diff --git a/DESCRIPTION b/DESCRIPTION index 34dc998..60c4710 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -26,6 +26,7 @@ Imports: tidyr, tools Suggests: + bookdown, knitr, rmarkdown, testthat (>= 3.1.7) diff --git a/data-raw/example_series.R b/data-raw/example_series.R index 5b6a665..04ccb87 100644 --- a/data-raw/example_series.R +++ b/data-raw/example_series.R @@ -166,7 +166,18 @@ generate_example_series_2 <- function() { dplyr::mutate(x = as.integer(x), y = as.integer(y)) + df4c <- df4 %>% + dplyr::mutate(y = replace(y, + c(38:43), + y[38:43] + c(6,1,1,-7,-1,-3))) %>% + f_extend_df(rpois, + n = 4, + lambda = 24) %>% + dplyr::mutate(x = as.integer(x), + y = as.integer(y)) + return(list(example_series_2a = df4, - example_series_2b = df4b)) + example_series_2b = df4b, + example_series_2c = df4c)) } diff --git a/data/example_series_2c.rda b/data/example_series_2c.rda new file mode 100644 index 0000000..cf72ed7 Binary files /dev/null and b/data/example_series_2c.rda differ diff --git a/renv.lock b/renv.lock index 379e34d..958e3c3 100644 --- a/renv.lock +++ b/renv.lock @@ -9,30 +9,6 @@ ] }, "Packages": { - "Deriv": { - "Package": "Deriv", - "Version": "4.2.0", - "Source": "Repository", - "Type": "Package", - "Title": "Symbolic Differentiation", - "Date": "2025-06-20", - "Authors@R": "c(person(given=\"Andrew\", family=\"Clausen\", role=\"aut\"), person(given=\"Serguei\", family=\"Sokol\", role=c(\"aut\", \"cre\"), email=\"sokol@insa-toulouse.fr\", comment = c(ORCID = \"0000-0002-5674-3327\")), person(given=\"Andreas\", family=\"Rappold\", role=\"ctb\", email=\"arappold@gmx.at\"))", - "Description": "R-based solution for symbolic differentiation. It admits user-defined function as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.", - "License": "GPL (>= 3)", - "Suggests": [ - "testthat (>= 0.11.0)" - ], - "BugReports": "https://github.com/sgsokol/Deriv/issues", - "RoxygenNote": "7.3.1", - "Imports": [ - "methods" - ], - "Encoding": "UTF-8", - "NeedsCompilation": "no", - "Author": "Andrew Clausen [aut], Serguei Sokol [aut, cre] (ORCID: ), Andreas Rappold [ctb]", - "Maintainer": "Serguei Sokol ", - "Repository": "CRAN" - }, "DiagrammeR": { "Package": "DiagrammeR", "Version": "1.0.11", @@ -85,24 +61,6 @@ "Maintainer": "Richard Iannone ", "Repository": "CRAN" }, - "Formula": { - "Package": "Formula", - "Version": "1.2-5", - "Source": "Repository", - "Date": "2023-02-23", - "Title": "Extended Model Formulas", - "Description": "Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side (see ).", - "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 = \"Yves\", family = \"Croissant\", role = \"aut\", email = \"Yves.Croissant@univ-reunion.fr\"))", - "Depends": [ - "R (>= 2.0.0)", - "stats" - ], - "License": "GPL-2 | GPL-3", - "NeedsCompilation": "no", - "Author": "Achim Zeileis [aut, cre] (), Yves Croissant [aut]", - "Maintainer": "Achim Zeileis ", - "Repository": "CRAN" - }, "MASS": { "Package": "MASS", "Version": "7.3-65", @@ -184,36 +142,6 @@ "Maintainer": "Martin Maechler ", "Repository": "CRAN" }, - "MatrixModels": { - "Package": "MatrixModels", - "Version": "0.5-4", - "Source": "Repository", - "VersionNote": "Released 0.5-3 on 2023-11-06", - "Date": "2025-03-25", - "Title": "Modelling with Sparse and Dense Matrices", - "Contact": "Matrix-authors@R-project.org", - "Authors@R": "c( person(\"Douglas\", \"Bates\", role = \"aut\", email = \"bates@stat.wisc.edu\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")))", - "Description": "Generalized Linear Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes.", - "Depends": [ - "R (>= 3.6.0)" - ], - "Imports": [ - "stats", - "methods", - "Matrix (>= 1.6-0)", - "Matrix(< 1.8-0)" - ], - "ImportsNote": "_not_yet_stats4", - "Encoding": "UTF-8", - "LazyLoad": "yes", - "License": "GPL (>= 2)", - "URL": "https://Matrix.R-forge.R-project.org/, https://r-forge.r-project.org/R/?group_id=61", - "BugReports": "https://R-forge.R-project.org/tracker/?func=add&atid=294&group_id=61", - "NeedsCompilation": "no", - "Author": "Douglas Bates [aut] (), Martin Maechler [aut, cre] ()", - "Maintainer": "Martin Maechler ", - "Repository": "CRAN" - }, "R6": { "Package": "R6", "Version": "2.6.1", @@ -286,145 +214,29 @@ "Maintainer": "Dirk Eddelbuettel ", "Repository": "CRAN" }, - "RcppEigen": { - "Package": "RcppEigen", - "Version": "0.3.4.0.2", - "Source": "Repository", - "Type": "Package", - "Title": "'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library", - "Date": "2024-08-23", - "Authors@R": "c(person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Yixuan\", \"Qiu\", role = \"aut\", comment = c(ORCID = \"0000-0003-0109-6692\")), person(\"Authors of\", \"Eigen\", role = \"cph\", comment = \"Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS\"))", - "Copyright": "See the file COPYRIGHTS for various Eigen copyright details", - "Description": "R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library. Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", - "License": "GPL (>= 2) | file LICENSE", - "LazyLoad": "yes", - "Depends": [ - "R (>= 3.6.0)" - ], - "LinkingTo": [ - "Rcpp" - ], - "Imports": [ - "Rcpp (>= 0.11.0)", - "stats", - "utils" - ], - "Suggests": [ - "Matrix", - "inline", - "tinytest", - "pkgKitten", - "microbenchmark" - ], - "URL": "https://github.com/RcppCore/RcppEigen, https://dirk.eddelbuettel.com/code/rcpp.eigen.html", - "BugReports": "https://github.com/RcppCore/RcppEigen/issues", - "NeedsCompilation": "yes", - "Author": "Doug Bates [aut] (), Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), Yixuan Qiu [aut] (), Authors of Eigen [cph] (Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS)", - "Maintainer": "Dirk Eddelbuettel ", - "Repository": "CRAN" - }, - "Rdpack": { - "Package": "Rdpack", - "Version": "2.6.4", + "askpass": { + "Package": "askpass", + "Version": "1.2.1", "Source": "Repository", "Type": "Package", - "Title": "Update and Manipulate Rd Documentation Objects", - "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), email = \"georgi.boshnakov@manchester.ac.uk\", comment = c(ORCID = \"0000-0003-2839-346X\")), person(given = \"Duncan\", family = \"Murdoch\", role = \"ctb\", email = \"murdoch.duncan@gmail.com\") )", - "Description": "Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.", - "URL": "https://geobosh.github.io/Rdpack/ (doc), https://github.com/GeoBosh/Rdpack (devel)", - "BugReports": "https://github.com/GeoBosh/Rdpack/issues", - "Depends": [ - "R (>= 2.15.0)", - "methods" - ], - "Imports": [ - "tools", - "utils", - "rbibutils (>= 1.3)" - ], - "Suggests": [ - "grDevices", - "testthat", - "rstudioapi", - "rprojroot", - "gbRd" - ], - "License": "GPL (>= 2)", - "LazyLoad": "yes", - "RoxygenNote": "7.1.1", - "NeedsCompilation": "no", - "Author": "Georgi N. Boshnakov [aut, cre] (), Duncan Murdoch [ctb]", - "Maintainer": "Georgi N. Boshnakov ", - "Repository": "CRAN" - }, - "SparseM": { - "Package": "SparseM", - "Version": "1.84-2", - "Source": "Repository", - "Authors@R": "c( person(\"Roger\", \"Koenker\", role = c(\"cre\",\"aut\"), email = \"rkoenker@uiuc.edu\"), person(c(\"Pin\", \"Tian\"), \"Ng\", role = c(\"ctb\"), comment = \"Contributions to Sparse QR code\", email = \"pin.ng@nau.edu\") , person(\"Yousef\", \"Saad\", role = c(\"ctb\"), comment = \"author of sparskit2\") , person(\"Ben\", \"Shaby\", role = c(\"ctb\"), comment = \"author of chol2csr\") , person(\"Martin\", \"Maechler\", role = \"ctb\", comment = c(\"chol() tweaks; S4\", ORCID = \"0000-0002-8685-9910\")) )", - "Maintainer": "Roger Koenker ", - "Depends": [ - "R (>= 2.15)", - "methods" - ], + "Title": "Password Entry Utilities for R, Git, and SSH", + "Authors@R": "person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\"))", + "Description": "Cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key. Includes native programs for MacOS and Windows, hence no 'tcltk' is required. Password entry can be invoked in two different ways: directly from R via the askpass() function, or indirectly as password-entry back-end for 'ssh-agent' or 'git-credential' via the SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can be prompted for credentials or a passphrase if needed when R calls out to git or ssh.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.r-universe.dev/askpass", + "BugReports": "https://github.com/r-lib/askpass/issues", + "Encoding": "UTF-8", "Imports": [ - "graphics", - "stats", - "utils" + "sys (>= 2.1)" ], - "VignetteBuilder": "knitr", + "RoxygenNote": "7.2.3", "Suggests": [ - "knitr" - ], - "Description": "Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.", - "License": "GPL (>= 2)", - "Title": "Sparse Linear Algebra", - "URL": "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html", - "NeedsCompilation": "yes", - "Author": "Roger Koenker [cre, aut], Pin Tian Ng [ctb] (Contributions to Sparse QR code), Yousef Saad [ctb] (author of sparskit2), Ben Shaby [ctb] (author of chol2csr), Martin Maechler [ctb] (chol() tweaks; S4, )", - "Repository": "CRAN" - }, - "abind": { - "Package": "abind", - "Version": "1.4-8", - "Source": "Repository", - "Date": "2024-09-08", - "Title": "Combine Multidimensional Arrays", - "Authors@R": "c(person(\"Tony\", \"Plate\", email = \"tplate@acm.org\", role = c(\"aut\", \"cre\")), person(\"Richard\", \"Heiberger\", role = c(\"aut\")))", - "Maintainer": "Tony Plate ", - "Description": "Combine multidimensional arrays into a single array. This is a generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and higher-dimensional arrays (aka tensors). Also provides functions 'adrop', 'asub', and 'afill' for manipulating, extracting and replacing data in arrays.", - "Depends": [ - "R (>= 1.5.0)" - ], - "Imports": [ - "methods", - "utils" + "testthat" ], - "License": "MIT + file LICENSE", - "NeedsCompilation": "no", - "Author": "Tony Plate [aut, cre], Richard Heiberger [aut]", - "Repository": "CRAN" - }, - "backports": { - "Package": "backports", - "Version": "1.5.0", - "Source": "Repository", - "Type": "Package", - "Title": "Reimplementations of Functions Introduced Since R-3.0.0", - "Authors@R": "c( person(\"Michel\", \"Lang\", NULL, \"michellang@gmail.com\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Duncan\", \"Murdoch\", NULL, \"murdoch.duncan@gmail.com\", role = c(\"aut\")), person(\"R Core Team\", role = \"aut\"))", - "Maintainer": "Michel Lang ", - "Description": "Functions introduced or changed since R v3.0.0 are re-implemented in this package. The backports are conditionally exported in order to let R resolve the function name to either the implemented backport, or the respective base version, if available. Package developers can make use of new functions or arguments by selectively importing specific backports to support older installations.", - "URL": "https://github.com/r-lib/backports", - "BugReports": "https://github.com/r-lib/backports/issues", - "License": "GPL-2 | GPL-3", + "Language": "en-US", "NeedsCompilation": "yes", - "ByteCompile": "yes", - "Depends": [ - "R (>= 3.0.0)" - ], - "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", - "Author": "Michel Lang [cre, aut] (), Duncan Murdoch [aut], R Core Team [aut]", + "Author": "Jeroen Ooms [aut, cre] ()", + "Maintainer": "Jeroen Ooms ", "Repository": "CRAN" }, "base64enc": { @@ -513,33 +325,6 @@ "Maintainer": "Michael Chirico ", "Repository": "CRAN" }, - "boot": { - "Package": "boot", - "Version": "1.3-31", - "Source": "Repository", - "Priority": "recommended", - "Date": "2024-08-28", - "Authors@R": "c(person(\"Angelo\", \"Canty\", role = \"aut\", email = \"cantya@mcmaster.ca\", comment = \"author of original code for S\"), person(\"Brian\", \"Ripley\", role = c(\"aut\", \"trl\"), email = \"ripley@stats.ox.ac.uk\", comment = \"conversion to R, maintainer 1999--2022, author of parallel support\"), person(\"Alessandra R.