diff --git a/renv/activate.R b/renv/activate.R index c9f59425..90b251ca 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.1.2" + version <- "1.1.4" attr(version, "sha") <- NULL # the project directory @@ -695,11 +695,19 @@ local({ } - renv_bootstrap_platform_prefix <- function() { + renv_bootstrap_platform_prefix_default <- function() { - # construct version prefix - version <- paste(R.version$major, R.version$minor, sep = ".") - prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + # read version component + version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v") + + # expand placeholders + placeholders <- list( + list("%v", format(getRversion()[1, 1:2])), + list("%V", format(getRversion()[1, 1:3])) + ) + + for (placeholder in placeholders) + version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE) # include SVN revision for development versions of R # (to avoid sharing platform-specific artefacts with released versions of R) @@ -708,10 +716,19 @@ local({ identical(R.version[["nickname"]], "Unsuffered Consequences") if (devel) - prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + version <- paste(version, R.version[["svn rev"]], sep = "-r") + + version + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- renv_bootstrap_platform_prefix_default() # build list of path components - components <- c(prefix, R.version$platform) + components <- c(version, R.version$platform) # include prefix if provided by user prefix <- renv_bootstrap_platform_prefix_impl() @@ -950,14 +967,14 @@ local({ } renv_bootstrap_validate_version_dev <- function(version, description) { - + expected <- description[["RemoteSha"]] if (!is.character(expected)) return(FALSE) - + pattern <- sprintf("^\\Q%s\\E", version) grepl(pattern, expected, perl = TRUE) - + } renv_bootstrap_validate_version_release <- function(version, description) { @@ -1198,86 +1215,89 @@ local({ } renv_json_read_patterns <- function() { - + list( - + # objects - list("{", "\t\n\tobject(\t\n\t"), - list("}", "\t\n\t)\t\n\t"), - + list("{", "\t\n\tobject(\t\n\t", TRUE), + list("}", "\t\n\t)\t\n\t", TRUE), + # arrays - list("[", "\t\n\tarray(\t\n\t"), - list("]", "\n\t\n)\n\t\n"), - + list("[", "\t\n\tarray(\t\n\t", TRUE), + list("]", "\n\t\n)\n\t\n", TRUE), + # maps - list(":", "\t\n\t=\t\n\t") - + list(":", "\t\n\t=\t\n\t", TRUE), + + # newlines + list("\\u000a", "\n", FALSE) + ) - + } renv_json_read_envir <- function() { envir <- new.env(parent = emptyenv()) - + envir[["+"]] <- `+` envir[["-"]] <- `-` - + envir[["object"]] <- function(...) { result <- list(...) names(result) <- as.character(names(result)) result } - + envir[["array"]] <- list - + envir[["true"]] <- TRUE envir[["false"]] <- FALSE envir[["null"]] <- NULL - + envir - + } renv_json_read_remap <- function(object, patterns) { - + # repair names if necessary if (!is.null(names(object))) { - + nms <- names(object) for (pattern in patterns) nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) names(object) <- nms - + } - + # repair strings if necessary if (is.character(object)) { for (pattern in patterns) object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) } - + # recurse for other objects if (is.recursive(object)) for (i in seq_along(object)) object[i] <- list(renv_json_read_remap(object[[i]], patterns)) - + # return remapped object object - + } renv_json_read_default <- function(file = NULL, text = NULL) { # read json text text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") - + # convert into something the R parser will understand patterns <- renv_json_read_patterns() transformed <- text for (pattern in patterns) transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) - + # parse it rfile <- tempfile("renv-json-", fileext = ".R") on.exit(unlink(rfile), add = TRUE) @@ -1287,9 +1307,10 @@ local({ # evaluate in safe environment result <- eval(json, envir = renv_json_read_envir()) - # fix up strings if necessary + # fix up strings if necessary -- do so only with reversible patterns + patterns <- Filter(function(pattern) pattern[[3L]], patterns) renv_json_read_remap(result, patterns) - + } diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index 74927987..e9dfb1ec 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.4.2", + "Version": "4.4.3", "Repositories": [ { "Name": "CRAN", @@ -24,7 +24,8 @@ "NeedsCompilation": "no", "Author": "Dirk Eddelbuettel [aut, cre] (), John W. Emerson [aut], Michael J. Kane [aut] ()", "Maintainer": "Dirk Eddelbuettel ", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "DBI": { "Package": "DBI", @@ -187,10 +188,10 @@ }, "Matrix": { "Package": "Matrix", - "Version": "1.7-2", + "Version": "1.7-3", "Source": "Repository", "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", - "Date": "2025-01-20", + "Date": "2025-03-05", "Priority": "recommended", "Title": "Sparse and Dense Matrix Classes and Methods", "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.", @@ -232,7 +233,7 @@ }, "QuickJSR": { "Package": "QuickJSR", - "Version": "1.6.0", + "Version": "1.7.0", "Source": "Repository", "Title": "Interface for the 'QuickJS' Lightweight 'JavaScript' Engine", "Authors@R": "c( person(c(\"Andrew\", \"R.\"), \"Johnson\", , \"andrew.johnson@arjohnsonau.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7000-8065\")), person(\"QuickJS\", \"Authors\", role = c(\"cph\"), comment = \"QuickJS sources and headers\"), person(\"QuickJS-NG\", \"Authors\", role = c(\"cph\"), comment = \"QuickJS-NG sources and headers\") )", @@ -248,7 +249,7 @@ "Encoding": "UTF-8", "Language": "en-AU", "NeedsCompilation": "yes", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "SystemRequirements": "GNU make", "VignetteBuilder": "knitr", "Author": "Andrew R. Johnson [aut, cre] (), QuickJS Authors [cph] (QuickJS sources and headers), QuickJS-NG Authors [cph] (QuickJS-NG sources and headers)", @@ -306,7 +307,8 @@ "URL": "https://github.com/HenrikBengtsson/R.oo", "BugReports": "https://github.com/HenrikBengtsson/R.oo/issues", "NeedsCompilation": "no", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "R.utils": { "Package": "R.utils", @@ -336,7 +338,8 @@ "URL": "https://henrikbengtsson.github.io/R.utils/, https://github.com/HenrikBengtsson/R.utils", "BugReports": "https://github.com/HenrikBengtsson/R.utils/issues", "NeedsCompilation": "no", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "R6": { "Package": "R6", @@ -460,11 +463,11 @@ }, "Rdpack": { "Package": "Rdpack", - "Version": "2.6.2", + "Version": "2.6.3", "Source": "Repository", "Type": "Package", "Title": "Update and Manipulate Rd Documentation Objects", - "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), email = \"georgi.boshnakov@manchester.ac.uk\"), person(given = \"Duncan\", family = \"Murdoch\", role = \"ctb\", email = \"murdoch.duncan@gmail.com\") )", + "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", @@ -488,10 +491,9 @@ "LazyLoad": "yes", "RoxygenNote": "7.1.1", "NeedsCompilation": "no", - "Author": "Georgi N. Boshnakov [aut, cre], Duncan Murdoch [ctb]", + "Author": "Georgi N. Boshnakov [aut, cre] (), Duncan Murdoch [ctb]", "Maintainer": "Georgi N. Boshnakov ", - "Repository": "CRAN", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "StanHeaders": { "Package": "StanHeaders", @@ -586,50 +588,6 @@ "Repository": "RSPM", "Encoding": "UTF-8" }, - "arsenal": { - "Package": "arsenal", - "Version": "3.6.3", - "Source": "Repository", - "Title": "An Arsenal of 'R' Functions for Large-Scale Statistical Summaries", - "Date": "2021-06-04", - "Authors@R": "c( person(\"Ethan\", \"Heinzen\", email = \"heinzen.ethan@mayo.edu\", role = c(\"aut\", \"cre\")), person(\"Jason\", \"Sinnwell\", role=\"aut\"), person(\"Elizabeth\", \"Atkinson\", role=\"aut\"), person(\"Tina\", \"Gunderson\", role=\"aut\"), person(\"Gregory\", \"Dougherty\", role=\"aut\"), person(\"Patrick\", \"Votruba\", role=\"ctb\"), person(\"Ryan\", \"Lennon\", role=\"ctb\"), person(\"Andrew\", \"Hanson\", role=\"ctb\"), person(\"Krista\", \"Goergen\", role=\"ctb\"), person(\"Emily\", \"Lundt\", role=\"ctb\"), person(\"Brendan\", \"Broderick\", role=\"ctb\"), person(\"Maddie\", \"McCullough\", role=\"art\") )", - "Description": "An Arsenal of 'R' functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in 'R' and 'RStudio' and which use formulas and versatile summary statistics for summary tables and models. The primary functions include tableby(), a Table-1-like summary of multiple variable types 'by' the levels of one or more categorical variables; paired(), a Table-1-like summary of multiple variable types paired across two time points; modelsum(), which performs simple model fits on one or more endpoints for many variables (univariate or adjusted for covariates); freqlist(), a powerful frequency table across many categorical variables; comparedf(), a function for comparing data.frames; and write2(), a function to output tables to a document.", - "Suggests": [ - "broom (>= 0.7.1)", - "magrittr", - "rmarkdown", - "testthat", - "xtable", - "pander", - "survival (>= 2.43-1)", - "coin", - "pROC", - "MASS", - "splines", - "rpart", - "yaml", - "geepack" - ], - "Depends": [ - "R (>= 3.4.0)", - "stats (>= 3.4.0)" - ], - "Imports": [ - "knitr (>= 1.29)", - "utils (>= 3.4.0)" - ], - "URL": "https://github.com/mayoverse/arsenal, https://cran.r-project.org/package=arsenal, https://mayoverse.github.io/arsenal/", - "BugReports": "https://github.com/mayoverse/arsenal/issues", - "VignetteBuilder": "knitr", - "License": "GPL (>= 2)", - "RoxygenNote": "7.1.1", - "LazyData": "true", - "Encoding": "UTF-8", - "NeedsCompilation": "no", - "Author": "Ethan Heinzen [aut, cre], Jason Sinnwell [aut], Elizabeth Atkinson [aut], Tina Gunderson [aut], Gregory Dougherty [aut], Patrick Votruba [ctb], Ryan Lennon [ctb], Andrew Hanson [ctb], Krista Goergen [ctb], Emily Lundt [ctb], Brendan Broderick [ctb], Maddie McCullough [art]", - "Maintainer": "Ethan Heinzen ", - "Repository": "RSPM" - }, "askpass": { "Package": "askpass", "Version": "1.2.1", @@ -699,19 +657,15 @@ }, "bit": { "Package": "bit", - "Version": "4.5.0.1", + "Version": "4.6.0", "Source": "Repository", - "Type": "Package", "Title": "Classes and Methods for Fast Memory-Efficient Boolean Selections", - "Date": "2024-09-17", - "Authors@R": "c(person(given = \"Jens\", family = \"Oehlschlägel\", role = c(\"aut\", \"cre\"), email = \"Jens.Oehlschlaegel@truecluster.com\"), person(given = \"Brian\", family = \"Ripley\", role = \"ctb\"))", - "Author": "Jens Oehlschlägel [aut, cre], Brian Ripley [ctb]", - "Maintainer": "Jens Oehlschlägel ", + "Authors@R": "c( person(\"Michael\", \"Chirico\", email = \"MichaelChirico4@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Jens\", \"Oehlschlägel\", role = \"aut\"), person(\"Brian\", \"Ripley\", role = \"ctb\") )", "Depends": [ "R (>= 3.4.0)" ], "Suggests": [ - "testthat (>= 0.11.0)", + "testthat (>= 3.0.0)", "roxygen2", "knitr", "markdown", @@ -725,10 +679,13 @@ "LazyLoad": "yes", "ByteCompile": "yes", "Encoding": "UTF-8", - "URL": "https://github.com/truecluster/bit", + "URL": "https://github.com/r-lib/bit", "VignetteBuilder": "knitr, rmarkdown", "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", "NeedsCompilation": "yes", + "Author": "Michael Chirico [aut, cre], Jens Oehlschlägel [aut], Brian Ripley [ctb]", + "Maintainer": "Michael Chirico ", "Repository": "CRAN" }, "bit64": { @@ -825,7 +782,7 @@ }, "broom": { "Package": "broom", - "Version": "1.0.7", + "Version": "1.0.8", "Source": "Repository", "Type": "Package", "Title": "Convert Statistical Objects into Tidy Tibbles", @@ -839,12 +796,13 @@ ], "Imports": [ "backports", + "cli", "dplyr (>= 1.0.0)", "generics (>= 0.0.2)", "glue", "lifecycle", "purrr", - "rlang", + "rlang (>= 1.1.0)", "stringr", "tibble (>= 3.0.0)", "tidyr (>= 1.0.0)" @@ -909,7 +867,6 @@ "multcomp", "network", "nnet", - "orcutt (>= 2.2)", "ordinal", "plm", "poLCA", @@ -927,7 +884,7 @@ "survey", "survival (>= 3.6-4)", "systemfit", - "testthat (>= 2.1.0)", + "testthat (>= 3.0.0)", "tseries", "vars", "zoo" @@ -937,7 +894,8 @@ "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Language": "en-US", - "Collate": "'aaa-documentation-helper.R' 'null-and-default-tidiers.R' 'aer-tidiers.R' 'auc-tidiers.R' 'base-tidiers.R' 'bbmle-tidiers.R' 'betareg-tidiers.R' 'biglm-tidiers.R' 'bingroup-tidiers.R' 'boot-tidiers.R' 'broom-package.R' 'broom.R' 'btergm-tidiers.R' 'car-tidiers.R' 'caret-tidiers.R' 'cluster-tidiers.R' 'cmprsk-tidiers.R' 'data-frame-tidiers.R' 'deprecated-0-7-0.R' 'drc-tidiers.R' 'emmeans-tidiers.R' 'epiR-tidiers.R' 'ergm-tidiers.R' 'fixest-tidiers.R' 'gam-tidiers.R' 'geepack-tidiers.R' 'glmnet-cv-glmnet-tidiers.R' 'glmnet-glmnet-tidiers.R' 'gmm-tidiers.R' 'hmisc-tidiers.R' 'joinerml-tidiers.R' 'kendall-tidiers.R' 'ks-tidiers.R' 'lavaan-tidiers.R' 'leaps-tidiers.R' 'lfe-tidiers.R' 'list-irlba.R' 'list-optim-tidiers.R' 'list-svd-tidiers.R' 'list-tidiers.R' 'list-xyz-tidiers.R' 'lm-beta-tidiers.R' 'lmodel2-tidiers.R' 'lmtest-tidiers.R' 'maps-tidiers.R' 'margins-tidiers.R' 'mass-fitdistr-tidiers.R' 'mass-negbin-tidiers.R' 'mass-polr-tidiers.R' 'mass-ridgelm-tidiers.R' 'stats-lm-tidiers.R' 'mass-rlm-tidiers.R' 'mclust-tidiers.R' 'mediation-tidiers.R' 'metafor-tidiers.R' 'mfx-tidiers.R' 'mgcv-tidiers.R' 'mlogit-tidiers.R' 'muhaz-tidiers.R' 'multcomp-tidiers.R' 'nnet-tidiers.R' 'nobs.R' 'orcutt-tidiers.R' 'ordinal-clm-tidiers.R' 'ordinal-clmm-tidiers.R' 'plm-tidiers.R' 'polca-tidiers.R' 'psych-tidiers.R' 'stats-nls-tidiers.R' 'quantreg-nlrq-tidiers.R' 'quantreg-rq-tidiers.R' 'quantreg-rqs-tidiers.R' 'robust-glmrob-tidiers.R' 'robust-lmrob-tidiers.R' 