytemplate", "Encoding": "UTF-8", "RoxygenNote": "7.3.0.9000", "NeedsCompilation": "yes", "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut], Posit Software, PBC [cph, fnd]", "Maintainer": "Lionel Henry ", "Repository": "CRAN" }, "timechange": { "Package": "timechange", "Version": "0.3.0", "Source": "Repository", "Title": "Efficient Manipulation of Date-Times", "Authors@R": "c(person(\"Vitalie\", \"Spinu\", email = \"spinuvit@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Google Inc.\", role = c(\"ctb\", \"cph\")))", "Description": "Efficient routines for manipulation of date-time objects while accounting for time-zones and daylight saving times. The package includes utilities for updating of date-time components (year, month, day etc.), modification of time-zones, rounding of date-times, period addition and subtraction etc. Parts of the 'CCTZ' source code, released under the Apache 2.0 License, are included in this package. See for more details.", "Depends": [ "R (>= 3.3)" ], "License": "GPL (>= 3)", "Encoding": "UTF-8", "LinkingTo": [ "cpp11 (>= 0.2.7)" ], "Suggests": [ "testthat (>= 0.7.1.99)", "knitr" ], "SystemRequirements": "A system with zoneinfo data (e.g. /usr/share/zoneinfo) as well as a recent-enough C++11 compiler (such as g++-4.8 or later). On Windows the zoneinfo included with R is used.", "BugReports": "https://github.com/vspinu/timechange/issues", "URL": "https://github.com/vspinu/timechange/", "RoxygenNote": "7.2.1", "NeedsCompilation": "yes", "Author": "Vitalie Spinu [aut, cre], Google Inc. [ctb, cph]", "Maintainer": "Vitalie Spinu ", "Repository": "RSPM" }, "tinytex": { "Package": "tinytex", "Version": "0.57", "Source": "Repository", "Type": "Package", "Title": "Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents", "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Devon\", \"Ryan\", role = \"ctb\", email = \"dpryan79@gmail.com\", comment = c(ORCID = \"0000-0002-8549-0971\")), person(\"Ethan\", \"Heinzen\", role = \"ctb\"), person(\"Fernando\", \"Cagua\", role = \"ctb\"), person() )", "Description": "Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", "Imports": [ "xfun (>= 0.48)" ], "Suggests": [ "testit", "rstudioapi" ], "License": "MIT + file LICENSE", "URL": "https://github.com/rstudio/tinytex", "BugReports": "https://github.com/rstudio/tinytex/issues", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Author": "Yihui Xie [aut, cre, cph] (), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (), Devon Ryan [ctb] (), Ethan Heinzen [ctb], Fernando Cagua [ctb]", "Maintainer": "Yihui Xie ", "Repository": "RSPM" }, "tweenr": { "Package": "tweenr", "Version": "2.0.3", "Source": "Repository", "Type": "Package", "Title": "Interpolate Data for Smooth Animations", "Authors@R": "c(person(given = \"Thomas Lin\", family = \"Pedersen\", role = c(\"aut\", \"cre\"), email = \"thomasp85@gmail.com\", comment = c(ORCID = \"0000-0002-5147-4711\")))", "Maintainer": "Thomas Lin Pedersen ", "Description": "In order to create smooth animation between states of data, tweening is necessary. This package provides a range of functions for creating tweened data that can be used as basis for animation. Furthermore it adds a number of vectorized interpolaters for common R data types such as numeric, date and colour.", "URL": "https://github.com/thomasp85/tweenr", "BugReports": "https://github.com/thomasp85/tweenr/issues", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Depends": [ "R (>= 3.2.0)" ], "Imports": [ "farver", "magrittr", "rlang", "vctrs" ], "LinkingTo": [ "cpp11 (>= 0.4.2)" ], "RoxygenNote": "7.2.3", "Suggests": [ "testthat", "covr" ], "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [aut, cre] ()", "Repository": "RSPM" }, "txtq": { "Package": "txtq", "Version": "0.2.4", "Source": "Repository", "Title": "A Small Message Queue for Parallel Processes", "Description": "This queue is a data structure that lets parallel processes send and receive messages, and it can help coordinate the work of complicated parallel tasks. 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This is a complete re-implementation in R (and C++, via the 'Rcpp' package): no Python installation is required. 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Other functions help aligning a matrix or data.frame to a reference using partial matching or to mine an experimental setup to extract patterns of replicate samples. Many times large experimental datasets need some additional filtering, adequate functions are provided. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too. 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Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]", "Encoding": "UTF-8" }, "yaml": { "Package": "yaml", "Version": "2.3.10", "Source": "Repository", "Type": "Package", "Title": "Methods to Convert R Data to YAML and Back", "Date": "2024-07-22", "Suggests": [ "RUnit" ], "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. 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Kamvar [ctb], Charlie Gao [ctb]", "Maintainer": "Shawn Garbett ", "License": "BSD_3_clause + file LICENSE", "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", "URL": "https://github.com/vubiostat/r-yaml/", "BugReports": "https://github.com/vubiostat/r-yaml/issues", "NeedsCompilation": "yes", "Repository": "RSPM", "Encoding": "UTF-8" }, "yulab.utils": { "Package": "yulab.utils", "Version": "0.2.0", "Source": "Repository", "Title": "Supporting Functions for Packages Maintained by 'YuLab-SMU'", "Authors@R": "c(person(\"Guangchuang\", \"Yu\", email = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6485-8781\")))", "Description": "Miscellaneous functions commonly used by 'YuLab-SMU'.", "Depends": [ "R (>= 4.2.0)" ], "Imports": [ "cli", "digest", "fs", "rlang", "tools", "utils" ], "Suggests": [ "httr2", "jsonlite", "openssl", "rappdirs" ], "ByteCompile": "true", "License": "Artistic-2.0", "URL": "https://yulab-smu.top/", "BugReports": "https://github.com/YuLab-SMU/yulab.utils/issues", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Author": "Guangchuang Yu [aut, cre] ()", "Maintainer": "Guangchuang Yu ", "Repository": "RSPM" }, "zip": { "Package": "zip", "Version": "2.3.3", "Source": "Repository", "Title": "Cross-Platform 'zip' Compression", "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kuba\", \"Podgórski\", role = \"ctb\"), person(\"Rich\", \"Geldreich\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.", "License": "MIT + file LICENSE", "URL": "https://github.com/r-lib/zip, https://r-lib.github.io/zip/", "BugReports": "https://github.com/r-lib/zip/issues", "Suggests": [ "covr", "pillar", "processx", "R6", "testthat", "withr" ], "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Config/usethis/last-upkeep": "2025-05-07", "Encoding": "UTF-8", "RoxygenNote": "7.3.2.9000", "NeedsCompilation": "yes", "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Gábor Csárdi ", "Repository": "RSPM" }, "zoo": { "Package": "zoo", "Version": "1.8-14", "Source": "Repository", "Date": "2025-04-09", "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", "Depends": [ "R (>= 3.1.0)", "stats" ], "Suggests": [ "AER", "coda", "chron", "ggplot2 (>= 3.5.0)", "mondate", "scales", "stinepack", "strucchange", "timeDate", "timeSeries", "tinyplot", "tis", "tseries", "xts" ], "Imports": [ "utils", "graphics", "grDevices", "lattice (>= 0.20-27)" ], "License": "GPL-2 | GPL-3", "URL": "https://zoo.R-Forge.R-project.org/", "NeedsCompilation": "yes", "Author": "Achim Zeileis [aut, cre] (), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", "Maintainer": "Achim Zeileis ", "Repository": "RSPM", "Encoding": "UTF-8" } } }