\", \"Brazzale\", role = c(\"ctb\", \"cre\"), email = \"brazzale@stat.unipd.it\", comment = \"minor bug fixes\"))", - "Maintainer": "Alessandra R. Brazzale ", - "Note": "Maintainers are not available to give advice on using a package they did not author.", - "Description": "Functions and datasets for bootstrapping from the book \"Bootstrap Methods and Their Application\" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.", - "Title": "Bootstrap Functions (Originally by Angelo Canty for S)", - "Depends": [ - "R (>= 3.0.0)", - "graphics", - "stats" - ], - "Suggests": [ - "MASS", - "survival" - ], - "LazyData": "yes", - "ByteCompile": "yes", - "License": "Unlimited", - "NeedsCompilation": "no", - "Author": "Angelo Canty [aut] (author of original code for S), Brian Ripley [aut, trl] (conversion to R, maintainer 1999--2022, author of parallel support), Alessandra R. Brazzale [ctb, cre] (minor bug fixes)", - "Repository": "CRAN" - }, "brio": { "Package": "brio", "Version": "1.1.5", @@ -566,128 +351,6 @@ "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" }, - "broom": { - "Package": "broom", - "Version": "1.0.9", - "Source": "Repository", - "Type": "Package", - "Title": "Convert Statistical Objects into Tidy Tibbles", - "Authors@R": "c( person(\"David\", \"Robinson\", , \"admiral.david@gmail.com\", role = \"aut\"), person(\"Alex\", \"Hayes\", , \"alexpghayes@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(\"Simon\", \"Couch\", , \"simon.couch@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5676-5107\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(\"Indrajeet\", \"Patil\", , \"patilindrajeet.science@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(\"Derek\", \"Chiu\", , \"dchiu@bccrc.ca\", role = \"ctb\"), person(\"Matthieu\", \"Gomez\", , \"mattg@princeton.edu\", role = \"ctb\"), person(\"Boris\", \"Demeshev\", , \"boris.demeshev@gmail.com\", role = \"ctb\"), person(\"Dieter\", \"Menne\", , \"dieter.menne@menne-biomed.de\", role = \"ctb\"), person(\"Benjamin\", \"Nutter\", , \"nutter@battelle.org\", role = \"ctb\"), person(\"Luke\", \"Johnston\", , \"luke.johnston@mail.utoronto.ca\", role = \"ctb\"), person(\"Ben\", \"Bolker\", , \"bolker@mcmaster.ca\", role = \"ctb\"), person(\"Francois\", \"Briatte\", , \"f.briatte@gmail.com\", role = \"ctb\"), person(\"Jeffrey\", \"Arnold\", , \"jeffrey.arnold@gmail.com\", role = \"ctb\"), person(\"Jonah\", \"Gabry\", , \"jsg2201@columbia.edu\", role = \"ctb\"), person(\"Luciano\", \"Selzer\", , \"luciano.selzer@gmail.com\", role = \"ctb\"), person(\"Gavin\", \"Simpson\", , \"ucfagls@gmail.com\", role = \"ctb\"), person(\"Jens\", \"Preussner\", , \"jens.preussner@mpi-bn.mpg.de\", role = \"ctb\"), person(\"Jay\", \"Hesselberth\", , \"jay.hesselberth@gmail.com\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"ctb\"), person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = \"ctb\"), person(\"Alessandro\", \"Gasparini\", , \"ag475@leicester.ac.uk\", role = \"ctb\"), person(\"Lukasz\", \"Komsta\", , \"lukasz.komsta@umlub.pl\", role = \"ctb\"), person(\"Frederick\", \"Novometsky\", role = \"ctb\"), person(\"Wilson\", \"Freitas\", role = \"ctb\"), person(\"Michelle\", \"Evans\", role = \"ctb\"), person(\"Jason Cory\", \"Brunson\", , \"cornelioid@gmail.com\", role = \"ctb\"), person(\"Simon\", \"Jackson\", , \"drsimonjackson@gmail.com\", role = \"ctb\"), person(\"Ben\", \"Whalley\", , \"ben.whalley@plymouth.ac.uk\", role = \"ctb\"), person(\"Karissa\", \"Whiting\", , \"karissa.whiting@gmail.com\", role = \"ctb\"), person(\"Yves\", \"Rosseel\", , \"yrosseel@gmail.com\", role = \"ctb\"), person(\"Michael\", \"Kuehn\", , \"mkuehn10@gmail.com\", role = \"ctb\"), person(\"Jorge\", \"Cimentada\", , \"cimentadaj@gmail.com\", role = \"ctb\"), person(\"Erle\", \"Holgersen\", , \"erle.holgersen@gmail.com\", role = \"ctb\"), person(\"Karl\", \"Dunkle Werner\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0523-7309\")), person(\"Ethan\", \"Christensen\", , \"christensen.ej@gmail.com\", role = \"ctb\"), person(\"Steven\", \"Pav\", , \"shabbychef@gmail.com\", role = \"ctb\"), person(\"Paul\", \"PJ\", , \"pjpaul.stephens@gmail.com\", role = \"ctb\"), person(\"Ben\", \"Schneider\", , \"benjamin.julius.schneider@gmail.com\", role = \"ctb\"), person(\"Patrick\", \"Kennedy\", , \"pkqstr@protonmail.com\", role = \"ctb\"), person(\"Lily\", \"Medina\", , \"lilymiru@gmail.com\", role = \"ctb\"), person(\"Brian\", \"Fannin\", , \"captain@pirategrunt.com\", role = \"ctb\"), person(\"Jason\", \"Muhlenkamp\", , \"jason.muhlenkamp@gmail.com\", role = \"ctb\"), person(\"Matt\", \"Lehman\", role = \"ctb\"), person(\"Bill\", \"Denney\", , \"wdenney@humanpredictions.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\")), person(\"Nic\", \"Crane\", role = \"ctb\"), person(\"Andrew\", \"Bates\", role = \"ctb\"), person(\"Vincent\", \"Arel-Bundock\", , \"vincent.arel-bundock@umontreal.ca\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2042-7063\")), person(\"Hideaki\", \"Hayashi\", role = \"ctb\"), person(\"Luis\", \"Tobalina\", role = \"ctb\"), person(\"Annie\", \"Wang\", , \"anniewang.uc@gmail.com\", role = \"ctb\"), person(\"Wei Yang\", \"Tham\", , \"weiyang.tham@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", , \"clara.wang.94@gmail.com\", role = \"ctb\"), person(\"Abby\", \"Smith\", , \"als1@u.northwestern.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3207-0375\")), person(\"Jasper\", \"Cooper\", , \"jaspercooper@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8639-3188\")), person(\"E Auden\", \"Krauska\", , \"krauskae@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1466-5850\")), person(\"Alex\", \"Wang\", , \"x249wang@uwaterloo.ca\", role = \"ctb\"), person(\"Malcolm\", \"Barrett\", , \"malcolmbarrett@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(\"Charles\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9978-011X\")), person(\"Jared\", \"Wilber\", role = \"ctb\"), person(\"Vilmantas\", \"Gegzna\", , \"GegznaV@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9500-5167\")), person(\"Eduard\", \"Szoecs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"Frederik\", \"Aust\", , \"frederik.aust@uni-koeln.de\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4900-788X\")), person(\"Angus\", \"Moore\", , \"angusmoore9@gmail.com\", role = \"ctb\"), person(\"Nick\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Marius\", \"Barth\", , \"marius.barth.uni.koeln@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3421-6665\")), person(\"Bruna\", \"Wundervald\", , \"brunadaviesw@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8163-220X\")), person(\"Joyce\", \"Cahoon\", , \"joyceyu48@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7217-4702\")), person(\"Grant\", \"McDermott\", , \"grantmcd@uoregon.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7883-8573\")), person(\"Kevin\", \"Zarca\", , \"kevin.zarca@gmail.com\", role = \"ctb\"), person(\"Shiro\", \"Kuriwaki\", , \"shirokuriwaki@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5687-2647\")), person(\"Lukas\", \"Wallrich\", , \"lukas.wallrich@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2121-5177\")), person(\"James\", \"Martherus\", , \"james@martherus.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8285-3300\")), person(\"Chuliang\", \"Xiao\", , \"cxiao@umich.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8466-9398\")), person(\"Joseph\", \"Larmarange\", , \"joseph@larmarange.net\", role = \"ctb\"), person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", , \"michal2992@gmail.com\", role = \"ctb\"), person(\"Hakon\", \"Malmedal\", , \"hmalmedal@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", role = \"ctb\"), person(\"Sergio\", \"Oller\", , \"sergioller@gmail.com\", role = \"ctb\"), person(\"Luke\", \"Sonnet\", , \"luke.sonnet@gmail.com\", role = \"ctb\"), person(\"Jim\", \"Hester\", , \"jim.hester@posit.co\", role = \"ctb\"), person(\"Ben\", \"Schneider\", , \"benjamin.julius.schneider@gmail.com\", role = \"ctb\"), person(\"Bernie\", \"Gray\", , \"bfgray3@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9190-6032\")), person(\"Mara\", \"Averick\", , \"mara@posit.co\", role = \"ctb\"), person(\"Aaron\", \"Jacobs\", , \"atheriel@gmail.com\", role = \"ctb\"), person(\"Andreas\", \"Bender\", , \"bender.at.R@gmail.com\", role = \"ctb\"), person(\"Sven\", \"Templer\", , \"sven.templer@gmail.com\", role = \"ctb\"), person(\"Paul-Christian\", \"Buerkner\", , \"paul.buerkner@gmail.com\", role = \"ctb\"), person(\"Matthew\", \"Kay\", , \"mjskay@umich.edu\", role = \"ctb\"), person(\"Erwan\", \"Le Pennec\", , \"lepennec@gmail.com\", role = \"ctb\"), person(\"Johan\", \"Junkka\", , \"johan.junkka@umu.se\", role = \"ctb\"), person(\"Hao\", \"Zhu\", , \"haozhu233@gmail.com\", role = \"ctb\"), person(\"Benjamin\", \"Soltoff\", , \"soltoffbc@uchicago.edu\", role = \"ctb\"), person(\"Zoe\", \"Wilkinson Saldana\", , \"zoewsaldana@gmail.com\", role = \"ctb\"), person(\"Tyler\", \"Littlefield\", , \"tylurp1@gmail.com\", role = \"ctb\"), person(\"Charles T.\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\"), person(\"Shabbh E.