'robustbase-glmrob-tidiers.R' 'robustbase-lmrob-tidiers.R' 'sp-tidiers.R' 'spdep-tidiers.R' 'speedglm-speedglm-tidiers.R' 'speedglm-speedlm-tidiers.R' 'stats-anova-tidiers.R' 'stats-arima-tidiers.R' 'stats-decompose-tidiers.R' 'stats-factanal-tidiers.R' 'stats-glm-tidiers.R' 'stats-htest-tidiers.R' 'stats-kmeans-tidiers.R' 'stats-loess-tidiers.R' 'stats-mlm-tidiers.R' 'stats-prcomp-tidiers.R' 'stats-smooth.spline-tidiers.R' 'stats-summary-lm-tidiers.R' 'stats-time-series-tidiers.R' 'survey-tidiers.R' 'survival-aareg-tidiers.R' 'survival-cch-tidiers.R' 'survival-coxph-tidiers.R' 'survival-pyears-tidiers.R' 'survival-survdiff-tidiers.R' 'survival-survexp-tidiers.R' 'survival-survfit-tidiers.R' 'survival-survreg-tidiers.R' 'systemfit-tidiers.R' 'tseries-tidiers.R' 'utilities.R' 'vars-tidiers.R' 'zoo-tidiers.R' 'zzz.R'", + "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'", + "Config/testthat/edition": "3", "NeedsCompilation": "no", "Author": "David Robinson [aut], Alex Hayes [aut] (), Simon Couch [aut, cre] (), Posit Software, PBC [cph, fnd], Indrajeet Patil [ctb] (), 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] (), 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] (), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (), Jasper Cooper [ctb] (), E Auden Krauska [ctb] (), Alex Wang [ctb], Malcolm Barrett [ctb] (), Charles Gray [ctb] (), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (), Eduard Szoecs [ctb], Frederik Aust [ctb] (), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (), Bruna Wundervald [ctb] (), Joyce Cahoon [ctb] (), Grant McDermott [ctb] (), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (), Lukas Wallrich [ctb] (), James Martherus [ctb] (), Chuliang Xiao [ctb] (), 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] (), 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] (), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (), Ilaria Prosdocimi [ctb] (), Daniel D. Sjoberg [ctb] (), Alex Reinhart [ctb] ()", "Maintainer": "Simon Couch ", @@ -1182,58 +1140,6 @@ "Author": "John Haman [cre, aut], Matthew Avery [aut], Institute for Defense Analyses [cph]", "Repository": "RSPM" }, - "cleanepi": { - "Package": "cleanepi", - "Version": "1.0.2", - "Source": "Repository", - "Title": "Clean and Standardize Epidemiological Data", - "Authors@R": "c( person(\"Karim\", \"Mané\", , \"karim.mane@lshtm.ac.uk\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9892-2999\")), person(\"Thibaut\", \"Jombart\", , \"thibautjombart@gmail.com\", role = \"cph\", comment = \"Thibault is the owner of the code in guess_dates.R file.\"), person(\"Bubacarr\", \"Bah\", , \"Bubacarr.Bah1@lshtm.ac.uk\", role = \"aut\", comment = c(ORCID = \"0000-0003-3318-6668\")), person(\"Bankolé\", \"Ahadzie\", , \"Bankole.Ahadzie@lshtm.ac.uk\", role = \"aut\"), person(\"Nuredin\", \"Mohammed\", , \"Nuredin.Mohammed@lshtm.ac.uk\", role = \"aut\"), person(\"Abdoelnaser\", \"Degoot\", , \"abdoelnaser-mahmood.degoot@lshtm.ac.uk\", role = \"aut\", comment = c(ORCID = \"0000-0001-8788-2496\")), person(\"Hugo\", \"Gruson\", , \"hugo@data.org\", role = \"rev\", comment = c(ORCID = \"0000-0002-4094-1476\")), person(\"Pratik R.\", \"Gupte\", , \"pratik.gupte@lshtm.ac.uk\", role = \"rev\", comment = c(ORCID = \"0000-0001-5294-7819\")), person(\"James M.\", \"Azam\", , \"james.azam@lshtm.ac.uk\", role = \"rev\", comment = c(ORCID = \"0000-0001-5782-7330\")), person(\"Joshua W.\", \"Lambert\", , \"joshua.lambert@lshtm.ac.uk\", role = \"rev\", comment = c(ORCID = \"0000-0001-5218-3046\")), person(\"Chris\", \"Hartgerink\", , \"chris@data.org\", role = \"rev\", comment = c(ORCID = \"0000-0003-1050-6809\")), person(\"London School of Hygiene and Tropical Medicine, LSHTM\", role = \"cph\"), person(\"data.org\", role = \"fnd\") )", - "Description": "Cleaning and standardizing tabular data package, tailored specifically for curating epidemiological data. It streamlines various data cleaning tasks that are typically expected when working with datasets in epidemiology. It returns the processed data in the same format, ensuring seamless integration into existing workflows. Additionally, it generates a comprehensive report detailing the outcomes of each cleaning task.", - "License": "MIT + file LICENSE", - "URL": "https://epiverse-trace.github.io/cleanepi/, https://github.com/epiverse-trace/cleanepi", - "BugReports": "https://github.com/epiverse-trace/cleanepi/issues", - "Imports": [ - "arsenal", - "checkmate", - "dplyr", - "janitor", - "linelist (>= 1.0.0)", - "lubridate", - "magrittr", - "matchmaker", - "numberize", - "readr", - "rlang", - "snakecase", - "utils", - "withr" - ], - "Suggests": [ - "htmlwidgets", - "kableExtra", - "knitr", - "lintr", - "markdown", - "reactable", - "rmarkdown", - "spelling", - "testthat (>= 3.0.0)" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "epiverse-trace/epiversetheme", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "Language": "en-US", - "LazyData": "true", - "RoxygenNote": "7.3.1", - "NeedsCompilation": "no", - "Author": "Karim Mané [aut, cre] (), Thibaut Jombart [cph] (Thibault is the owner of the code in guess_dates.R file.), Bubacarr Bah [aut] (), Bankolé Ahadzie [aut], Nuredin Mohammed [aut], Abdoelnaser Degoot [aut] (), Hugo Gruson [rev] (), Pratik R. Gupte [rev] (), James M. Azam [rev] (), Joshua W. Lambert [rev] (), Chris Hartgerink [rev] (), London School of Hygiene and Tropical Medicine, LSHTM [cph], data.org [fnd]", - "Maintainer": "Karim Mané ", - "Depends": [ - "R (>= 3.5.0)" - ], - "Repository": "RSPM" - }, "cli": { "Package": "cli", "Version": "3.6.4", @@ -1426,7 +1332,7 @@ }, "countrycode": { "Package": "countrycode", - "Version": "1.6.0", + "Version": "1.6.1", "Source": "Repository", "Type": "Package", "Title": "Convert Country Names and Country Codes", @@ -1449,11 +1355,11 @@ "Encoding": "UTF-8", "LazyData": "yes", "LazyLoad": "yes", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Author": "Vincent Arel-Bundock [aut, cre] (), CJ Yetman [ctb] (), Nils Enevoldsen [ctb] (), Etienne Bacher [ctb] (), Samuel Meichtry [ctb] ()", "Maintainer": "Vincent Arel-Bundock ", - "Repository": "RSPM" + "Repository": "CRAN" }, "cpp11": { "Package": "cpp11", @@ -1534,7 +1440,7 @@ }, "curl": { "Package": "curl", - "Version": "6.2.1", + "Version": "6.2.2", "Source": "Repository", "Type": "Package", "Title": "A Modern and Flexible Web Client for R", @@ -1981,48 +1887,6 @@ "Maintainer": "Winston Chang ", "Repository": "RSPM" }, - "fitdistrplus": { - "Package": "fitdistrplus", - "Version": "1.2-2", - "Source": "Repository", - "Title": "Help to Fit of a Parametric Distribution to Non-Censored or Censored Data", - "Authors@R": "c(person(\"Marie-Laure\", \"Delignette-Muller\", role = \"aut\", email = \"marielaure.delignettemuller@vetagro-sup.fr\", comment = c(ORCID = \"0000-0001-5453-3994\")), person(\"Christophe\", \"Dutang\", role = \"aut\", email = \"christophe.dutang@ensimag.fr\", comment = c(ORCID = \"0000-0001-6732-1501\")), person(\"Regis\", \"Pouillot\", role = \"ctb\"), person(\"Jean-Baptiste\", \"Denis\", role = \"ctb\"), person(\"Aurélie\", \"Siberchicot\", role = c(\"aut\", \"cre\"), email = \"aurelie.siberchicot@univ-lyon1.fr\", comment = c(ORCID = \"0000-0002-7638-8318\")))", - "Description": "Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit estimation (MGE) and maximum spacing estimation (MSE) methods (available only for non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g. Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction to parametric estimation.", - "Depends": [ - "R (>= 3.5.0)", - "MASS", - "grDevices", - "survival", - "methods" - ], - "Imports": [ - "stats", - "rlang" - ], - "Suggests": [ - "actuar", - "rgenoud", - "mc2d", - "gamlss.dist", - "knitr", - "ggplot2", - "GeneralizedHyperbolic", - "rmarkdown", - "Hmisc", - "bookdown" - ], - "VignetteBuilder": "knitr", - "BuildVignettes": "true", - "License": "GPL (>= 2)", - "Encoding": "UTF-8", - "URL": "https://lbbe-software.github.io/fitdistrplus/, https://lbbe.univ-lyon1.fr/fr/fitdistrplus, https://github.com/lbbe-software/fitdistrplus", - "BugReports": "https://github.com/lbbe-software/fitdistrplus/issues", - "Contact": "Marie-Laure Delignette-Muller or Christophe Dutang ", - "NeedsCompilation": "no", - "Author": "Marie-Laure Delignette-Muller [aut] (), Christophe Dutang [aut] (), Regis Pouillot [ctb], Jean-Baptiste Denis [ctb], Aurélie Siberchicot [aut, cre] ()", - "Maintainer": "Aurélie Siberchicot ", - "Repository": "CRAN" - }, "fontawesome": { "Package": "fontawesome", "Version": "0.5.3", @@ -2514,11 +2378,11 @@ }, "grates": { "Package": "grates", - "Version": "1.4.1", + "Version": "1.4.3", "Source": "Repository", "Title": "Grouped Date Classes", "Authors@R": "c( person( given = \"Tim\", family = \"Taylor\", role = c(\"aut\", \"cre\"), email = \"tim.taylor@hiddenelephants.co.uk\", comment = c(ORCID = \"0000-0002-8587-7113\") ) )", - "Description": "Provides a coherent interface and implementation for creating grouped date classes. This package is part of the RECON () toolkit for outbreak analysis.", + "Description": "Provides a coherent interface and implementation for creating grouped date classes.", "URL": "https://www.reconverse.org/grates/, https://github.com/reconverse/grates", "License": "MIT + file LICENSE", "Encoding": "UTF-8", @@ -2843,12 +2707,12 @@ }, "incidence2": { "Package": "incidence2", - "Version": "2.6.0", + "Version": "2.6.1", "Source": "Repository", "Type": "Package", "Title": "Compute, Handle and Plot Incidence of Dated Events", "Authors@R": "c( person(\"Tim\", \"Taylor\", role = c(\"aut\", \"cre\"), email = \"tim.taylor@hiddenelephants.co.uk\", comment = c(ORCID = \"0000-0002-8587-7113\")), person(\"Thibaut\", \"Jombart\", role = \"ctb\", email = \"thibautjombart@gmail.com\") )", - "Description": "Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence2' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. This package is part of the RECON () toolkit for outbreak analysis ().", + "Description": "Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence2' is used to store computed incidence and can be easily manipulated, subsetted, and plotted.", "Encoding": "UTF-8", "License": "MIT + file LICENSE", "URL": "https://www.reconverse.org/incidence2/, https://github.com/reconverse/incidence2", @@ -2876,13 +2740,12 @@ "outbreaks", "ggplot2", "scales", - "knitr", - "markdown", + "litedown", "testthat (>= 3.0.0)", "ciTools", "withr" ], - "VignetteBuilder": "knitr", + "VignetteBuilder": "litedown", "Config/testthat/edition": "3", "LazyData": "true", "NeedsCompilation": "no", @@ -2913,7 +2776,8 @@ "NeedsCompilation": "no", "Author": "Oleg Sklyar [aut], Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), Mike Smith [ctb], Duncan Murdoch [ctb], Karline Soetaert [ctb] (), Johannes Ranke [ctb] ()", "Maintainer": "Dirk Eddelbuettel ", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "isoband": { "Package": "isoband", @@ -2951,52 +2815,6 @@ "Maintainer": "Hadley Wickham ", "Repository": "RSPM" }, - "janitor": { - "Package": "janitor", - "Version": "2.2.1", - "Source": "Repository", - "Title": "Simple Tools for Examining and Cleaning Dirty Data", - "Authors@R": "c(person(\"Sam\", \"Firke\", email = \"samuel.firke@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Bill\", \"Denney\", email = \"wdenney@humanpredictions.com\", role = \"ctb\"), person(\"Chris\", \"Haid\", email = \"chrishaid@gmail.com\", role = \"ctb\"), person(\"Ryan\", \"Knight\", email = \"ryangknight@gmail.com\", role = \"ctb\"), person(\"Malte\", \"Grosser\", email = \"malte.grosser@gmail.com\", role = \"ctb\"), person(\"Jonathan\", \"Zadra\", email = \"jonathan.zadra@sorensonimpact.com\", role = \"ctb\"))", - "Description": "The main janitor functions can: perfectly format data.frame column names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and explore duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the \"tidyverse\" and works well with the pipe function %>%. janitor was built with beginning-to-intermediate R users in mind and is optimized for user-friendliness.", - "URL": "https://github.com/sfirke/janitor, https://sfirke.github.io/janitor/", - "BugReports": "https://github.com/sfirke/janitor/issues", - "Depends": [ - "R (>= 3.1.2)" - ], - "Imports": [ - "dplyr (>= 1.0.0)", - "hms", - "lifecycle", - "lubridate", - "magrittr", - "purrr", - "rlang", - "stringi", - "stringr", - "snakecase (>= 0.9.2)", - "tidyselect (>= 1.0.0)", - "tidyr (>= 0.7.0)" - ], - "License": "MIT + file LICENSE", - "RoxygenNote": "7.2.3", - "Suggests": [ - "dbplyr", - "knitr", - "rmarkdown", - "RSQLite", - "sf", - "testthat (>= 3.0.0)", - "tibble", - "tidygraph" - ], - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "Config/testthat/edition": "3", - "NeedsCompilation": "no", - "Author": "Sam Firke [aut, cre], Bill Denney [ctb], Chris Haid [ctb], Ryan Knight [ctb], Malte Grosser [ctb], Jonathan Zadra [ctb]", - "Maintainer": "Sam Firke ", - "Repository": "CRAN" - }, "jquerylib": { "Package": "jquerylib", "Version": "0.1.4", @@ -3021,7 +2839,7 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.9.1", + "Version": "2.0.0", "Source": "Repository", "Title": "A Simple and Robust JSON Parser and Generator for R", "License": "MIT + file LICENSE", @@ -3043,7 +2861,7 @@ "R.rsp", "sf" ], - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "NeedsCompilation": "yes", "Author": "Jeroen Ooms [aut, cre] (), Duncan Temple Lang [ctb], Lloyd Hilaiel [cph] (author of bundled libyajl)", @@ -3051,11 +2869,11 @@ }, "knitr": { "Package": "knitr", - "Version": "1.49", + "Version": "1.50", "Source": "Repository", "Type": "Package", "Title": "A General-Purpose Package for Dynamic Report Generation in R", - "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Abhraneel\", \"Sarma\", role = \"ctb\"), person(\"Adam\", \"Vogt\", role = \"ctb\"), person(\"Alastair\", \"Andrew\", role = \"ctb\"), person(\"Alex\", \"Zvoleff\", role = \"ctb\"), person(\"Amar\", \"Al-Zubaidi\", role = \"ctb\"), person(\"Andre\", \"Simon\", role = \"ctb\", comment = \"the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de\"), person(\"Aron\", \"Atkins\", role = \"ctb\"), person(\"Aaron\", \"Wolen\", role = \"ctb\"), person(\"Ashley\", \"Manton\", role = \"ctb\"), person(\"Atsushi\", \"Yasumoto\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8335-495X\")), person(\"Ben\", \"Baumer\", role = \"ctb\"), person(\"Brian\", \"Diggs\", role = \"ctb\"), person(\"Brian\", \"Zhang\", role = \"ctb\"), person(\"Bulat\", \"Yapparov\", role = \"ctb\"), person(\"Cassio\", \"Pereira\", role = \"ctb\"), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person(\"David\", \"Hall\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", role = \"ctb\"), person(\"David\", \"Robinson\", role = \"ctb\"), person(\"Doug\", \"Hemken\", role = \"ctb\"), person(\"Duncan\", \"Murdoch\", role = \"ctb\"), person(\"Elio\", \"Campitelli\", role = \"ctb\"), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Emily\", \"Riederer\", role = \"ctb\"), person(\"Fabian\", \"Hirschmann\", role = \"ctb\"), person(\"Fitch\", \"Simeon\", role = \"ctb\"), person(\"Forest\", \"Fang\", role = \"ctb\"), person(c(\"Frank\", \"E\", \"Harrell\", \"Jr\"), role = \"ctb\", comment = \"the Sweavel package at inst/misc/Sweavel.sty\"), person(\"Garrick\", \"Aden-Buie\", role = \"ctb\"), person(\"Gregoire\", \"Detrez\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Hao\", \"Zhu\", role = \"ctb\"), person(\"Heewon\", \"Jeon\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Ian\", \"Lyttle\", role = \"ctb\"), person(\"Hodges\", \"Daniel\", role = \"ctb\"), person(\"Jacob\", \"Bien\", role = \"ctb\"), person(\"Jake\", \"Burkhead\", role = \"ctb\"), person(\"James\", \"Manton\", role = \"ctb\"), person(\"Jared\", \"Lander\", role = \"ctb\"), person(\"Jason\", \"Punyon\", role = \"ctb\"), person(\"Javier\", \"Luraschi\", role = \"ctb\"), person(\"Jeff\", \"Arnold\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", role = \"ctb\"), person(\"Jeremy\", \"Ashkenas\", role = c(\"ctb\", \"cph\"), comment = \"the CSS file at inst/misc/docco-classic.css\"), person(\"Jeremy\", \"Stephens\", role = \"ctb\"), person(\"Jim\", \"Hester\", role = \"ctb\"), person(\"Joe\", \"Cheng\", role = \"ctb\"), person(\"Johannes\", \"Ranke\", role = \"ctb\"), person(\"John\", \"Honaker\", role = \"ctb\"), person(\"John\", \"Muschelli\", role = \"ctb\"), person(\"Jonathan\", \"Keane\", role = \"ctb\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Johan\", \"Toloe\", role = \"ctb\"), person(\"Jonathan\", \"Sidi\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Julien\", \"Barnier\", role = \"ctb\"), person(\"Kaiyin\", \"Zhong\", role = \"ctb\"), person(\"Kamil\", \"Slowikowski\", role = \"ctb\"), person(\"Karl\", \"Forner\", role = \"ctb\"), person(c(\"Kevin\", \"K.\"), \"Smith\", role = \"ctb\"), person(\"Kirill\", \"Mueller\", role = \"ctb\"), person(\"Kohske\", \"Takahashi\", role = \"ctb\"), person(\"Lorenz\", \"Walthert\", role = \"ctb\"), person(\"Lucas\", \"Gallindo\", role = \"ctb\"), person(\"Marius\", \"Hofert\", role = \"ctb\"), person(\"Martin\", \"Modrák\", role = \"ctb\"), person(\"Michael\", \"Chirico\", role = \"ctb\"), person(\"Michael\", \"Friendly\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", role = \"ctb\"), person(\"Michel\", \"Kuhlmann\", role = \"ctb\"), person(\"Miller\", \"Patrick\", role = \"ctb\"), person(\"Nacho\", \"Caballero\", role = \"ctb\"), person(\"Nick\", \"Salkowski\", role = \"ctb\"), person(\"Niels Richard\", \"Hansen\", role = \"ctb\"), person(\"Noam\", \"Ross\", role = \"ctb\"), person(\"Obada\", \"Mahdi\", role = \"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role = \"ctb\", comment=c(ORCID = \"0000-0002-9101-3362\")), person(\"Pedro\", \"Faria\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\"), person(\"Ramnath\", \"Vaidyanathan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Robert\", \"Krzyzanowski\", role = \"ctb\"), person(\"Rodrigo\", \"Copetti\", role = \"ctb\"), person(\"Romain\", \"Francois\", role = \"ctb\"), person(\"Ruaridh\", \"Williamson\", role = \"ctb\"), person(\"Sagiru\", \"Mati\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1413-3974\")), person(\"Scott\", \"Kostyshak\", role = \"ctb\"), person(\"Sebastian\", \"Meyer\", role = \"ctb\"), person(\"Sietse\", \"Brouwer\", role = \"ctb\"), person(c(\"Simon\", \"de\"), \"Bernard\", role = \"ctb\"), person(\"Sylvain\", \"Rousseau\", role = \"ctb\"), person(\"Taiyun\", \"Wei\", role = \"ctb\"), person(\"Thibaut\", \"Assus\", role = \"ctb\"), person(\"Thibaut\", \"Lamadon\", role = \"ctb\"), person(\"Thomas\", \"Leeper\", role = \"ctb\"), person(\"Tim\", \"Mastny\", role = \"ctb\"), person(\"Tom\", \"Torsney-Weir\", role = \"ctb\"), person(\"Trevor\", \"Davis\", role = \"ctb\"), person(\"Viktoras\", \"Veitas\", role = \"ctb\"), person(\"Weicheng\", \"Zhu\", role = \"ctb\"), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Zachary\", \"Foster\", role = \"ctb\"), person(\"Zhian N.\", \"Kamvar\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1458-7108\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Abhraneel\", \"Sarma\", role = \"ctb\"), person(\"Adam\", \"Vogt\", role = \"ctb\"), person(\"Alastair\", \"Andrew\", role = \"ctb\"), person(\"Alex\", \"Zvoleff\", role = \"ctb\"), person(\"Amar\", \"Al-Zubaidi\", role = \"ctb\"), person(\"Andre\", \"Simon\", role = \"ctb\", comment = \"the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de\"), person(\"Aron\", \"Atkins\", role = \"ctb\"), person(\"Aaron\", \"Wolen\", role = \"ctb\"), person(\"Ashley\", \"Manton\", role = \"ctb\"), person(\"Atsushi\", \"Yasumoto\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8335-495X\")), person(\"Ben\", \"Baumer\", role = \"ctb\"), person(\"Brian\", \"Diggs\", role = \"ctb\"), person(\"Brian\", \"Zhang\", role = \"ctb\"), person(\"Bulat\", \"Yapparov\", role = \"ctb\"), person(\"Cassio\", \"Pereira\", role = \"ctb\"), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person(\"David\", \"Hall\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", role = \"ctb\"), person(\"David\", \"Robinson\", role = \"ctb\"), person(\"Doug\", \"Hemken\", role = \"ctb\"), person(\"Duncan\", \"Murdoch\", role = \"ctb\"), person(\"Elio\", \"Campitelli\", role = \"ctb\"), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Emily\", \"Riederer\", role = \"ctb\"), person(\"Fabian\", \"Hirschmann\", role = \"ctb\"), person(\"Fitch\", \"Simeon\", role = \"ctb\"), person(\"Forest\", \"Fang\", role = \"ctb\"), person(c(\"Frank\", \"E\", \"Harrell\", \"Jr\"), role = \"ctb\", comment = \"the Sweavel package at inst/misc/Sweavel.sty\"), person(\"Garrick\", \"Aden-Buie\", role = \"ctb\"), person(\"Gregoire\", \"Detrez\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Hao\", \"Zhu\", role = \"ctb\"), person(\"Heewon\", \"Jeon\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Ian\", \"Lyttle\", role = \"ctb\"), person(\"Hodges\", \"Daniel\", role = \"ctb\"), person(\"Jacob\", \"Bien\", role = \"ctb\"), person(\"Jake\", \"Burkhead\", role = \"ctb\"), person(\"James\", \"Manton\", role = \"ctb\"), person(\"Jared\", \"Lander\", role = \"ctb\"), person(\"Jason\", \"Punyon\", role = \"ctb\"), person(\"Javier\", \"Luraschi\", role = \"ctb\"), person(\"Jeff\", \"Arnold\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", role = \"ctb\"), person(\"Jeremy\", \"Ashkenas\", role = c(\"ctb\", \"cph\"), comment = \"the CSS file at inst/misc/docco-classic.css\"), person(\"Jeremy\", \"Stephens\", role = \"ctb\"), person(\"Jim\", \"Hester\", role = \"ctb\"), person(\"Joe\", \"Cheng\", role = \"ctb\"), person(\"Johannes\", \"Ranke\", role = \"ctb\"), person(\"John\", \"Honaker\", role = \"ctb\"), person(\"John\", \"Muschelli\", role = \"ctb\"), person(\"Jonathan\", \"Keane\", role = \"ctb\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Johan\", \"Toloe\", role = \"ctb\"), person(\"Jonathan\", \"Sidi\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Julien\", \"Barnier\", role = \"ctb\"), person(\"Kaiyin\", \"Zhong\", role = \"ctb\"), person(\"Kamil\", \"Slowikowski\", role = \"ctb\"), person(\"Karl\", \"Forner\", role = \"ctb\"), person(c(\"Kevin\", \"K.\"), \"Smith\", role = \"ctb\"), person(\"Kirill\", \"Mueller\", role = \"ctb\"), person(\"Kohske\", \"Takahashi\", role = \"ctb\"), person(\"Lorenz\", \"Walthert\", role = \"ctb\"), person(\"Lucas\", \"Gallindo\", role = \"ctb\"), person(\"Marius\", \"Hofert\", role = \"ctb\"), person(\"Martin\", \"Modrák\", role = \"ctb\"), person(\"Michael\", \"Chirico\", role = \"ctb\"), person(\"Michael\", \"Friendly\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", role = \"ctb\"), person(\"Michel\", \"Kuhlmann\", role = \"ctb\"), person(\"Miller\", \"Patrick\", role = \"ctb\"), person(\"Nacho\", \"Caballero\", role = \"ctb\"), person(\"Nick\", \"Salkowski\", role = \"ctb\"), person(\"Niels Richard\", \"Hansen\", role = \"ctb\"), person(\"Noam\", \"Ross\", role = \"ctb\"), person(\"Obada\", \"Mahdi\", role = \"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role = \"ctb\", comment=c(ORCID = \"0000-0002-9101-3362\")), person(\"Pedro\", \"Faria\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\"), person(\"Ramnath\", \"Vaidyanathan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Robert\", \"Krzyzanowski\", role = \"ctb\"), person(\"Rodrigo\", \"Copetti\", role = \"ctb\"), person(\"Romain\", \"Francois\", role = \"ctb\"), person(\"Ruaridh\", \"Williamson\", role = \"ctb\"), person(\"Sagiru\", \"Mati\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1413-3974\")), person(\"Scott\", \"Kostyshak\", role = \"ctb\"), person(\"Sebastian\", \"Meyer\", role = \"ctb\"), person(\"Sietse\", \"Brouwer\", role = \"ctb\"), person(c(\"Simon\", \"de\"), \"Bernard\", role = \"ctb\"), person(\"Sylvain\", \"Rousseau\", role = \"ctb\"), person(\"Taiyun\", \"Wei\", role = \"ctb\"), person(\"Thibaut\", \"Assus\", role = \"ctb\"), person(\"Thibaut\", \"Lamadon\", role = \"ctb\"), person(\"Thomas\", \"Leeper\", role = \"ctb\"), person(\"Tim\", \"Mastny\", role = \"ctb\"), person(\"Tom\", \"Torsney-Weir\", role = \"ctb\"), person(\"Trevor\", \"Davis\", role = \"ctb\"), person(\"Viktoras\", \"Veitas\", role = \"ctb\"), person(\"Weicheng\", \"Zhu\", role = \"ctb\"), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Zachary\", \"Foster\", role = \"ctb\"), person(\"Zhian N.\", \"Kamvar\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1458-7108\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", "Description": "Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.", "Depends": [ "R (>= 3.6.0)" @@ -3065,7 +2883,7 @@ "highr (>= 0.11)", "methods", "tools", - "xfun (>= 0.48)", + "xfun (>= 0.51)", "yaml (>= 2.1.19)" ], "Suggests": [ @@ -3095,7 +2913,7 @@ "testit", "tibble", "tikzDevice (>= 0.10)", - "tinytex (>= 0.46)", + "tinytex (>= 0.56)", "webshot", "rstudioapi", "svglite" @@ -3106,10 +2924,10 @@ "Encoding": "UTF-8", "VignetteBuilder": "litedown, knitr", "SystemRequirements": "Package vignettes based on R Markdown v2 or reStructuredText require Pandoc (http://pandoc.org). The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).", - "Collate": "'block.R' 'cache.R' 'utils.R' 'citation.R' 'hooks-html.R' 'plot.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", + "Collate": "'block.R' 'cache.R' 'citation.R' 'hooks-html.R' 'plot.R' 'utils.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", - "Author": "Yihui Xie [aut, cre] (), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. Kamvar [ctb] (), Posit Software, PBC [cph, fnd]", + "Author": "Yihui Xie [aut, cre] (, https://yihui.org), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. Kamvar [ctb] (), Posit Software, PBC [cph, fnd]", "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, @@ -3239,55 +3057,12 @@ "Maintainer": "Lionel Henry ", "Repository": "RSPM" }, - "linelist": { - "Package": "linelist", - "Version": "1.1.4", - "Source": "Repository", - "Title": "Tagging and Validating Epidemiological Data", - "Authors@R": "c( person(given = \"Hugo\", family = \"Gruson\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4094-1476\"), email = \"hugo@data.org\"), person(given = \"Thibaut\", family = \"Jombart\", role = c(\"aut\", \"ccp\")), person(given = \"Tim\", family = \"Taylor\", role = \"ctb\"), person(given = \"Chris\", family = \"Hartgerink\", role = \"rev\", comment = c(ORCID = \"0000-0003-1050-6809\")) )", - "Description": "Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.", - "License": "MIT + file LICENSE", - "URL": "https://epiverse-trace.github.io/linelist/, https://github.com/epiverse-trace/linelist", - "BugReports": "https://github.com/epiverse-trace/linelist/issues", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", - "Config/testthat/edition": "3", - "Config/testthat/parallel": "true", - "Config/Needs/README": "incidence2 (>= 2.1.1), ggplot2", - "Depends": [ - "R (>= 3.1.0)" - ], - "Imports": [ - "checkmate", - "dplyr", - "lifecycle", - "rlang", - "tidyselect" - ], - "Suggests": [ - "callr", - "knitr", - "magrittr", - "outbreaks", - "rmarkdown", - "spelling", - "testthat", - "tibble" - ], - "Config/Needs/website": "r-lib/pkgdown, epiverse-trace/epiversetheme", - "VignetteBuilder": "knitr", - "Language": "en-GB", - "NeedsCompilation": "no", - "Author": "Hugo Gruson [aut, cre] (), Thibaut Jombart [aut, ccp], Tim Taylor [ctb], Chris Hartgerink [rev] ()", - "Maintainer": "Hugo Gruson ", - "Repository": "RSPM" - }, "lme4": { "Package": "lme4", - "Version": "1.1-36", + "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\")) )", + "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)", @@ -3342,7 +3117,7 @@ "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] ()", + "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" }, @@ -3468,35 +3243,6 @@ "Maintainer": "Lionel Henry ", "Repository": "RSPM" }, - "matchmaker": { - "Package": "matchmaker", - "Version": "0.1.1", - "Source": "Repository", - "Title": "Flexible Dictionary-Based Cleaning", - "Authors@R": "c( person(given = \"Zhian N.