From 74897930327a1c4fec4ae1d299d69f07626771e4 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Wed, 23 Apr 2025 14:25:38 +0200 Subject: [PATCH] updating docs --- .Rbuildignore | 1 + R/app_version.R | 2 +- _pkgdown.yml | 1 + inst/apps/FreesearchR/app.R | 156 ++-- inst/apps/FreesearchR/ui.R | 20 +- man/data-plots.Rd | 15 +- renv.lock | 1217 ++---------------------------- tests/testthat/test-data_plots.R | 4 +- vignettes/data-types.Rmd | 1 + 9 files changed, 171 insertions(+), 1246 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index ed3805c..3a9512e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -12,3 +12,4 @@ ^docs$ ^pkgdown$ ^dev$ +^data-raw$ diff --git a/R/app_version.R b/R/app_version.R index d49df0c..1fbe1ec 100644 --- a/R/app_version.R +++ b/R/app_version.R @@ -1 +1 @@ -app_version <- function()'Version: 25.4.3.250422' +app_version <- function()'v25.4.3.250423' diff --git a/_pkgdown.yml b/_pkgdown.yml index 586880b..decca44 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -8,6 +8,7 @@ template: base_font: {google: "Montserrat"} heading_font: {google: "Public Sans"} # code_font: {google: "Open Sans"} + # Adding the switch destroys the theme colors light-switch: false navbar: diff --git a/inst/apps/FreesearchR/app.R b/inst/apps/FreesearchR/app.R index 293ccdc..5c205b3 100644 --- a/inst/apps/FreesearchR/app.R +++ b/inst/apps/FreesearchR/app.R @@ -10,7 +10,7 @@ #### Current file: /Users/au301842/FreesearchR/R//app_version.R ######## -app_version <- function()'Version: 25.4.3.250422' +app_version <- function()'v25.4.3.250423' ######## @@ -1801,7 +1801,7 @@ line_break <- function(data, lineLength = 20, force = FALSE) { #' @export #' wrap_plot_list <- function(data, tag_levels = NULL) { - if (ggplot2::is.ggplot(data[[1]])) { + if (ggplot2::is_ggplot(data[[1]])) { if (length(data) > 1) { out <- data |> (\(.x){ @@ -1838,7 +1838,7 @@ wrap_plot_list <- function(data, tag_levels = NULL) { align_axes <- function(...) { # https://stackoverflow.com/questions/62818776/get-axis-limits-from-ggplot-object # https://github.com/thomasp85/patchwork/blob/main/R/plot_multipage.R#L150 - if (ggplot2::is.ggplot(..1)) { + if (ggplot2::is_ggplot(..1)) { ## Assumes list of ggplots p <- list(...) } else if (is.list(..1)) { @@ -2497,7 +2497,7 @@ read_input <- function(file, consider.na = c("NA", '""', "")) { if (ext == "csv") { df <- readr::read_csv(file = file, na = consider.na) } else if (ext %in% c("xls", "xlsx")) { - df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na) + df <- readxl::read_excel(file = file, na.strings = consider.na) } else if (ext == "dta") { df <- haven::read_dta(file = file) } else if (ext == "ods") { @@ -2838,7 +2838,7 @@ sort_by <- function(x, y, na.rm = FALSE, ...) { get_ggplot_label <- function(data, label) { - assertthat::assert_that(ggplot2::is.ggplot(data)) + assertthat::assert_that(ggplot2::is_ggplot(data)) data$labels[[label]] } @@ -3312,7 +3312,7 @@ import_file_server <- function(id, req(input$file) if (!all(input$sheet %in% temporary_rv$sheets)) { - sheets <- 1 + sheets <- 1 } else { sheets <- input$sheet } @@ -3368,31 +3368,33 @@ import_file_server <- function(id, ) observeEvent(input$see_data, { - tryCatch({ - datamods:::show_data(default_parsing(temporary_rv$data), title = datamods:::i18n("Imported data"), type = show_data_in) - }, - # warning = function(warn) { - # showNotification(warn, type = "warning") - # }, - error = function(err) { - showNotification(err, type = "err") - } + tryCatch( + { + datamods:::show_data(default_parsing(temporary_rv$data), title = datamods:::i18n("Imported data"), type = show_data_in) + }, + # warning = function(warn) { + # showNotification(warn, type = "warning") + # }, + error = function(err) { + showNotification(err, type = "err") + } ) }) output$table <- toastui::renderDatagrid2({ req(temporary_rv$data) - tryCatch({ - toastui::datagrid( - data = setNames(head(temporary_rv$data, 5),make.names(names(temporary_rv$data),unique = TRUE)), - theme = "striped", - colwidths = "guess", - minBodyHeight = 250 - ) - }, - error = function(err) { - showNotification(err, type = "err") - } + tryCatch( + { + toastui::datagrid( + data = setNames(head(temporary_rv$data, 5), make.names(names(temporary_rv$data), unique = TRUE)), + theme = "striped", + colwidths = "guess", + minBodyHeight = 250 + ) + }, + error = function(err) { + showNotification(err, type = "err") + } ) }) @@ -3488,13 +3490,22 @@ import_xls <- function(file, sheet, skip, na.strings) { sheet |> purrr::map(\(.x){ - openxlsx2::read_xlsx( - file = file, + readxl::read_excel( + path = file, sheet = .x, - skip_empty_rows = TRUE, - start_row = skip - 1, - na.strings = na.strings + na = na.strings, + skip = skip, + .name_repair = "unique_quiet", + trim_ws = TRUE ) + + # openxlsx2::read_xlsx( + # file = file, + # sheet = .x, + # skip_empty_rows = TRUE, + # start_row = skip - 1, + # na.strings = na.strings + # ) }) |> purrr::reduce(dplyr::full_join) }, @@ -3738,13 +3749,14 @@ plot_box <- function(data, pri, sec, ter = NULL) { #' @export #' #' @examples +#' mtcars |> plot_box_single("mpg") #' mtcars |> plot_box_single("mpg","cyl") plot_box_single <- function(data, pri, sec=NULL, seed = 2103) { set.seed(seed) if (is.null(sec)) { sec <- "All" - data[[y]] <- sec + data[[sec]] <- sec } discrete <- !data_type(data[[sec]]) %in% "continuous" @@ -4075,7 +4087,7 @@ sankey_ready <- function(data, pri, sec, numbers = "count", ...) { data[c(pri, sec)] <- data[c(pri, sec)] |> dplyr::mutate(dplyr::across(!dplyr::where(is.factor), forcats::as_factor)) - out <- dplyr::count(data, !!dplyr::sym(pri), !!dplyr::sym(sec)) + out <- dplyr::count(data, !!dplyr::sym(pri), !!dplyr::sym(sec), .drop = FALSE) out <- out |> dplyr::group_by(!!dplyr::sym(pri)) |> @@ -4126,9 +4138,17 @@ str_remove_last <- function(data, pattern = "\n") { #' @examples #' ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) #' ds |> plot_sankey("first", "last") -#' ds |> plot_sankey("first", "last", color.group = "y") -#' ds |> plot_sankey("first", "last", z = "g", color.group = "y") -plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "x", colors = NULL) { +#' ds |> plot_sankey("first", "last", color.group = "sec") +#' ds |> plot_sankey("first", "last", ter = "g", color.group = "sec") +#' mtcars |> +#' default_parsing() |> +#' plot_sankey("cyl", "gear", "am", color.group = "pri") +#' ## In this case, the last plot as the secondary variable in wrong order +#' ## Dont know why... +#' mtcars |> +#' default_parsing() |> +#' plot_sankey("cyl", "gear", "vs", color.group = "pri") +plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors = NULL) { if (!is.null(ter)) { ds <- split(data, data[ter]) } else { @@ -4136,16 +4156,12 @@ plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "x", colors = } out <- lapply(ds, \(.ds){ - plot_sankey_single(.ds, x = pri, y = sec, color.group = color.group, colors = colors) + plot_sankey_single(.ds, pri = pri, sec = sec, color.group = color.group, colors = colors) }) patchwork::wrap_plots(out) } -default_theme <- function() { - theme_void() -} - #' Beautiful sankey plot #' #' @param color.group set group to colour by. "x" or "y". @@ -4159,15 +4175,26 @@ default_theme <- function() { #' @examples #' ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) #' ds |> plot_sankey_single("first", "last") -#' ds |> plot_sankey_single("first", "last", color.group = "y") +#' ds |> plot_sankey_single("first", "last", color.group = "sec") #' data.frame( #' g = sample(LETTERS[1:2], 100, TRUE), #' first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), #' last = sample(c(TRUE, FALSE, FALSE), 100, TRUE) #' ) |> #' plot_sankey_single("first", "last", color.group = "pri") +#' mtcars |> +#' default_parsing() |> +#' str() +#' plot_sankey_single("cyl", "vs", color.group = "pri") plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), colors = NULL, ...) { color.group <- match.arg(color.group) + + data_orig <- data + data[c(pri, sec)] <- data[c(pri, sec)] |> + dplyr::mutate(dplyr::across(dplyr::where(is.factor), forcats::fct_drop)) + + # browser() + data <- data |> sankey_ready(pri = pri, sec = sec, ...) library(ggalluvial) @@ -4177,11 +4204,17 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co if (is.null(colors)) { if (color.group == "sec") { - main.colors <- viridisLite::viridis(n = length(levels(data[[sec]]))) + main.colors <- viridisLite::viridis(n = length(levels(data_orig[[sec]]))) + ## Only keep colors for included levels + main.colors <- main.colors[match(levels(data[[sec]]), levels(data_orig[[sec]]))] + secondary.colors <- rep(na.color, length(levels(data[[pri]]))) label.colors <- Reduce(c, lapply(list(secondary.colors, rev(main.colors)), contrast_text)) } else { - main.colors <- viridisLite::viridis(n = length(levels(data[[pri]]))) + main.colors <- viridisLite::viridis(n = length(levels(data_orig[[pri]]))) + ## Only keep colors for included levels + main.colors <- main.colors[match(levels(data[[pri]]), levels(data_orig[[pri]]))] + secondary.colors <- rep(na.color, length(levels(data[[sec]]))) label.colors <- Reduce(c, lapply(list(rev(main.colors), secondary.colors), contrast_text)) } @@ -4199,7 +4232,11 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co if (color.group == "sec") { p <- p + ggalluvial::geom_alluvium( - ggplot2::aes(fill = !!dplyr::sym(sec), color = !!dplyr::sym(sec)), + ggplot2::aes( + fill = !!dplyr::sym(sec) # , + ## Including will print strings when levels are empty + # color = !!dplyr::sym(sec) + ), width = 1 / 16, alpha = .8, knot.pos = 0.4, @@ -4211,7 +4248,10 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co } else { p <- p + ggalluvial::geom_alluvium( - ggplot2::aes(fill = !!dplyr::sym(pri), color = !!dplyr::sym(pri)), + ggplot2::aes( + fill = !!dplyr::sym(pri) # , + # color = !!dplyr::sym(pri) + ), width = 1 / 16, alpha = .8, knot.pos = 0.4, @@ -4235,7 +4275,7 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co labels = group_labels ) + ggplot2::scale_fill_manual(values = colors[-1], na.value = colors[1]) + - ggplot2::scale_color_manual(values = main.colors) + + # ggplot2::scale_color_manual(values = main.colors) + ggplot2::theme_void() + ggplot2::theme( legend.position = "none", @@ -8399,7 +8439,7 @@ ui_elements <- list( shiny::uiOutput(outputId = "column_filter"), shiny::helpText("Variable ", tags$a( "data type", - href = "https://agdamsbo.github.io/FreesearchR/articles/FreesearchR.html", + href = "https://agdamsbo.github.io/FreesearchR/articles/data-types.html", target = "_blank", rel = "noopener noreferrer" ), " filtering."), @@ -8596,15 +8636,13 @@ ui_elements <- list( data_visuals_ui("visuals"), shiny::tagList( bslib::nav_spacer(), - bslib::nav_panel( - title = "Notes", - shiny::fluidRow( - shiny::column(width = 2), - shiny::column( - width = 8, - shiny::markdown(readLines("www/notes_visuals.md")), - shiny::column(width = 2) - ) + bslib::nav_item( + # shiny::img(shiny::icon("book")), + shiny::tags$a( + href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html", + "Notes (external)", + target = "_blank", + rel = "noopener noreferrer" ) ) ) @@ -8774,11 +8812,11 @@ ui <- bslib::page_fixed( style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;", shiny::p( style = "margin: 1", - "Data is only stored for analyses and deleted immediately afterwards." + "Data is only stored for analyses and deleted when the app is