\", \"Banks\", role = \"ctb\"), person(\"Serina\", \"Robinson\", , \"robi0916@umn.edu\", role = \"ctb\"), person(\"Roger\", \"Bivand\", , \"Roger.Bivand@nhh.no\", role = \"ctb\"), person(\"Riinu\", \"Ots\", , \"riinuots@gmail.com\", role = \"ctb\"), person(\"Nicholas\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Nina\", \"Jakobsen\", role = \"ctb\"), person(\"Michael\", \"Weylandt\", , \"michael.weylandt@gmail.com\", role = \"ctb\"), person(\"Lisa\", \"Lendway\", , \"llendway@macalester.edu\", role = \"ctb\"), person(\"Karl\", \"Hailperin\", , \"khailper@gmail.com\", role = \"ctb\"), person(\"Josue\", \"Rodriguez\", , \"jerrodriguez@ucdavis.edu\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", , \"jenny@posit.co\", role = \"ctb\"), person(\"Chris\", \"Jarvis\", , \"Christopher1.jarvis@gmail.com\", role = \"ctb\"), person(\"Greg\", \"Macfarlane\", , \"gregmacfarlane@gmail.com\", role = \"ctb\"), person(\"Brian\", \"Mannakee\", , \"bmannakee@gmail.com\", role = \"ctb\"), person(\"Drew\", \"Tyre\", , \"atyre2@unl.edu\", role = \"ctb\"), person(\"Shreyas\", \"Singh\", , \"shreyas.singh.298@gmail.com\", role = \"ctb\"), person(\"Laurens\", \"Geffert\", , \"laurensgeffert@gmail.com\", role = \"ctb\"), person(\"Hong\", \"Ooi\", , \"hongooi@microsoft.com\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", , \"henrikb@braju.com\", role = \"ctb\"), person(\"Eduard\", \"Szocs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", , \"davidhughjones@gmail.com\", role = \"ctb\"), person(\"Matthieu\", \"Stigler\", , \"Matthieu.Stigler@gmail.com\", role = \"ctb\"), person(\"Hugo\", \"Tavares\", , \"hm533@cam.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(\"R. Willem\", \"Vervoort\", , \"Willemvervoort@gmail.com\", role = \"ctb\"), person(\"Brenton M.\", \"Wiernik\", , \"brenton@wiernik.org\", role = \"ctb\"), person(\"Josh\", \"Yamamoto\", , \"joshuayamamoto5@gmail.com\", role = \"ctb\"), person(\"Jasme\", \"Lee\", role = \"ctb\"), person(\"Taren\", \"Sanders\", , \"taren.sanders@acu.edu.au\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(\"Ilaria\", \"Prosdocimi\", , \"prosdocimi.ilaria@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(\"Alex\", \"Reinhart\", , \"areinhar@stat.cmu.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-6658-514X\")) )", - "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", - "License": "MIT + file LICENSE", - "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", - "BugReports": "https://github.com/tidymodels/broom/issues", - "Depends": [ - "R (>= 4.1)" - ], - "Imports": [ - "backports", - "cli", - "dplyr (>= 1.0.0)", - "generics (>= 0.0.2)", - "glue", - "lifecycle", - "purrr", - "rlang (>= 1.1.0)", - "stringr", - "tibble (>= 3.0.0)", - "tidyr (>= 1.0.0)" - ], - "Suggests": [ - "AER", - "AUC", - "bbmle", - "betareg (>= 3.2-1)", - "biglm", - "binGroup", - "boot", - "btergm (>= 1.10.6)", - "car (>= 3.1-2)", - "carData", - "caret", - "cluster", - "cmprsk", - "coda", - "covr", - "drc", - "e1071", - "emmeans", - "epiR (>= 2.0.85)", - "ergm (>= 3.10.4)", - "fixest (>= 0.9.0)", - "gam (>= 1.15)", - "gee", - "geepack", - "ggplot2", - "glmnet", - "glmnetUtils", - "gmm", - "Hmisc", - "interp", - "irlba", - "joineRML", - "Kendall", - "knitr", - "ks", - "Lahman", - "lavaan (>= 0.6.18)", - "leaps", - "lfe", - "lm.beta", - "lme4", - "lmodel2", - "lmtest (>= 0.9.38)", - "lsmeans", - "maps", - "margins", - "MASS", - "mclust", - "mediation", - "metafor", - "mfx", - "mgcv", - "mlogit", - "modeldata", - "modeltests (>= 0.1.6)", - "muhaz", - "multcomp", - "network", - "nnet", - "ordinal", - "plm", - "poLCA", - "psych", - "quantreg", - "rmarkdown", - "robust", - "robustbase", - "rsample", - "sandwich", - "spatialreg", - "spdep (>= 1.1)", - "speedglm", - "spelling", - "survey", - "survival (>= 3.6-4)", - "systemfit", - "testthat (>= 3.0.0)", - "tseries", - "vars", - "zoo" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Config/usethis/last-upkeep": "2025-04-25", - "Encoding": "UTF-8", - "Language": "en-US", - "RoxygenNote": "7.3.2", - "Collate": "'aaa-documentation-helper.R' 'null-and-default.R' 'aer.R' 'auc.R' 'base.R' 'bbmle.R' 'betareg.R' 'biglm.R' 'bingroup.R' 'boot.R' 'broom-package.R' 'broom.R' 'btergm.R' 'car.R' 'caret.R' 'cluster.R' 'cmprsk.R' 'data-frame.R' 'deprecated-0-7-0.R' 'drc.R' 'emmeans.R' 'epiR.R' 'ergm.R' 'fixest.R' 'gam.R' 'geepack.R' 'glmnet-cv-glmnet.R' 'glmnet-glmnet.R' 'gmm.R' 'hmisc.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'joinerml.R' 'kendall.R' 'ks.R' 'lavaan.R' 'leaps.R' 'lfe.R' 'list-irlba.R' 'list-optim.R' 'list-svd.R' 'list-xyz.R' 'list.R' 'lm-beta.R' 'lmodel2.R' 'lmtest.R' 'maps.R' 'margins.R' 'mass-fitdistr.R' 'mass-negbin.R' 'mass-polr.R' 'mass-ridgelm.R' 'stats-lm.R' 'mass-rlm.R' 'mclust.R' 'mediation.R' 'metafor.R' 'mfx.R' 'mgcv.R' 'mlogit.R' 'muhaz.R' 'multcomp.R' 'nnet.R' 'nobs.R' 'ordinal-clm.R' 'ordinal-clmm.R' 'plm.R' 'polca.R' 'psych.R' 'stats-nls.R' 'quantreg-nlrq.R' 'quantreg-rq.R' 'quantreg-rqs.R' 'robust-glmrob.R' 'robust-lmrob.R' 'robustbase-glmrob.R' 'robustbase-lmrob.R' 'sp.R' 'spdep.R' 'speedglm-speedglm.R' 'speedglm-speedlm.R' 'stats-anova.R' 'stats-arima.R' 'stats-decompose.R' 'stats-factanal.R' 'stats-glm.R' 'stats-htest.R' 'stats-kmeans.R' 'stats-loess.R' 'stats-mlm.R' 'stats-prcomp.R' 'stats-smooth.spline.R' 'stats-summary-lm.R' 'stats-time-series.R' 'survey.R' 'survival-aareg.R' 'survival-cch.R' 'survival-coxph.R' 'survival-pyears.R' 'survival-survdiff.R' 'survival-survexp.R' 'survival-survfit.R' 'survival-survreg.R' 'systemfit.R' 'tseries.R' 'utilities.R' 'vars.R' 'zoo.R' 'zzz.R'", - "NeedsCompilation": "no", - "Author": "David Robinson [aut], Alex Hayes [aut] (ORCID: ), Simon Couch [aut, cre] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: ), Indrajeet Patil [ctb] (ORCID: ), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (ORCID: ), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (ORCID: ), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (ORCID: ), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (ORCID: ), Jasper Cooper [ctb] (ORCID: ), E Auden Krauska [ctb] (ORCID: ), Alex Wang [ctb], Malcolm Barrett [ctb] (ORCID: ), Charles Gray [ctb] (ORCID: ), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (ORCID: ), Eduard Szoecs [ctb], Frederik Aust [ctb] (ORCID: ), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (ORCID: ), Bruna Wundervald [ctb] (ORCID: ), Joyce Cahoon [ctb] (ORCID: ), Grant McDermott [ctb] (ORCID: ), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (ORCID: ), Lukas Wallrich [ctb] (ORCID: ), James Martherus [ctb] (ORCID: ), Chuliang Xiao [ctb] (ORCID: ), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (ORCID: ), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (ORCID: ), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (ORCID: ), Ilaria Prosdocimi [ctb] (ORCID: ), Daniel D. Sjoberg [ctb] (ORCID: ), Alex Reinhart [ctb] (ORCID: )", - "Maintainer": "Simon Couch ", - "Repository": "CRAN" - }, "bslib": { "Package": "bslib", "Version": "0.9.0", @@ -811,90 +474,6 @@ "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" }, - "car": { - "Package": "car", - "Version": "3.1-3", - "Source": "Repository", - "Date": "2024-09-23", - "Title": "Companion to Applied Regression", - "Authors@R": "c(person(\"John\", \"Fox\", role = c(\"aut\", \"cre\"), email = \"jfox@mcmaster.ca\"), person(\"Sanford\", \"Weisberg\", role = \"aut\", email = \"sandy@umn.edu\"), person(\"Brad\", \"Price\", role = \"aut\", email = \"brad.price@mail.wvu.edu\"), person(\"Daniel\", \"Adler\", role=\"ctb\"), person(\"Douglas\", \"Bates\", role = \"ctb\"), person(\"Gabriel\", \"Baud-Bovy\", role = \"ctb\"), person(\"Ben\", \"Bolker\", role=\"ctb\"), person(\"Steve\", \"Ellison\", role=\"ctb\"), person(\"David\", \"Firth\", role = \"ctb\"), person(\"Michael\", \"Friendly\", role = \"ctb\"), person(\"Gregor\", \"Gorjanc\", role = \"ctb\"), person(\"Spencer\", \"Graves\", role = \"ctb\"), person(\"Richard\", \"Heiberger\", role = \"ctb\"), person(\"Pavel\", \"Krivitsky\", role = \"ctb\"), person(\"Rafael\", \"Laboissiere\", role = \"ctb\"), person(\"Martin\", \"Maechler\", role=\"ctb\"), person(\"Georges\", \"Monette\", role = \"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Henric\", \"Nilsson\", role = \"ctb\"), person(\"Derek\", \"Ogle\", role = \"ctb\"), person(\"Brian\", \"Ripley\", role = \"ctb\"), person(\"Tom\", \"Short\", role=\"ctb\"), person(\"William\", \"Venables\", role = \"ctb\"), person(\"Steve\", \"Walker\", role=\"ctb\"), person(\"David\", \"Winsemius\", role=\"ctb\"), person(\"Achim\", \"Zeileis\", role = \"ctb\"), person(\"R-Core\", role=\"ctb\"))", - "Depends": [ - "R (>= 3.5.0)", - "carData (>= 3.0-0)" - ], - "Imports": [ - "abind", - "Formula", - "MASS", - "mgcv", - "nnet", - "pbkrtest (>= 0.4-4)", - "quantreg", - "grDevices", - "utils", - "stats", - "graphics", - "lme4 (>= 1.1-27.1)", - "nlme", - "scales" - ], - "Suggests": [ - "alr4", - "boot", - "coxme", - "effects", - "knitr", - "leaps", - "lmtest", - "Matrix", - "MatrixModels", - "ordinal", - "plotrix", - "mvtnorm", - "rgl (>= 0.111.3)", - "rio", - "sandwich", - "SparseM", - "survival", - "survey" - ], - "ByteCompile": "yes", - "LazyLoad": "yes", - "Description": "Functions to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage, 2019.", - "License": "GPL (>= 2)", - "URL": "https://r-forge.r-project.org/projects/car/, https://CRAN.R-project.org/package=car, https://www.john-fox.ca/Companion/index.html", - "VignetteBuilder": "knitr", - "NeedsCompilation": "no", - "Author": "John Fox [aut, cre], Sanford Weisberg [aut], Brad Price [aut], Daniel Adler [ctb], Douglas Bates [ctb], Gabriel Baud-Bovy [ctb], Ben Bolker [ctb], Steve Ellison [ctb], David Firth [ctb], Michael Friendly [ctb], Gregor Gorjanc [ctb], Spencer Graves [ctb], Richard Heiberger [ctb], Pavel Krivitsky [ctb], Rafael Laboissiere [ctb], Martin Maechler [ctb], Georges Monette [ctb], Duncan Murdoch [ctb], Henric Nilsson [ctb], Derek Ogle [ctb], Brian Ripley [ctb], Tom Short [ctb], William Venables [ctb], Steve Walker [ctb], David Winsemius [ctb], Achim Zeileis [ctb], R-Core [ctb]", - "Maintainer": "John Fox ", - "Repository": "CRAN" - }, - "carData": { - "Package": "carData", - "Version": "3.0-5", - "Source": "Repository", - "Date": "2022-01-05", - "Title": "Companion to Applied Regression Data Sets", - "Authors@R": "c(person(\"John\", \"Fox\", role = c(\"aut\", \"cre\"), email = \"jfox@mcmaster.ca\"), person(\"Sanford\", \"Weisberg\", role = \"aut\", email = \"sandy@umn.edu\"), person(\"Brad\", \"Price\", role = \"aut\", email = \"brad.price@mail.wvu.edu\"))", - "Depends": [ - "R (>= 3.5.0)" - ], - "Suggests": [ - "car (>= 3.0-0)" - ], - "LazyLoad": "yes", - "LazyData": "yes", - "Description": "Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage (2019).", - "License": "GPL (>= 2)", - "URL": "https://r-forge.r-project.org/projects/car/, https://CRAN.R-project.org/package=carData, https://socialsciences.mcmaster.ca/jfox/Books/Companion/index.html", - "Author": "John Fox [aut, cre], Sanford Weisberg [aut], Brad Price [aut]", - "Maintainer": "John Fox ", - "Repository": "CRAN", - "Repository/R-Forge/Project": "car", - "Repository/R-Forge/Revision": "694", - "Repository/R-Forge/DateTimeStamp": "2022-01-05 19:40:37", - "NeedsCompilation": "no" - }, "cli": { "Package": "cli", "Version": "3.6.5", @@ -973,34 +552,6 @@ "Maintainer": "Matthew Lincoln ", "Repository": "CRAN" }, - "corrplot": { - "Package": "corrplot", - "Version": "0.95", - "Source": "Repository", - "Type": "Package", - "Title": "Visualization of a Correlation Matrix", - "Date": "2024-10-14", - "Authors@R": "c( person('Taiyun', 'Wei', email = 'weitaiyun@gmail.com', role = c('cre', 'aut')), person('Viliam', 'Simko', email = 'viliam.simko@gmail.com', role = 'aut'), person('Michael', 'Levy', email = 'michael.levy@healthcatalyst.com', role = 'ctb'), person('Yihui', 'Xie', email = 'xie@yihui.name', role = 'ctb'), person('Yan', 'Jin', email = 'jyfeather@gmail.com', role = 'ctb'), person('Jeff', 'Zemla', email = 'zemla@wisc.edu', role = 'ctb'), person('Moritz', 'Freidank', email = 'freidankm@googlemail.com', role = 'ctb'), person('Jun', 'Cai', email = 'cai-j12@mails.tsinghua.edu.cn', role = 'ctb'), person('Tomas', 'Protivinsky', email = 'tomas.protivinsky@gmail.com', role = 'ctb') )", - "Maintainer": "Taiyun Wei ", - "Suggests": [ - "seriation", - "knitr", - "RColorBrewer", - "rmarkdown", - "magrittr", - "prettydoc", - "testthat" - ], - "Description": "Provides a visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/taiyun/corrplot", - "BugReports": "https://github.com/taiyun/corrplot/issues", - "VignetteBuilder": "knitr", - "RoxygenNote": "7.2.1", - "NeedsCompilation": "no", - "Author": "Taiyun Wei [cre, aut], Viliam Simko [aut], Michael Levy [ctb], Yihui Xie [ctb], Yan Jin [ctb], Jeff Zemla [ctb], Moritz Freidank [ctb], Jun Cai [ctb], Tomas Protivinsky [ctb]", - "Repository": "CRAN" - }, "cowplot": { "Package": "cowplot", "Version": "1.2.0", @@ -1128,6 +679,40 @@ "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" }, + "curl": { + "Package": "curl", + "Version": "7.0.0", + "Source": "Repository", + "Type": "Package", + "Title": "A Modern and Flexible Web Client for R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Posit Software, PBC\", role = \"cph\"))", + "Description": "Bindings to 'libcurl' for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.73): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, "desc": { "Package": "desc", "Version": "1.4.3", @@ -1228,52 +813,49 @@ "Maintainer": "Dirk Eddelbuettel ", "Repository": "CRAN" }, - "doBy": { - "Package": "doBy", - "Version": "4.7.0", + "downlit": { + "Package": "downlit", + "Version": "0.4.4", "Source": "Repository", - "Title": "Groupwise Statistics, LSmeans, Linear Estimates, Utilities", - "Authors@R": "c( person(given = \"Ulrich\", family = \"Halekoh\", email = \"uhalekoh@health.sdu.dk\", role = c(\"aut\", \"cph\")), person(given = \"Søren\", family = \"Højsgaard\", email = \"sorenh@math.aau.dk\", role = c(\"aut\", \"cre\", \"cph\")) )", - "Description": "Utility package containing: Main categories: Working with grouped data: 'do' something to data when stratified 'by' some variables. General linear estimates. Data handling utilities. Functional programming, in particular restrict functions to a smaller domain. Miscellaneous functions for data handling. Model stability in connection with model selection. Miscellaneous other tools.", - "Encoding": "UTF-8", - "VignetteBuilder": "knitr", - "LazyData": "true", - "LazyDataCompression": "xz", - "URL": "https://github.com/hojsgaard/doBy", - "License": "GPL (>= 2)", + "Title": "Syntax Highlighting and Automatic Linking", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Syntax highlighting of R code, specifically designed for the needs of 'RMarkdown' packages like 'pkgdown', 'hugodown', and 'bookdown'. It includes linking of function calls to their documentation on the web, and automatic translation of ANSI escapes in output to the equivalent HTML.", + "License": "MIT + file LICENSE", + "URL": "https://downlit.r-lib.org/, https://github.com/r-lib/downlit", + "BugReports": "https://github.com/r-lib/downlit/issues", "Depends": [ - "R (>= 4.2.0)", - "methods" + "R (>= 4.0.0)" ], "Imports": [ - "boot", - "broom", - "cowplot", - "Deriv", - "dplyr", - "ggplot2", - "MASS", - "Matrix", - "modelr", - "microbenchmark", + "brio", + "desc", + "digest", + "evaluate", + "fansi", + "memoise", "rlang", - "tibble", - "tidyr" + "vctrs", + "withr", + "yaml" ], "Suggests": [ - "geepack", - "knitr", - "lme4", - "markdown", - "multcomp", - "pbkrtest (>= 0.5.2)", - "survival", - "testthat (>= 2.1.0)" + "covr", + "htmltools", + "jsonlite", + "MASS", + "MassSpecWavelet", + "pkgload", + "rmarkdown", + "testthat (>= 3.0.0)", + "xml2" ], - "RoxygenNote": "7.3.2", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", "NeedsCompilation": "no", - "Author": "Ulrich Halekoh [aut, cph], Søren Højsgaard [aut, cre, cph]", - "Maintainer": "Søren Højsgaard ", + "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, "dplyr": { @@ -1375,6 +957,37 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, + "fansi": { + "Package": "fansi", + "Version": "1.0.6", + "Source": "Repository", + "Title": "ANSI Control Sequence Aware String Functions", + "Description": "Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.", + "Authors@R": "c( person(\"Brodie\", \"Gaslam\", email=\"brodie.gaslam@yahoo.com\", role=c(\"aut\", \"cre\")), person(\"Elliott\", \"Sales De Andrade\", role=\"ctb\"), person(family=\"R Core Team\", email=\"R-core@r-project.org\", role=\"cph\", comment=\"UTF8 byte length calcs from src/util.c\" ))", + "Depends": [ + "R (>= 3.1.0)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://github.com/brodieG/fansi", + "BugReports": "https://github.com/brodieG/fansi/issues", + "VignetteBuilder": "knitr", + "Suggests": [ + "unitizer", + "knitr", + "rmarkdown" + ], + "Imports": [ + "grDevices", + "utils" + ], + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "Collate": "'constants.R' 'fansi-package.R' 'internal.R' 'load.R' 'misc.R' 'nchar.R' 'strwrap.R' 'strtrim.R' 'strsplit.R' 'substr2.R' 'trimws.R' 'tohtml.R' 'unhandled.R' 'normalize.R' 'sgr.R'", + "NeedsCompilation": "yes", + "Author": "Brodie Gaslam [aut, cre], Elliott Sales De Andrade [ctb], R Core Team [cph] (UTF8 byte length calcs from src/util.c)", + "Maintainer": "Brodie Gaslam ", + "Repository": "CRAN" + }, "farver": { "Package": "farver", "Version": "2.1.2", @@ -1683,58 +1296,6 @@ "Author": "Pedro J. Aphalo [aut, cre] (ORCID: ), Kamil Slowikowski [ctb] (ORCID: ), Michał Krassowski [ctb] (ORCID: ), Daniel Sabanés Bové [ctb], Stella Banjo [ctb]", "Repository": "CRAN" }, - "ggpubr": { - "Package": "ggpubr", - "Version": "0.6.1", - "Source": "Repository", - "Type": "Package", - "Title": "'ggplot2' Based Publication Ready Plots", - "Date": "2025-06-27", - "Authors@R": "c( person(\"Alboukadel\", \"Kassambara\", role = c(\"aut\", \"cre\"), email = \"alboukadel.kassambara@gmail.com\"))", - "Description": "The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.", - "License": "GPL (>= 2)", - "LazyData": "TRUE", - "Encoding": "UTF-8", - "Depends": [ - "R (>= 3.1.0)", - "ggplot2 (>= 3.5.2)" - ], - "Imports": [ - "ggrepel (>= 0.9.2)", - "grid", - "ggsci", - "stats", - "utils", - "tidyr (>= 1.3.0)", - "purrr", - "dplyr (>= 0.7.1)", - "cowplot (>= 1.1.1)", - "ggsignif", - "scales", - "gridExtra", - "glue", - "polynom", - "rlang (>= 0.4.6)", - "rstatix (>= 0.7.2)", - "tibble", - "magrittr" - ], - "Suggests": [ - "grDevices", - "knitr", - "RColorBrewer", - "gtable", - "testthat" - ], - "URL": "https://rpkgs.datanovia.com/ggpubr/", - "BugReports": "https://github.com/kassambara/ggpubr/issues", - "RoxygenNote": "7.3.2", - "Collate": "'utilities_color.R' 'utilities_base.R' 'desc_statby.R' 'utilities.R' 'add_summary.R' 'annotate_figure.R' 'as_ggplot.R' 'as_npc.R' 'axis_scale.R' 'background_image.R' 'bgcolor.R' 'border.R' 'compare_means.R' 'create_aes.R' 'diff_express.R' 'facet.R' 'font.R' 'gene_citation.R' 'gene_expression.R' 'geom_bracket.R' 'geom_exec.R' 'utils-aes.R' 'utils_stat_test_label.R' 'geom_pwc.R' 'get_breaks.R' 'get_coord.R' 'get_legend.R' 'get_palette.R' 'ggadd.R' 'ggadjust_pvalue.R' 'ggarrange.R' 'ggballoonplot.R' 'ggpar.R' 'ggbarplot.R' 'ggboxplot.R' 'ggdensity.R' 'ggpie.R' 'ggdonutchart.R' 'stat_conf_ellipse.R' 'stat_chull.R' 'ggdotchart.R' 'ggdotplot.R' 'ggecdf.R' 'ggerrorplot.R' 'ggexport.R' 'gghistogram.R' 'ggline.R' 'ggmaplot.R' 'ggpaired.R' 'ggparagraph.R' 'ggpubr-package.R' 'ggpubr_args.R' 'ggpubr_options.R' 'ggqqplot.R' 'utilities_label.R' 'stat_cor.R' 'stat_stars.R' 'ggscatter.R' 'ggscatterhist.R' 'ggstripchart.R' 'ggsummarystats.R' 'ggtext.R' 'ggtexttable.R' 'ggviolin.R' 'gradient_color.R' 'grids.R' 'npc_to_data_coord.R' 'reexports.R' 'rotate.R' 'rotate_axis_text.R' 'rremove.R' 'set_palette.R' 'shared_docs.R' 'show_line_types.R' 'show_point_shapes.R' 'stat_anova_test.R' 'stat_central_tendency.R' 'stat_compare_means.R' 'stat_friedman_test.R' 'stat_kruskal_test.R' 'stat_mean.R' 'stat_overlay_normal_density.R' 'stat_pvalue_manual.R' 'stat_regline_equation.R' 'stat_welch_anova_test.R' 'text_grob.R' 'theme_pubr.R' 'theme_transparent.R' 'utils-geom-signif.R' 'utils-pipe.R' 'utils-tidyr.R'", - "NeedsCompilation": "no", - "Author": "Alboukadel Kassambara [aut, cre]", - "Maintainer": "Alboukadel Kassambara ", - "Repository": "CRAN" - }, "ggrepel": { "Package": "ggrepel", "Version": "0.9.6", @@ -1784,69 +1345,6 @@ "Maintainer": "Kamil Slowikowski ", "Repository": "CRAN" }, - "ggsci": { - "Package": "ggsci", - "Version": "3.2.0", - "Source": "Repository", - "Type": "Package", - "Title": "Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'", - "Authors@R": "c( person(\"Nan\", \"Xiao\", email = \"me@nanx.me\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0250-5673\")), person(\"Joshua\", \"Cook\", email = \"joshuacook0023@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Jégousse\", email = \"cat3@hi.is\", role = \"ctb\"), person(\"Hui\", \"Chen\", email = \"huichen@zju.edu.cn\", role = \"ctb\"), person(\"Miaozhu\", \"Li\", email = \"miaozhu.li@duke.edu\", role = \"ctb\") )", - "Maintainer": "Nan Xiao ", - "Description": "A collection of 'ggplot2' color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.", - "License": "GPL (>= 3)", - "URL": "https://nanx.me/ggsci/, https://github.com/nanxstats/ggsci", - "BugReports": "https://github.com/nanxstats/ggsci/issues", - "Depends": [ - "R (>= 3.5.0)" - ], - "Imports": [ - "ggplot2 (>= 2.0.0)", - "grDevices", - "scales" - ], - "Suggests": [ - "gridExtra", - "knitr", - "ragg", - "rmarkdown" - ], - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", - "NeedsCompilation": "no", - "Author": "Nan Xiao [aut, cre] (), Joshua Cook [ctb], Clara Jégousse [ctb], Hui Chen [ctb], Miaozhu Li [ctb]", - "Repository": "CRAN" - }, - "ggsignif": { - "Package": "ggsignif", - "Version": "0.6.4", - "Source": "Repository", - "Type": "Package", - "Title": "Significance Brackets for 'ggplot2'", - "Authors@R": "c( person(given = \"Constantin\", family = \"Ahlmann-Eltze\", role = c(\"aut\", \"cre\", \"ctb\"), email = \"artjom31415@googlemail.com\", comment = c(ORCID = \"0000-0002-3762-068X\", Twitter = \"@const_ae\")), person(given = \"Indrajeet\", family = \"Patil\", role = c(\"aut\", \"ctb\"), email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\", Twitter = \"@patilindrajeets\")) )", - "Description": "Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.", - "License": "GPL-3 | file LICENSE", - "URL": "https://const-ae.github.io/ggsignif/, https://github.com/const-ae/ggsignif", - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "Language": "en-US", - "Imports": [ - "ggplot2 (>= 3.3.5)" - ], - "Suggests": [ - "knitr", - "rmarkdown", - "testthat", - "vdiffr (>= 1.0.2)" - ], - "RoxygenNote": "7.2.1", - "Config/testthat/edition": "3", - "Config/testthat/parallel": "true", - "NeedsCompilation": "no", - "Author": "Constantin Ahlmann-Eltze [aut, cre, ctb] (, @const_ae), Indrajeet Patil [aut, ctb] (, @patilindrajeets)", - "Maintainer": "Constantin Ahlmann-Eltze ", - "Repository": "CRAN" - }, "glue": { "Package": "glue", "Version": "1.8.0", @@ -2099,6 +1597,64 @@ "Maintainer": "Carson Sievert ", "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": "CRAN" + }, "igraph": { "Package": "igraph", "Version": "2.1.4", @@ -2414,70 +1970,6 @@ "Maintainer": "Lionel Henry ", "Repository": "CRAN" }, - "lme4": { - "Package": "lme4", - "Version": "1.1-37", - "Source": "Repository", - "Title": "Linear Mixed-Effects Models using 'Eigen' and S4", - "Authors@R": "c( person(\"Douglas\",\"Bates\", role=\"aut\", comment=c(ORCID=\"0000-0001-8316-9503\")), person(\"Martin\",\"Maechler\", role=\"aut\", comment=c(ORCID=\"0000-0002-8685-9910\")), person(\"Ben\",\"Bolker\",email=\"bbolker+lme4@gmail.com\", role=c(\"aut\",\"cre\"), comment=c(ORCID=\"0000-0002-2127-0443\")), person(\"Steven\",\"Walker\",role=\"aut\", comment=c(ORCID=\"0000-0002-4394-9078\")), person(\"Rune Haubo Bojesen\",\"Christensen\", role=\"ctb\", comment=c(ORCID=\"0000-0002-4494-3399\")), person(\"Henrik\",\"Singmann\", role=\"ctb\", comment=c(ORCID=\"0000-0002-4842-3657\")), person(\"Bin\", \"Dai\", role=\"ctb\"), person(\"Fabian\", \"Scheipl\", role=\"ctb\", comment=c(ORCID=\"0000-0001-8172-3603\")), person(\"Gabor\", \"Grothendieck\", role=\"ctb\"), person(\"Peter\", \"Green\", role=\"ctb\", comment=c(ORCID=\"0000-0002-0238-9852\")), person(\"John\", \"Fox\", role=\"ctb\"), person(\"Alexander\", \"Bauer\", role=\"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role=c(\"ctb\",\"cph\"), comment=c(ORCID=\"0000-0002-9101-3362\", \"shared copyright on simulate.formula\")), person(\"Emi\", \"Tanaka\", role = \"ctb\", comment = c(ORCID=\"0000-0002-1455-259X\")), person(\"Mikael\", \"Jagan\", role = \"ctb\", comment = c(ORCID=\"0000-0002-3542-2938\")), person(\"Ross D.\", \"Boylan\", email=\"ross.boylan@ucsf.edu\", role=(\"ctb\"), comment = c(ORCID=\"0009-0003-4123-8090\")) )", - "Description": "Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' \"glue\".", - "Depends": [ - "R (>= 3.6.0)", - "Matrix", - "methods", - "stats" - ], - "LinkingTo": [ - "Rcpp (>= 0.10.5)", - "RcppEigen (>= 0.3.3.9.4)", - "Matrix (>= 1.2-3)" - ], - "Imports": [ - "graphics", - "grid", - "splines", - "utils", - "parallel", - "MASS", - "lattice", - "boot", - "nlme (>= 3.1-123)", - "minqa (>= 1.1.15)", - "nloptr (>= 1.0.4)", - "reformulas (>= 0.3.0)" - ], - "Suggests": [ - "knitr", - "rmarkdown", - "MEMSS", - "testthat (>= 0.8.1)", - "ggplot2", - "mlmRev", - "optimx (>= 2013.8.6)", - "gamm4", - "pbkrtest", - "HSAUR3", - "numDeriv", - "car", - "dfoptim", - "mgcv", - "statmod", - "rr2", - "semEff", - "tibble", - "merDeriv" - ], - "VignetteBuilder": "knitr", - "LazyData": "yes", - "License": "GPL (>= 2)", - "URL": "https://github.com/lme4/lme4/", - "BugReports": "https://github.com/lme4/lme4/issues", - "Encoding": "UTF-8", - "NeedsCompilation": "yes", - "Author": "Douglas Bates [aut] (), Martin Maechler [aut] (), Ben Bolker [aut, cre] (), Steven Walker [aut] (), Rune Haubo Bojesen Christensen [ctb] (), Henrik Singmann [ctb] (), Bin Dai [ctb], Fabian Scheipl [ctb] (), Gabor Grothendieck [ctb], Peter Green [ctb] (), John Fox [ctb], Alexander Bauer [ctb], Pavel N. Krivitsky [ctb, cph] (, shared copyright on simulate.formula), Emi Tanaka [ctb] (), Mikael Jagan [ctb] (), Ross D. Boylan [ctb] ()", - "Maintainer": "Ben Bolker ", - "Repository": "CRAN" - }, "lubridate": { "Package": "lubridate", "Version": "1.9.4", @@ -2618,35 +2110,6 @@ "Maintainer": "Simon Wood ", "Repository": "CRAN" }, - "microbenchmark": { - "Package": "microbenchmark", - "Version": "1.5.0", - "Source": "Repository", - "Title": "Accurate Timing Functions", - "Description": "Provides infrastructure to accurately measure and compare the execution time of R expressions.", - "Authors@R": "c(person(\"Olaf\", \"Mersmann\", role=c(\"aut\")), person(\"Claudia\", \"Beleites\", role=c(\"ctb\")), person(\"Rainer\", \"Hurling\", role=c(\"ctb\")), person(\"Ari\", \"Friedman\", role=c(\"ctb\")), person(given=c(\"Joshua\",\"M.\"), family=\"Ulrich\", role=\"cre\", email=\"josh.m.ulrich@gmail.com\"))", - "URL": "https://github.com/joshuaulrich/microbenchmark/", - "BugReports": "https://github.com/joshuaulrich/microbenchmark/issues/", - "License": "BSD_2_clause + file LICENSE", - "Depends": [ - "R (>= 3.2.0)" - ], - "Imports": [ - "graphics", - "stats" - ], - "Suggests": [ - "ggplot2", - "multcomp", - "RUnit" - ], - "SystemRequirements": "On a Unix-alike, one of the C functions mach_absolute_time (macOS), clock_gettime or gethrtime. If none of these is found, the obsolescent POSIX function gettimeofday will be tried.", - "ByteCompile": "yes", - "NeedsCompilation": "yes", - "Author": "Olaf Mersmann [aut], Claudia Beleites [ctb], Rainer Hurling [ctb], Ari Friedman [ctb], Joshua M. Ulrich [cre]", - "Maintainer": "Joshua M. Ulrich ", - "Repository": "CRAN" - }, "mime": { "Package": "mime", "Version": "0.13", @@ -2668,67 +2131,6 @@ "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, - "minqa": { - "Package": "minqa", - "Version": "1.2.8", - "Source": "Repository", - "Type": "Package", - "Title": "Derivative-Free Optimization Algorithms by Quadratic Approximation", - "Authors@R": "c(person(given = \"Douglas\", family = \"Bates\", role = \"aut\"), person(given = c(\"Katharine\", \"M.\"), family = \"Mullen\", role = c(\"aut\", \"cre\"), email = \"katharine.mullen@stat.ucla.edu\"), person(given = c(\"John\", \"C.\"), family = \"Nash\", role = \"aut\"), person(given = \"Ravi\", family = \"Varadhan\", role = \"aut\"))", - "Maintainer": "Katharine M. Mullen ", - "Description": "Derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.", - "License": "GPL-2", - "URL": "http://optimizer.r-forge.r-project.org", - "Imports": [ - "Rcpp (>= 0.9.10)" - ], - "LinkingTo": [ - "Rcpp" - ], - "SystemRequirements": "GNU make", - "NeedsCompilation": "yes", - "Repository": "CRAN", - "Author": "Douglas Bates [aut], Katharine M. Mullen [aut, cre], John C. Nash [aut], Ravi Varadhan [aut]" - }, - "modelr": { - "Package": "modelr", - "Version": "0.1.11", - "Source": "Repository", - "Title": "Modelling Functions that Work with the Pipe", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.", - "License": "GPL-3", - "URL": "https://modelr.tidyverse.org, https://github.com/tidyverse/modelr", - "BugReports": "https://github.com/tidyverse/modelr/issues", - "Depends": [ - "R (>= 3.2)" - ], - "Imports": [ - "broom", - "magrittr", - "purrr (>= 0.2.2)", - "rlang (>= 1.0.6)", - "tibble", - "tidyr (>= 0.8.0)", - "tidyselect", - "vctrs" - ], - "Suggests": [ - "compiler", - "covr", - "ggplot2", - "testthat (>= 3.0.0)" - ], - "Config/Needs/website": "tidyverse/tidytemplate", - "Encoding": "UTF-8", - "LazyData": "true", - "RoxygenNote": "7.2.3", - "Config/testthat/edition": "3", - "NeedsCompilation": "no", - "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]", - "Maintainer": "Hadley Wickham ", - "Repository": "CRAN" - }, "nlme": { "Package": "nlme", "Version": "3.1-168", @@ -2763,112 +2165,37 @@ "Maintainer": "R Core Team ", "Repository": "CRAN" }, - "nloptr": { - "Package": "nloptr", - "Version": "2.2.1", + "openssl": { + "Package": "openssl", + "Version": "2.3.3", "Source": "Repository", "Type": "Package", - "Title": "R Interface to NLopt", - "Authors@R": "c(person(\"Jelmer\", \"Ypma\", role = \"aut\", email = \"uctpjyy@ucl.ac.uk\"), person(c(\"Steven\", \"G.\"), \"Johnson\", role = \"aut\", comment = \"author of the NLopt C library\"), person(\"Aymeric\", \"Stamm\", role = c(\"ctb\", \"cre\"), email = \"aymeric.stamm@cnrs.fr\", comment = c(ORCID = \"0000-0002-8725-3654\")), person(c(\"Hans\", \"W.\"), \"Borchers\", role = \"ctb\", email = \"hwborchers@googlemail.com\"), person(\"Dirk\", \"Eddelbuettel\", role = \"ctb\", email = \"edd@debian.org\"), person(\"Brian\", \"Ripley\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Kurt\", \"Hornik\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Julien\", \"Chiquet\", role = \"ctb\"), person(\"Avraham\", \"Adler\", role = \"ctb\", email = \"Avraham.Adler@gmail.com\", comment = c(ORCID = \"0000-0002-3039-0703\")), person(\"Xiongtao\", \"Dai\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\", email = \"jeroen@berkeley.edu\"), person(\"Tomas\", \"Kalibera\", role = \"ctb\"), person(\"Mikael\", \"Jagan\", role = \"ctb\"))", - "Description": "Solve optimization problems using an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See for more information on the available algorithms. Building from included sources requires 'CMake'. On Linux and 'macOS', if a suitable system build of NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from included sources via 'CMake'. On Windows, NLopt is obtained through 'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for 'R >= 4.2.0'.", - "License": "LGPL (>= 3)", - "SystemRequirements": "cmake (>= 3.2.0) which is used only on Linux or macOS systems when no system build of nlopt (>= 2.7.0) can be found.", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "Suggests": [ - "knitr", - "rmarkdown", - "covr", - "tinytest" - ], - "VignetteBuilder": "knitr", - "URL": "https://github.com/astamm/nloptr, https://astamm.github.io/nloptr/", - "BugReports": "https://github.com/astamm/nloptr/issues", - "NeedsCompilation": "yes", - "UseLTO": "yes", - "Author": "Jelmer Ypma [aut], Steven G. Johnson [aut] (author of the NLopt C library), Aymeric Stamm [ctb, cre] (), Hans W. Borchers [ctb], Dirk Eddelbuettel [ctb], Brian Ripley [ctb] (build process on multiple OS), Kurt Hornik [ctb] (build process on multiple OS), Julien Chiquet [ctb], Avraham Adler [ctb] (), Xiongtao Dai [ctb], Jeroen Ooms [ctb], Tomas Kalibera [ctb], Mikael Jagan [ctb]", - "Maintainer": "Aymeric Stamm ", - "Repository": "CRAN" - }, - "nnet": { - "Package": "nnet", - "Version": "7.3-20", - "Source": "Repository", - "Priority": "recommended", - "Date": "2025-01-01", - "Depends": [ - "R (>= 3.0.0)", - "stats", - "utils" - ], - "Suggests": [ - "MASS" - ], - "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Brian.Ripley@R-project.org\"), person(\"William\", \"Venables\", role = \"cph\"))", - "Description": "Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.", - "Title": "Feed-Forward Neural Networks and Multinomial Log-Linear Models", - "ByteCompile": "yes", - "License": "GPL-2 | GPL-3", - "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", - "NeedsCompilation": "yes", - "Author": "Brian Ripley [aut, cre, cph], William Venables [cph]", - "Maintainer": "Brian Ripley ", - "Repository": "CRAN" - }, - "numDeriv": { - "Package": "numDeriv", - "Version": "2016.8-1.1", - "Source": "Repository", - "Title": "Accurate Numerical Derivatives", - "Description": "Methods for calculating (usually) accurate numerical first and second order derivatives. Accurate calculations are done using 'Richardson''s' extrapolation or, when applicable, a complex step derivative is available. A simple difference method is also provided. Simple difference is (usually) less accurate but is much quicker than 'Richardson''s' extrapolation and provides a useful cross-check. Methods are provided for real scalar and vector valued functions.", - "Depends": [ - "R (>= 2.11.1)" - ], - "LazyLoad": "yes", - "ByteCompile": "yes", - "License": "GPL-2", - "Copyright": "2006-2011, Bank of Canada. 