\", family = \"Kamvar\", role = c(\"aut\", \"cre\"), email = \"zkamvar@gmail.com\", comment = c(ORCID = \"0000-0003-1458-7108\")), person(given = \"Thibaut\", family = \"Jombart\", email = \"thibautjombart@gmail.com\", role = c(\"ctb\")), person(given = \"Patrick\", family = \"Barks\", email = \"patrick.barks@epicentre.msf.org\", role = c(\"ctb\")))", - "Description": "Provides flexible dictionary-based cleaning that allows users to specify implicit and explicit missing data, regular expressions for both data and columns, and global matches, while respecting ordering of factors. This package is part of the 'RECON' () toolkit for outbreak analysis.", - "URL": "https://www.repidemicsconsortium.org/matchmaker, https://github.com/reconhub/matchmaker", - "License": "GPL-3", - "Suggests": [ - "testthat (>= 2.1.0)", - "covr", - "knitr", - "rmarkdown" - ], - "Encoding": "UTF-8", - "LazyData": "true", - "RoxygenNote": "7.0.2", - "Imports": [ - "rlang", - "forcats", - "cli" - ], - "VignetteBuilder": "knitr", - "NeedsCompilation": "no", - "Author": "Zhian N. Kamvar [aut, cre] (), Thibaut Jombart [ctb], Patrick Barks [ctb]", - "Maintainer": "Zhian N. Kamvar ", - "Repository": "RSPM" - }, "matrixStats": { "Package": "matrixStats", "Version": "1.5.0", @@ -3527,7 +3273,8 @@ "URL": "https://github.com/HenrikBengtsson/matrixStats", "BugReports": "https://github.com/HenrikBengtsson/matrixStats/issues", "RoxygenNote": "7.3.2", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "memoise": { "Package": "memoise", @@ -3593,11 +3340,11 @@ }, "mime": { "Package": "mime", - "Version": "0.12", + "Version": "0.13", "Source": "Repository", "Type": "Package", "Title": "Map Filenames to MIME Types", - "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"Beilei\", \"Bian\", role = \"ctb\") )", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"Beilei\", \"Bian\", role = \"ctb\") )", "Description": "Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.", "Imports": [ "tools" @@ -3605,12 +3352,12 @@ "License": "GPL", "URL": "https://github.com/yihui/mime", "BugReports": "https://github.com/yihui/mime/issues", - "RoxygenNote": "7.1.1", + "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "NeedsCompilation": "yes", - "Author": "Yihui Xie [aut, cre] (), Jeffrey Horner [ctb], Beilei Bian [ctb]", + "Author": "Yihui Xie [aut, cre] (, https://yihui.org), Jeffrey Horner [ctb], Beilei Bian [ctb]", "Maintainer": "Yihui Xie ", - "Repository": "RSPM" + "Repository": "CRAN" }, "minqa": { "Package": "minqa", @@ -3735,17 +3482,16 @@ }, "nloptr": { "Package": "nloptr", - "Version": "2.1.1", + "Version": "2.2.1", "Source": "Repository", "Type": "Package", "Title": "R Interface to NLopt", - "Authors@R": "c(person(\"Jelmer\", \"Ypma\", role = \"aut\", email = \"uctpjyy@ucl.ac.uk\"), person(c(\"Steven\", \"G.\"), \"Johnson\", role = \"aut\", comment = \"author of the NLopt C library\"), person(\"Aymeric\", \"Stamm\", role = c(\"ctb\", \"cre\"), email = \"aymeric.stamm@cnrs.fr\", comment = c(ORCID = \"0000-0002-8725-3654\")), person(c(\"Hans\", \"W.\"), \"Borchers\", role = \"ctb\", email = \"hwborchers@googlemail.com\"), person(\"Dirk\", \"Eddelbuettel\", role = \"ctb\", email = \"edd@debian.org\"), person(\"Brian\", \"Ripley\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Kurt\", \"Hornik\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Julien\", \"Chiquet\", role = \"ctb\"), person(\"Avraham\", \"Adler\", role = \"ctb\", email = \"Avraham.Adler@gmail.com\", comment = c(ORCID = \"0000-0002-3039-0703\")), person(\"Xiongtao\", \"Dai\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\", email = \"jeroen@berkeley.edu\"))", + "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.", - "Biarch": "true", "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "Suggests": [ "knitr", "rmarkdown", @@ -3756,9 +3502,10 @@ "URL": "https://github.com/astamm/nloptr, https://astamm.github.io/nloptr/", "BugReports": "https://github.com/astamm/nloptr/issues", "NeedsCompilation": "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]", + "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": "RSPM" + "Repository": "CRAN" }, "numDeriv": { "Package": "numDeriv", @@ -3780,37 +3527,6 @@ "Repository": "RSPM", "Encoding": "UTF-8" }, - "numberize": { - "Package": "numberize", - "Version": "1.0.1", - "Source": "Repository", - "Title": "Convert Words to Numbers in Multiple Languages", - "Authors@R": "c( person(\"Chris\", \"Hartgerink\", , \"chris@libscie.org\", role = \"rev\", comment = c(ORCID = \"0000-0003-1050-6809\")), person(\"Joshua W.\", \"Lambert\", , \"joshua.lambert@lshtm.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0001-5218-3046\")), person(\"Karim\", \"Mané\", , \"karim.mane@lshtm.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9892-2999\")), person(\"Hugo\", \"Gruson\", , \"hugo.gruson+R@normalesup.org\", role = \"aut\", comment = c(ORCID = \"0000-0002-4094-1476\")), person(\"Bankole\", \"Ahadzie\", , \"bankole.ahadzie@lshtm.ac.uk\", role = c(\"aut\", \"cre\", \"cph\")) )", - "Description": "Converts written out numbers into their equivalent numbers. Supports numbers written out in English, French, or Spanish.