2012-2016, Paul Gilbert", - "Author": "Paul Gilbert and Ravi Varadhan", - "Maintainer": "Paul Gilbert ", - "URL": "http://optimizer.r-forge.r-project.org/", - "NeedsCompilation": "no", - "Repository": "CRAN" - }, - "pbkrtest": { - "Package": "pbkrtest", - "Version": "0.5.5", - "Source": "Repository", - "Title": "Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models", - "Authors@R": "c( person(given = \"Ulrich\", family = \"Halekoh\", email = \"uhalekoh@health.sdu.dk\", role = c(\"aut\", \"cph\")), person(given = \"Søren\", family = \"Højsgaard\", email = \"sorenh@math.aau.dk\", role = c(\"aut\", \"cre\", \"cph\")) )", - "Maintainer": "Søren Højsgaard ", - "Description": "Computes p-values based on (a) Satterthwaite or Kenward-Rogers degree of freedom methods and (b) parametric bootstrap for mixed effects models as implemented in the 'lme4' package. Implements parametric bootstrap test for generalized linear mixed models as implemented in 'lme4' and generalized linear models. The package is documented in the paper by Halekoh and Højsgaard, (2012, ). Please see 'citation(\"pbkrtest\")' for citation details.", - "URL": "https://people.math.aau.dk/~sorenh/software/pbkrtest/", - "Depends": [ - "R (>= 4.2.0)", - "lme4 (>= 1.1.31)" - ], - "Imports": [ - "broom", - "dplyr", - "MASS", - "methods", - "numDeriv", - "Matrix (>= 1.2.3)", - "doBy (>= 4.6.22)" - ], - "Suggests": [ - "nlme", - "markdown", - "knitr" - ], - "Encoding": "UTF-8", + "Title": "Toolkit for Encryption, Signatures and Certificates Based on OpenSSL", + "Authors@R": "c(person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Oliver\", \"Keyes\", role = \"ctb\"))", + "Description": "Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. 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", - "License": "GPL (>= 2)", - "ByteCompile": "Yes", + "Imports": [ + "askpass" + ], + "Suggests": [ + "curl", + "testthat (>= 2.1.0)", + "digest", + "knitr", + "rmarkdown", + "jsonlite", + "jose", + "sodium" + ], "RoxygenNote": "7.3.2", - "LazyData": "true", - "NeedsCompilation": "no", - "Author": "Ulrich Halekoh [aut, cph], Søren Højsgaard [aut, cre, cph]", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Oliver Keyes [ctb]", + "Maintainer": "Jeroen Ooms ", "Repository": "CRAN" }, "pillar": { @@ -2991,6 +2318,75 @@ "NeedsCompilation": "no", "Repository": "CRAN" }, + "pkgdown": { + "Package": "pkgdown", + "Version": "2.1.3", + "Source": "Repository", + "Title": "Make Static HTML Documentation for a Package", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jay\", \"Hesselberth\", role = \"aut\", comment = c(ORCID = \"0000-0002-6299-179X\")), person(\"Maëlle\", \"Salmon\", role = \"aut\", comment = c(ORCID = \"0000-0002-2815-0399\")), person(\"Olivier\", \"Roy\", role = \"aut\"), person(\"Salim\", \"Brüggemann\", role = \"aut\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.", + "License": "MIT + file LICENSE", + "URL": "https://pkgdown.r-lib.org/, https://github.com/r-lib/pkgdown", + "BugReports": "https://github.com/r-lib/pkgdown/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Imports": [ + "bslib (>= 0.5.1)", + "callr (>= 3.7.3)", + "cli (>= 3.6.1)", + "desc (>= 1.4.0)", + "downlit (>= 0.4.4)", + "fontawesome", + "fs (>= 1.4.0)", + "httr2 (>= 1.0.2)", + "jsonlite", + "openssl", + "purrr (>= 1.0.0)", + "ragg (>= 1.4.0)", + "rlang (>= 1.1.4)", + "rmarkdown (>= 2.27)", + "tibble", + "whisker", + "withr (>= 2.4.3)", + "xml2 (>= 1.3.1)", + "yaml" + ], + "Suggests": [ + "covr", + "diffviewer", + "evaluate (>= 0.24.0)", + "gert", + "gt", + "htmltools", + "htmlwidgets", + "knitr (>= 1.50)", + "lifecycle", + "magick", + "methods", + "pkgload (>= 1.0.2)", + "quarto", + "rsconnect", + "rstudioapi", + "rticles", + "sass", + "testthat (>= 3.1.3)", + "tools" + ], + "VignetteBuilder": "knitr, quarto", + "Config/Needs/website": "usethis, servr", + "Config/potools/style": "explicit", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/testthat/start-first": "build-article, build-quarto-article, build-reference", + "Encoding": "UTF-8", + "SystemRequirements": "pandoc", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre] (ORCID: ), Jay Hesselberth [aut] (ORCID: ), Maëlle Salmon [aut] (ORCID: ), Olivier Roy [aut], Salim Brüggemann [aut] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, "pkgload": { "Package": "pkgload", "Version": "1.4.0", @@ -3267,43 +2663,41 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "quantreg": { - "Package": "quantreg", - "Version": "6.1", + "ragg": { + "Package": "ragg", + "Version": "1.4.0", "Source": "Repository", - "Title": "Quantile Regression", - "Description": "Estimation and inference methods for models for conditional quantile functions: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press, and Koenker, R. et al. (2017) Handbook of Quantile Regression, CRC Press, .", - "Authors@R": "c( person(\"Roger\", \"Koenker\", role = c(\"cre\",\"aut\"), email = \"rkoenker@illinois.edu\"), person(\"Stephen\", \"Portnoy\", role = c(\"ctb\"), comment = \"Contributions to Censored QR code\", email = \"sportnoy@illinois.edu\"), person(c(\"Pin\", \"Tian\"), \"Ng\", role = c(\"ctb\"), comment = \"Contributions to Sparse QR code\", email = \"pin.ng@nau.edu\"), person(\"Blaise\", \"Melly\", role = c(\"ctb\"), comment = \"Contributions to preprocessing code\", email = \"mellyblaise@gmail.com\"), person(\"Achim\", \"Zeileis\", role = c(\"ctb\"), comment = \"Contributions to dynrq code essentially identical to his dynlm code\", email = \"Achim.Zeileis@uibk.ac.at\"), person(\"Philip\", \"Grosjean\", role = c(\"ctb\"), comment = \"Contributions to nlrq code\", email = \"phgrosjean@sciviews.org\"), person(\"Cleve\", \"Moler\", role = c(\"ctb\"), comment = \"author of several linpack routines\"), person(\"Yousef\", \"Saad\", role = c(\"ctb\"), comment = \"author of sparskit2\"), person(\"Victor\", \"Chernozhukov\", role = c(\"ctb\"), comment = \"contributions to extreme value inference code\"), person(\"Ivan\", \"Fernandez-Val\", role = c(\"ctb\"), comment = \"contributions to extreme value inference code\"), person(\"Martin\", \"Maechler\", role = \"ctb\", comment = c(\"tweaks (src/chlfct.f, 'tiny','Large')\", ORCID = \"0000-0002-8685-9910\")), person(c(\"Brian\", \"D\"), \"Ripley\", role = c(\"trl\",\"ctb\"), comment = \"Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice\", email = \"ripley@stats.ox.ac.uk\"))", - "Maintainer": "Roger Koenker ", - "Repository": "CRAN", - "Depends": [ - "R (>= 3.5)", - "stats", - "SparseM" - ], + "Type": "Package", + "Title": "Graphic Devices Based on AGG", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Maxim\", \"Shemanarev\", role = c(\"aut\", \"cph\"), comment = \"Author of AGG\"), person(\"Tony\", \"Juricic\", , \"tonygeek@yahoo.com\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Milan\", \"Marusinec\", , \"milan@marusinec.sk\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Spencer\", \"Garrett\", role = \"ctb\", comment = \"Contributor to AGG\"), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Maintainer": "Thomas Lin Pedersen ", + "Description": "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The 'ragg' package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://ragg.r-lib.org, https://github.com/r-lib/ragg", + "BugReports": "https://github.com/r-lib/ragg/issues", "Imports": [ - "methods", - "graphics", - "Matrix", - "MatrixModels", - "survival", - "MASS" + "systemfonts (>= 1.0.3)", + "textshaping (>= 0.3.0)" ], "Suggests": [ - "interp", - "rgl", - "logspline", - "nor1mix", - "Formula", - "zoo", - "R.rsp", - "conquer" + "covr", + "graphics", + "grid", + "testthat (>= 3.0.0)" ], - "License": "GPL (>= 2)", - "URL": "https://www.r-project.org", + "LinkingTo": [ + "systemfonts", + "textshaping" + ], + "Config/Needs/website": "ggplot2, devoid, magick, bench, tidyr, ggridges, hexbin, sessioninfo, pkgdown, tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "freetype2, libpng, libtiff, libjpeg", + "Config/testthat/edition": "3", + "Config/build/compilation-database": "true", "NeedsCompilation": "yes", - "VignetteBuilder": "R.rsp", - "Author": "Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Blaise Melly [ctb] (Contributions to preprocessing code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Cleve Moler [ctb] (author of several linpack routines), Yousef Saad [ctb] (author of sparskit2), Victor Chernozhukov [ctb] (contributions to extreme value inference code), Ivan Fernandez-Val [ctb] (contributions to extreme value inference code), Martin Maechler [ctb] (tweaks (src/chlfct.f, 'tiny','Large'), ), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)" + "Author": "Thomas Lin Pedersen [cre, aut] (), Maxim Shemanarev [aut, cph] (Author of AGG), Tony Juricic [ctb, cph] (Contributor to AGG), Milan Marusinec [ctb, cph] (Contributor to AGG), Spencer Garrett [ctb] (Contributor to AGG), Posit, PBC [cph, fnd]", + "Repository": "CRAN" }, "rappdirs": { "Package": "rappdirs", @@ -3334,34 +2728,6 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "rbibutils": { - "Package": "rbibutils", - "Version": "2.3", - "Source": "Repository", - "Type": "Package", - "Title": "Read 'Bibtex' Files and Convert Between Bibliography Formats", - "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), \t email = \"georgi.boshnakov@manchester.ac.uk\", comment = \"R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)\" ), person(given = \"Chris\", family = \"Putman\", role = \"aut\", comment = \"src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/\"), person(given = \"Richard\", family = \"Mathar\", role = \"ctb\", comment = \"src/addsout.c\"), person(given = \"Johannes\", family = \"Wilm\", role = \"ctb\", comment = \"src/biblatexin.c, src/bltypes.c\"), person(\"R Core Team\", role = \"ctb\", comment = \"base R's bibentry and bibstyle implementation\") )", - "Description": "Read and write 'Bibtex' files. Convert between bibliography formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam . Supports all bibliography formats and character encodings implemented in 'bibutils'.", - "License": "GPL-2", - "URL": "https://geobosh.github.io/rbibutils/ (doc), https://github.com/GeoBosh/rbibutils (devel)", - "BugReports": "https://github.com/GeoBosh/rbibutils/issues", - "Depends": [ - "R (>= 2.10)" - ], - "Imports": [ - "utils", - "tools" - ], - "Suggests": [ - "testthat" - ], - "Encoding": "UTF-8", - "NeedsCompilation": "yes", - "Config/Needs/memcheck": "devtools, rcmdcheck", - "Author": "Georgi N. Boshnakov [aut, cre] (R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)), Chris Putman [aut] (src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/), Richard Mathar [ctb] (src/addsout.c), Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c), R Core Team [ctb] (base R's bibentry and bibstyle implementation)", - "Maintainer": "Georgi N. Boshnakov ", - "Repository": "CRAN" - }, "readr": { "Package": "readr", "Version": "2.1.5", @@ -3418,34 +2784,6 @@ "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, - "reformulas": { - "Package": "reformulas", - "Version": "0.4.1", - "Source": "Repository", - "Title": "Machinery for Processing Random Effect Formulas", - "Authors@R": "person(given = \"Ben\", family = \"Bolker\", role = c(\"aut\", \"cre\"), email = \"bolker@mcmaster.ca\", comment=c(ORCID=\"0000-0002-2127-0443\"))", - "Description": "Takes formulas including random-effects components (formatted as in 'lme4', 'glmmTMB', etc.) and processes them. Includes various helper functions.", - "URL": "https://github.com/bbolker/reformulas", - "License": "GPL-3", - "Encoding": "UTF-8", - "Imports": [ - "stats", - "methods", - "Matrix", - "Rdpack" - ], - "RdMacros": "Rdpack", - "Suggests": [ - "lme4", - "tinytest", - "glmmTMB" - ], - "RoxygenNote": "7.3.2.9000", - "NeedsCompilation": "no", - "Author": "Ben Bolker [aut, cre] (ORCID: )", - "Maintainer": "Ben Bolker ", - "Repository": "CRAN" - }, "renv": { "Package": "renv", "Version": "1.1.5", @@ -3641,55 +2979,6 @@ "Maintainer": "Kirill Müller ", "Repository": "CRAN" }, - "rstatix": { - "Package": "rstatix", - "Version": "0.7.2", - "Source": "Repository", - "Type": "Package", - "Title": "Pipe-Friendly Framework for Basic Statistical Tests", - "Authors@R": "c( person(\"Alboukadel\", \"Kassambara\", role = c(\"aut\", \"cre\"), email = \"alboukadel.kassambara@gmail.com\"))", - "Description": "Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy, for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. The output of each test is automatically transformed into a tidy data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs (repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs. It's also possible to compute several effect size metrics, including \"eta squared\" for ANOVA, \"Cohen's d\" for t-test and 'Cramer V' for the association between categorical variables. The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.", - "License": "GPL-2", - "Encoding": "UTF-8", - "Depends": [ - "R (>= 3.3.0)" - ], - "Imports": [ - "stats", - "utils", - "tidyr (>= 1.0.0)", - "purrr", - "broom (>= 0.7.4)", - "rlang (>= 0.3.1)", - "tibble (>= 2.1.3)", - "dplyr (>= 0.7.1)", - "magrittr", - "corrplot", - "tidyselect (>= 1.2.0)", - "car", - "generics (>= 0.0.2)" - ], - "Suggests": [ - "knitr", - "rmarkdown", - "ggpubr", - "graphics", - "emmeans", - "coin", - "boot", - "testthat", - "spelling" - ], - "URL": "https://rpkgs.datanovia.com/rstatix/", - "BugReports": "https://github.com/kassambara/rstatix/issues", - "RoxygenNote": "7.2.3", - "Collate": "'utilities.R' 'add_significance.R' 'adjust_pvalue.R' 'factorial_design.R' 'utilities_two_sample_test.R' 'anova_summary.R' 'anova_test.R' 'as_cor_mat.R' 'binom_test.R' 'box_m.R' 'chisq_test.R' 'cochran_qtest.R' 'cohens_d.R' 'cor_as_symbols.R' 'replace_triangle.R' 'pull_triangle.R' 'cor_mark_significant.R' 'cor_mat.R' 'cor_plot.R' 'cor_reorder.R' 'cor_reshape.R' 'cor_select.R' 'cor_test.R' 'counts_to_cases.R' 'cramer_v.R' 'df.R' 'doo.R' 't_test.R' 'dunn_test.R' 'emmeans_test.R' 'eta_squared.R' 'factors.R' 'fisher_test.R' 'freq_table.R' 'friedman_test.R' 'friedman_effsize.R' 'games_howell_test.R' 'get_comparisons.R' 'get_manova_table.R' 'get_mode.R' 'get_pvalue_position.R' 'get_summary_stats.R' 'get_test_label.R' 'kruskal_effesize.R' 'kruskal_test.R' 'levene_test.R' 'mahalanobis_distance.R' 'make_clean_names.R' 'mcnemar_test.R' 'multinom_test.R' 'outliers.R' 'p_value.R' 'prop_test.R' 'prop_trend_test.R' 'reexports.R' 'remove_ns.R' 'sample_n_by.R' 'shapiro_test.R' 'sign_test.R' 'tukey_hsd.R' 'utils-manova.R' 'utils-pipe.R' 'welch_anova_test.R' 'wilcox_effsize.R' 'wilcox_test.R'", - "Language": "en-US", - "NeedsCompilation": "no", - "Author": "Alboukadel Kassambara [aut, cre]", - "Maintainer": "Alboukadel Kassambara ", - "Repository": "CRAN" - }, "rstudioapi": { "Package": "rstudioapi", "Version": "0.17.1", @@ -3869,34 +3158,73 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "survival": { - "Package": "survival", - "Version": "3.8-3", + "sys": { + "Package": "sys", + "Version": "3.4.3", "Source": "Repository", - "Title": "Survival Analysis", - "Priority": "recommended", - "Date": "2024-12-17", + "Type": "Package", + "Title": "Powerful and Reliable Tools for Running System Commands in R", + "Authors@R": "c(person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = \"ctb\"))", + "Description": "Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. 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": "CRAN" + }, + "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 (>= 3.5.0)" + "R (>= 3.2.0)" ], "Imports": [ - "graphics", - "Matrix", - "methods", - "splines", - "stats", + "base64enc", + "grid", + "jsonlite", + "lifecycle", + "tools", "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", + "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": "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 ", + "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": "CRAN" }, "testthat": { @@ -3958,6 +3286,50 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, + "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": "CRAN" + }, "tibble": { "Package": "tibble", "Version": "3.3.0", @@ -4456,6 +3828,25 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, + "whisker": { + "Package": "whisker", + "Version": "0.4.1", + "Source": "Repository", + "Maintainer": "Edwin de Jonge ", + "License": "GPL-3", + "Title": "{{mustache}} for R, Logicless Templating", + "Type": "Package", + "LazyLoad": "yes", + "Author": "Edwin de Jonge", + "Description": "Implements 'Mustache' logicless templating.", + "URL": "https://github.com/edwindj/whisker", + "Suggests": [ + "markdown" + ], + "RoxygenNote": "6.1.1", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, "withr": { "Package": "withr", "Version": "3.0.2", @@ -4542,6 +3933,47 @@ "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, + "xml2": { + "Package": "xml2", + "Version": "1.4.0", + "Source": "Repository", + "Title": "Parse XML", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", email = \"jeroenooms@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"R Foundation\", role = \"ctb\", comment = \"Copy of R-project homepage cached as example\") )", + "Description": "Bindings to 'libxml2' for working with XML data using a simple, consistent interface based on 'XPath' expressions. Also supports XML schema validation; for 'XSLT' transformations see the 'xslt' package.", + "License": "MIT + file LICENSE", + "URL": "https://xml2.r-lib.org, https://r-lib.r-universe.dev/xml2", + "BugReports": "https://github.com/r-lib/xml2/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "cli", + "methods", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "curl", + "httr", + "knitr", + "magrittr", + "mockery", + "rmarkdown", + "testthat (>= 3.2.0)", + "xslt" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "libxml2: libxml2-dev (deb), libxml2-devel (rpm)", + "Collate": "'S4.R' 'as_list.R' 'xml_parse.R' 'as_xml_document.R' 'classes.R' 'format.R' 'import-standalone-obj-type.R' 'import-standalone-purrr.R' 'import-standalone-types-check.R' 'init.R' 'nodeset_apply.R' 'paths.R' 'utils.R' 'xml2-package.R' 'xml_attr.R' 'xml_children.R' 'xml_document.R' 'xml_find.R' 'xml_missing.R' 'xml_modify.R' 'xml_name.R' 'xml_namespaces.R' 'xml_node.R' 'xml_nodeset.R' 'xml_path.R' 'xml_schema.R' 'xml_serialize.R' 'xml_structure.R' 'xml_text.R' 'xml_type.R' 'xml_url.R' 'xml_write.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Jeroen Ooms [aut, cre], Posit Software, PBC [cph, fnd], R Foundation [ctb] (Copy of R-project homepage cached as example)", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, "xts": { "Package": "xts", "Version": "0.14.1", diff --git a/vignettes/stable-shift-algorithm.Rmd b/vignettes/stable-shift-algorithm.Rmd index daf76fa..42b2f0f 100644 --- a/vignettes/stable-shift-algorithm.Rmd +++ b/vignettes/stable-shift-algorithm.Rmd @@ -1,9 +1,13 @@ --- title: "The Stable Shift Algorithm" output: - rmarkdown::html_vignette: + bookdown::html_document2: + base_format: rmarkdown::html_vignette + fig_caption: yes toc: true number_sections: true +pkgdown: + as_is: true vignette: > %\VignetteIndexEntry{The Stable Shift Algorithm} %\VignetteEngine{knitr::rmarkdown} @@ -29,7 +33,10 @@ library(DiagrammeR) The *autospc* package implements the *Stable Shift Algorithm* for re-establishing control limits in statistical process control (SPC) analysis. This vignette describes the problem the algorithm addresses, sets out some -useful terminology, and describes the algorithm. +useful terminology, describes the algorithm, and explains how to use the +algorithm log. +\ +\ # The problem @@ -42,9 +49,11 @@ A standard approach in SPC analysis for quality improvement goes as follows: 2. Extend the baseline limits into the future 3. Add data to the chart as time progresses, without updating the control limits -This is exemplified in the following three charts. +An example is shown in Figure \@ref(fig:extending-limits). This uses the +`ed_attendances_monthly` dataset included with `autospc`. For more information +on this dataset see `?ed_attendances_monthly`. -```{r 2.0, fig.width=7, fig.height=9} +```{r extending-limits, fig.width=7, fig.height=7, fig.cap="Extending