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/epiverse-trace/numberize", - "BugReports": "https://github.com/epiverse-trace/numberize/issues", - "Depends": [ - "R (>= 3.5.0)" - ], - "Suggests": [ - "spelling", - "testthat (>= 3.0.0)" - ], - "Config/Department": "Centre for the Mathematical Modelling of Infectious Diseases", - "Config/DepartmentURL": "https://www.lshtm.ac.uk/research/centres/centre-mathematical-modelling-infectious-diseases", - "Config/Institution": "London School of Hygiene and Tropical Medicine", - "Config/Needs/website": "epiverse-trace/epiversetheme", - "Config/Recon": "stable", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "Language": "en-US", - "RoxygenNote": "7.3.1", - "NeedsCompilation": "no", - "Author": "Chris Hartgerink [rev] (), Joshua W. Lambert [ctb] (), Karim Mané [ctb] (), Hugo Gruson [aut] (), Bankole Ahadzie [aut, cre, cph]", - "Maintainer": "Bankole Ahadzie ", - "Repository": "CRAN" - }, "oai": { "Package": "oai", "Version": "0.4.0", @@ -3982,7 +3698,7 @@ }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.4.6", + "Version": "1.4.7", "Source": "Repository", "Title": "Find Tools Needed to Build R Packages", "Authors@R": "c( person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -4462,7 +4178,7 @@ }, "readxl": { "Package": "readxl", - "Version": "1.4.4", + "Version": "1.4.5", "Source": "Repository", "Title": "Read Excel Files", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = \"Copyright holder of all R code and all C/C++ code without explicit copyright attribution\"), person(\"Marcin\", \"Kalicinski\", role = c(\"ctb\", \"cph\"), comment = \"Author of included RapidXML code\"), person(\"Komarov Valery\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Christophe Leitienne\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Bob Colbert\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"David Hoerl\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Evan Miller\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\") )", @@ -4574,7 +4290,7 @@ }, "renv": { "Package": "renv", - "Version": "1.1.2", + "Version": "1.1.4", "Source": "Repository", "Type": "Package", "Title": "Project Environments", @@ -4829,7 +4545,7 @@ }, "rstan": { "Package": "rstan", - "Version": "2.32.6", + "Version": "2.32.7", "Source": "Repository", "Type": "Package", "Title": "R Interface to Stan", @@ -4883,7 +4599,7 @@ "Config/testthat/edition": "3", "Author": "Jiqiang Guo [aut], Jonah Gabry [aut], Ben Goodrich [cre, aut], Andrew Johnson [aut], Sebastian Weber [aut], Hamada S. Badr [aut] (), Daniel Lee [ctb], Krzysztof Sakrejda [ctb], Modrak Martin [ctb], Trustees of Columbia University [cph], Oleg Sklyar [cph] (R/cxxfunplus.R), The R Core Team [cph] (R/pairs.R, R/dynGet.R), Jens Oehlschlaegel-Akiyoshi [cph] (R/pairs.R), John Maddock [cph] (gamma.hpp), Paul Bristow [cph] (gamma.hpp), Nikhar Agrawal [cph] (gamma.hpp), Christopher Kormanyos [cph] (gamma.hpp), Bronder Steve [ctb]", "Maintainer": "Ben Goodrich ", - "Repository": "RSPM" + "Repository": "CRAN" }, "rstantools": { "Package": "rstantools", @@ -5197,41 +4913,6 @@ "RemoteSha": "c0018a7eae3a8858a873d85eeda55120489fb03f", "RemoteHost": "api.github.com" }, - "snakecase": { - "Package": "snakecase", - "Version": "0.11.1", - "Source": "Repository", - "Date": "2023-08-27", - "Title": "Convert Strings into any Case", - "Description": "A consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others.", - "Authors@R": "c( person(\"Malte\", \"Grosser\", , \"malte.grosser@gmail.com\", role = c(\"aut\", \"cre\")))", - "Maintainer": "Malte Grosser ", - "Depends": [ - "R (>= 3.2)" - ], - "Imports": [ - "stringr", - "stringi" - ], - "Suggests": [ - "testthat", - "covr", - "tibble", - "purrrlyr", - "knitr", - "rmarkdown", - "magrittr" - ], - "URL": "https://github.com/Tazinho/snakecase", - "BugReports": "https://github.com/Tazinho/snakecase/issues", - "Encoding": "UTF-8", - "License": "GPL-3", - "RoxygenNote": "6.1.1", - "VignetteBuilder": "knitr", - "NeedsCompilation": "no", - "Author": "Malte Grosser [aut, cre]", - "Repository": "RSPM" - }, "socialmixr": { "Package": "socialmixr", "Version": "0.4.0", @@ -5279,9 +4960,9 @@ }, "stringi": { "Package": "stringi", - "Version": "1.8.4", + "Version": "1.8.7", "Source": "Repository", - "Date": "2024-05-06", + "Date": "2025-03-27", "Title": "Fast and Portable Character String Processing Facilities", "Description": "A collection of character string/text/natural language processing tools for pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date-time formatting and parsing, and many more. They are fast, consistent, convenient, and - thanks to 'ICU' (International Components for Unicode) - portable across all locales and platforms. Documentation about 'stringi' is provided via its website at and the paper by Gagolewski (2022, ).", "URL": "https://stringi.gagolewski.com/, https://github.com/gagolews/stringi, https://icu.unicode.org/", @@ -5298,13 +4979,14 @@ ], "Biarch": "TRUE", "License": "file LICENSE", - "Author": "Marek Gagolewski [aut, cre, cph] (), Bartek Tartanus [ctb], and others (stringi source code); Unicode, Inc. and others (ICU4C source code, Unicode Character Database)", - "Maintainer": "Marek Gagolewski ", - "RoxygenNote": "7.2.3", + "Authors@R": "c(person(given = \"Marek\", family = \"Gagolewski\", role = c(\"aut\", \"cre\", \"cph\"), email = \"marek@gagolewski.com\", comment = c(ORCID = \"0000-0003-0637-6028\")), person(given = \"Bartek\", family = \"Tartanus\", role = \"ctb\"), person(\"Unicode, Inc. and others\", role=\"ctb\", comment = \"ICU4C source code, Unicode Character Database\") )", + "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "NeedsCompilation": "yes", + "Author": "Marek Gagolewski [aut, cre, cph] (), Bartek Tartanus [ctb], Unicode, Inc. and others [ctb] (ICU4C source code, Unicode Character Database)", + "Maintainer": "Marek Gagolewski ", "License_is_FOSS": "yes", - "Repository": "RSPM" + "Repository": "CRAN" }, "stringr": { "Package": "stringr", @@ -5812,7 +5494,7 @@ }, "tzdb": { "Package": "tzdb", - "Version": "0.4.0", + "Version": "0.5.0", "Source": "Repository", "Title": "Time Zone Database Information", "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -5821,24 +5503,24 @@ "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", "BugReports": "https://github.com/r-lib/tzdb/issues", "Depends": [ - "R (>= 3.5.0)" + "R (>= 4.0.0)" ], "Suggests": [ "covr", "testthat (>= 3.0.0)" ], "LinkingTo": [ - "cpp11 (>= 0.4.2)" + "cpp11 (>= 0.5.2)" ], "Biarch": "yes", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.2", "NeedsCompilation": "yes", "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", "Maintainer": "Davis Vaughan ", - "Repository": "RSPM" + "Repository": "CRAN" }, "utf8": { "Package": "utf8", @@ -5887,7 +5569,8 @@ "URL": "https://www.rforge.net/uuid", "BugReports": "https://github.com/s-u/uuid/issues", "NeedsCompilation": "yes", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "vctrs": { "Package": "vctrs", @@ -6193,7 +5876,7 @@ }, "xml2": { "Package": "xml2", - "Version": "1.3.7", + "Version": "1.3.8", "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\") )", @@ -6249,7 +5932,8 @@ "URL": "https://github.com/vubiostat/r-yaml/", "BugReports": "https://github.com/vubiostat/r-yaml/issues", "NeedsCompilation": "yes", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "ympes": { "Package": "ympes",