baseline control limits"} facet_stages( ed_attendances_monthly %>% filter(row_number() <= 32L), @@ -70,13 +79,18 @@ the new process. Whilst various textbooks and online resources offer opinions on this issue, there is no universally accepted approach. The Stable Shift Algorithm (SSA) offers an automated, consistent and rigorous approach to re-establishing control limits. +\ +\ -# The Stable Shift Algorithm: Overview +# The Stable Shift Algorithm + +## Overview The main idea of the SSA is to only re-establish limits where: -1. There is evidence that the process has shifted to a new level -2. This shift persists for long enough to compute new control limits +A. There is evidence that the process has shifted to a new level + +B. This shift persists for long enough to compute new control limits In other words, the SSA re-establishes limits at shift rule breaks, provided that the shift is not "transient" in some sense. Here "transient" means that @@ -84,55 +98,158 @@ once we calculate the new control limits, there is not a shift rule break back towards the original process. In the next two sections we make this idea precise and describe how it is operationalised in the SSA. -# Some terminology +## Some terminology + +First, it is useful to introduce some terminology. We will refer to Figure +\@ref(fig:example-1) to illustrate the concepts introduced in this section. This +figure shows a C-chart for the first 35 data points of the simulated +`example_series_2a` data included with `autospc`, which for the purpose of this +section we shall interpret as daily values of a count measure of interest. -First, it is useful to introduce some terminology. +```{r example-1, fig.width=7, fig.height=5, fig.cap="Example 1"} +plot_auto_SPC(example_series_2a %>% + filter(row_number() <= 35L), + override_y_title = "Count", + chartType = "C", + extend_limits_to = 47L) +``` -## Calculation and display periods -## Rule-breaking run -A *rule-breaking run* is a run whose length is greater than or equal to the -threshold for a rule break (`runRuleLength`), set to $8$ by default in -`plot_auto_SPC()`. +### Calculation and display periods + +The data used to calculate a set of control limits comes from a contiguous +period of time, with the possible exception of some excluded points. This period +of time is referred to as the *calculation period* of the limits. -Runs that are subsets of longer runs count here, so for example with the default -`runRuleLength = 8`, a run of length 10 actually comprises three rule-breaking -runs, commencing at the first, second and third points in the length 10 run. -In this example, the first rule-breaking run has length 10, the second 9, and -the third 8. The run that commences on the fourth point of the length 10 run is -not rule-breaking, since it is of length 7 only. +When the limits are extended into the future, beyond their calculation period, +the period over which they are extended is referred to as the *display period*. -## Triggering rule break -In the SSA, a rule breaking run can trigger consideration of whether to -re-establish limits. Such a run is referred to as a *triggering rule break*. +In charts produced by *autospc*, limits are displayed as black dashed lines over +their calculation period, and grey dashed lines over their display period. For +example, in \@ref(fig:example-1), there is one calculation period, covering +days 1 to 21 inclusive, extended into its display period covering day 22 +onwards. -## Candidate limits +### Rule-breaking run +A *rule-breaking run* is a run whose length is greater than or equal to the +threshold for a shift rule break (`runRuleLength`), set to $8$ by default in +`plot_auto_SPC()`. In \@ref(fig:example-1), there is a rule-breaking run of +length 10 starting on day 22. By default, rule-breaking runs are highlighted in +blue by `autospc`. + +Runs that are subsets of longer runs with the same end point count here, so for +example with the default `runRuleLength = 8`, the run of length 10 in +\@ref(fig:example-1) actually comprises three rule-breaking runs, commencing at +the first, second and third points in the length 10 run. In this example, the +first rule-breaking run starts on day 22 and has length 10, the second starts on +day 23 and has length 9, and the third starts on day 24 and has length 8. The +run that commences on day 25, the fourth point of the length 10 run, is not +rule-breaking, since it is of length 7 only. + +### Triggering rule break +In the SSA, a rule-breaking run commencing during a display period triggers +consideration of whether to re-establish limits. Such a run is referred to as a +*triggering rule break*. + +In \@ref(fig:example-1) the highlighted rule-breaking run is a triggering rule +break. + +### Candidate limits In order to decide whether to re-establish control limits at a triggering rule -break, the -SSA requires consideration of the set of limits that _would_ be established. -These are referred to as *candidate limits* until they are either rejected or -accepted. Candidate limits are formed from the first `periodMin` points starting -at the first point of the triggering rule break, and this period is referred to -as the *candidate calculation period*. - -## Opposing rule break +break, the SSA requires consideration of the set of limits that _would_ be +established. These are referred to as *candidate limits* until they are either +rejected or accepted. Candidate limits are formed from the first `periodMin` +points starting at the first point of the triggering rule break, and this +period is referred to as the *candidate calculation period*. + +In Figure \@ref(fig:example-1), there are fewer than `periodMin` (here 21) +points on or after the start of the triggering rule break (day 22), so it is not +possible to re-establish limits at day 22, and there are no candidate limits to +consider. + +In Figure \@ref(fig:example-2) we imagine rolling time forward, so that we have +more data to add to the chart in \@ref(fig:example-1). Figure +\@ref(fig:example-2) shows the data against the (baseline) calculation limits. +Figure \@ref(fig:example-3) shows candidate limits established at the start of +the triggering rule break, i.e. day 22. + +```{r example-2, fig.width=7, fig.height=5, fig.cap="Example 2"} +plot_auto_SPC(example_series_2a, + override_y_title = "Count", + chartType = "C", + noRecals = TRUE, + extend_limits_to = 47L) +``` + +```{r example-3, fig.width=7, fig.height=5, fig.cap="Example 3"} +plot_auto_SPC(example_series_2a, + override_y_title = "Count", + chartType = "C", + extend_limits_to = 47L) +``` + +### Opposing rule break If there is a rule break within the candidate calculation period, and that rule break is in the opposite direction to the triggering rule break, it is referred to as an *opposing rule break*. We also sometimes refer to such a rule break as -a *reversion*, as in reverting to the original limits. If the rule break only -reaches the `runRuleLength` threshold after the end of the candidate calculation -period, it is referred to as an *overhanging reversion*. +a *reversion*, as in reverting to the original limits. + +In Figure \@ref(fig:example-3) there is no opposing rule break within the +candidate calculation period. Figure \@ref(fig:example-4) shows an alternative +continuation of the baseline time series we have considered so far. This series +is identical to the first up to day 26, and differs thereafter. There is still +a triggering rule break against the baseline limits commencing at day 22. Figure +\@ref(fig:example-5) shows candidate limits established from the start of this +triggering rule break, i.e. from day 22. There is an opposing rule break in +Figure \@ref(fig:example-5), commencing on day 31. + +```{r example-4, fig.width=7, fig.height=5, fig.cap="Example 4"} +plot_auto_SPC(example_series_2b, + override_y_title = "Count", + chartType = "C", + noRecals = TRUE, + extend_limits_to = 47L) +``` + +```{r example-5, fig.width=7, fig.height=5, fig.cap="Example 5"} +plot_auto_SPC(example_series_2b, + override_y_title = "Count", + chartType = "C", + recalEveryShift = TRUE, + extend_limits_to = 47L) +``` + + +If an opposing rule break only reaches the `runRuleLength` threshold after the +end of the candidate calculation period, it is referred to as an +*overhanging reversion*. Figure \@ref(fig:example-6) shows another alternative +continuation of our example time series, this time showing an +overhanging reversion commencing on day 40, against the candidate limits. -## Minimum period length +```{r example-6, fig.width=7, fig.height=5, fig.cap="Example 6"} +plot_auto_SPC(example_series_2c, + override_y_title = "Count", + chartType = "C", + recalEveryShift = TRUE) +``` + +### Minimum period length The SSA requires specification of a minimum number of data points to be used for calculation of control limits, $n_{min}$. Whilst those using SPC in practice may not often make such a minimum explicit, in a way it is always there implicitly - nobody would compute control limits from two data points would they? In fact, various authors offer guidance on what such a minimum should be, -with values ranging from 17 to 25 points. In `plot_auto_SPC()`, $n_{min}$ is -specified by the `periodMin` argument, defaulting to 21. +with values ranging from 17 to 25 points. + +In `plot_auto_SPC()`, $n_{min}$ is specified by the `periodMin` argument, +defaulting to 21. This default is above the commonly recommended minimum values +and represents a convenient choice for daily data, since it is a multiple of 7. +This means that in the presence of weekly "seasonal" (periodic) variation over +the 7 day period the limits are not unduly affected by which day of the week the +limit calculation period begins on. When using monthly data, it is preferable to +use $n_{min} = 24$, for the same reason. -# The Stable Shift Algorithm: Details +## Details of the algorithm The steps of the algorithm are as follows: @@ -168,7 +285,7 @@ points beginning at the counter. 7. Decide whether to accept or reject the candidate limits: - i. If there at least one opposing rule break commencing within the candidate + i. If there is at least one opposing rule break commencing within the candidate calculation period, then the candidate limits are rejected, the counter is set to the next rule-breaking run (after the triggering rule break) against the prevailing limits, and the algorithm continues from (3). @@ -190,7 +307,7 @@ The algorithm is visualised in the flow chart below. ```{r 5.1, fig.width=7, fig.height=7} grViz(autospc:::algorithm_flow_chart_string) ``` - +\ # Using the algorithm log @@ -211,7 +328,8 @@ plot_auto_SPC( y = Att_All, verbosity = 1, x_break = 365, - x_date_format = "%Y-%b" + x_date_format = "%Y-%b", + point_size = 1L ) ```