closed." ), shiny::p( style = "margin: 1; color: #888;", - "AG Damsbo | v", app_version(), " | ", shiny::tags$a("AGPLv3 license", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer") + shiny::tags$a("AG Damsbo", href = "https://andreas.gdamsbo.dk/", target = "_blank", rel = "noopener noreferrer")," | ", app_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer") ), ) ) diff --git a/inst/apps/FreesearchR/ui.R b/inst/apps/FreesearchR/ui.R index 6fb9b0d..8dac445 100644 --- a/inst/apps/FreesearchR/ui.R +++ b/inst/apps/FreesearchR/ui.R @@ -359,15 +359,13 @@ ui_elements <- list( data_visuals_ui("visuals"), shiny::tagList( bslib::nav_spacer(), - bslib::nav_panel( - title = "Notes", - shiny::fluidRow( - shiny::column(width = 2), - shiny::column( - width = 8, - shiny::markdown(readLines("www/notes_visuals.md")), - shiny::column(width = 2) - ) + bslib::nav_item( + # shiny::img(shiny::icon("book")), + shiny::tags$a( + href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html", + "Notes (external)", + target = "_blank", + rel = "noopener noreferrer" ) ) ) @@ -537,11 +535,11 @@ ui <- bslib::page_fixed( style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;", shiny::p( style = "margin: 1", - "Data is only stored for analyses and deleted immediately afterwards." + "Data is only stored for analyses and deleted when the app is closed." ), shiny::p( style = "margin: 1; color: #888;", - "AG Damsbo | v", app_version(), " | ", shiny::tags$a("AGPLv3 license", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer") + shiny::tags$a("AG Damsbo", href = "https://andreas.gdamsbo.dk/", target = "_blank", rel = "noopener noreferrer")," | ", app_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer") ), ) ) diff --git a/man/data-plots.Rd b/man/data-plots.Rd index 171c45f..6a42b99 100644 --- a/man/data-plots.Rd +++ b/man/data-plots.Rd @@ -32,7 +32,7 @@ plot_ridge(data, x, y, z = NULL, ...) sankey_ready(data, pri, sec, numbers = "count", ...) -plot_sankey(data, pri, sec, ter = NULL, color.group = "x", colors = NULL) +plot_sankey(data, pri, sec, ter = NULL, color.group = "pri", colors = NULL) plot_scatter(data, pri, sec, ter = NULL) @@ -103,6 +103,7 @@ mtcars |> plot_box(pri = "mpg", sec = "cyl", ter = "gear") mtcars |> default_parsing() |> plot_box(pri = "mpg", sec = "cyl", ter = "gear") +mtcars |> plot_box_single("mpg") mtcars |> plot_box_single("mpg","cyl") mtcars |> plot_hbars(pri = "carb", sec = "cyl") mtcars |> plot_hbars(pri = "carb", sec = NULL) @@ -121,8 +122,16 @@ data.frame( sankey_ready("first", "last") ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) ds |> plot_sankey("first", "last") -ds |> plot_sankey("first", "last", color.group = "y") -ds |> plot_sankey("first", "last", z = "g", color.group = "y") +ds |> plot_sankey("first", "last", color.group = "sec") +ds |> plot_sankey("first", "last", ter = "g", color.group = "sec") +mtcars |> + default_parsing() |> + plot_sankey("cyl", "gear", "am", color.group = "pri") +## In this case, the last plot as the secondary variable in wrong order +## Dont know why... +mtcars |> + default_parsing() |> + plot_sankey("cyl", "gear", "vs", color.group = "pri") mtcars |> plot_scatter(pri = "mpg", sec = "wt") mtcars |> plot_violin(pri = "mpg", sec = "cyl", ter = "gear") } diff --git a/renv.lock b/renv.lock index 521be62..1a38674 100644 --- a/renv.lock +++ b/renv.lock @@ -146,27 +146,6 @@ "Maintainer": "Achim Zeileis ", "Repository": "CRAN" }, - "GPArotation": { - "Package": "GPArotation", - "Version": "2024.3-1", - "Source": "Repository", - "Title": "Gradient Projection Factor Rotation", - "Authors@R": "c( person(\"Coen\", \"Bernaards\", email = \"cab.gparotation@gmail.com\", role = c(\"aut\",\"cre\")), person(\"Paul\", \"Gilbert\", email = \"pgilbert.ttv9z@ncf.ca\", role = \"aut\"), person(\"Robert\", \"Jennrich\", role = \"aut\") )", - "Depends": [ - "R (>= 2.0.0)" - ], - "Description": "Gradient Projection Algorithms for Factor Rotation. For details see ?GPArotation. When using this package, please cite: Bernaards and Jennrich (2005) . \"Gradient Projection Algorithms and Software for Arbitrary Rotation Criteria in Factor Analysis\".", - "LazyData": "yes", - "Imports": [ - "stats" - ], - "License": "GPL (>= 2)", - "URL": "https://optimizer.r-forge.r-project.org/GPArotation_www/", - "NeedsCompilation": "no", - "Author": "Coen Bernaards [aut, cre], Paul Gilbert [aut], Robert Jennrich [aut]", - "Maintainer": "Coen Bernaards ", - "Repository": "CRAN" - }, "GenSA": { "Package": "GenSA", "Version": "1.1.14.1", @@ -1441,67 +1420,6 @@ "Maintainer": "Joseph Larmarange ", "Repository": "CRAN" }, - "broom.mixed": { - "Package": "broom.mixed", - "Version": "0.2.9.6", - "Source": "Repository", - "Type": "Package", - "Title": "Tidying Methods for Mixed Models", - "Authors@R": "c( person(\"Ben\", \"Bolker\", email = \"bolker@mcmaster.ca\", role = c(\"aut\", \"cre\"), comment=c(ORCID=\"0000-0002-2127-0443\")), person(\"David\", \"Robinson\", email = \"admiral.david@gmail.com\", role = \"aut\"), person(\"Dieter\", \"Menne\", role = \"ctb\"), person(\"Jonah\", \"Gabry\", role = \"ctb\"), person(\"Paul\", \"Buerkner\", role = \"ctb\"), person(\"Christopher\", \"Hua\", role = \"ctb\"), person(\"William\", \"Petry\", role = \"ctb\", comment=c(ORCID=\"0000-0002-5230-5987\")), person(\"Joshua\", \"Wiley\", role = \"ctb\", comment=c(ORCID=\"0000-0002-0271-6702\")), person(\"Patrick\", \"Kennedy\", role = \"ctb\"), person(\"Eduard\", \"Szöcs\", role = \"ctb\", comment=c(ORCID = \"0000-0001-5376-1194\", sponsor = \"BASF SE\")), person(\"Indrajeet\", \"Patil\", role=\"ctb\"), person(\"Vincent\", \"Arel-Bundock\", email = \"vincent.arel-bundock@umontreal.ca\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2042-7063\")), person(\"Bill\", \"Denney\", role = \"ctb\"), person(\"Cory\", \"Brunson\", role = \"ctb\"), person(\"Joe\", \"Wasserman\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9705-1853\")), person(\"Alexey\", \"Stukalov\", role = \"ctb\"), person(\"Matthieu\", \"Bruneaux\", role = \"ctb\") )", - "Maintainer": "Ben Bolker ", - "Description": "Convert fitted objects from various R mixed-model packages into tidy data frames along the lines of the 'broom' package. The package provides three S3 generics for each model: tidy(), which summarizes a model's statistical findings such as coefficients of a regression; augment(), which adds columns to the original data such as predictions, residuals and cluster assignments; and glance(), which provides a one-row summary of model-level statistics.", - "Imports": [ - "broom", - "coda", - "dplyr", - "forcats", - "methods", - "nlme", - "purrr", - "stringr", - "tibble", - "tidyr", - "furrr" - ], - "Suggests": [ - "brms", - "dotwhisker", - "knitr", - "testthat", - "gamlss", - "gamlss.data", - "ggplot2", - "GLMMadaptive", - "glmmADMB", - "glmmTMB", - "lmerTest", - "lme4", - "Matrix", - "MCMCglmm", - "mediation", - "mgcv", - "ordinal", - "pander", - "pbkrtest", - "posterior", - "rstan", - "rstanarm", - "rstantools", - "R2jags", - "TMB", - "rmarkdown" - ], - "URL": "https://github.com/bbolker/broom.mixed", - "BugReports": "https://github.com/bbolker/broom.mixed/issues", - "License": "GPL-3", - "Encoding": "UTF-8", - "Additional_repositories": "http://bbolker.github.io/drat", - "VignetteBuilder": "knitr", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "no", - "Author": "Ben Bolker [aut, cre] (), David Robinson [aut], Dieter Menne [ctb], Jonah Gabry [ctb], Paul Buerkner [ctb], Christopher Hua [ctb], William Petry [ctb] (), Joshua Wiley [ctb] (), Patrick Kennedy [ctb], Eduard Szöcs [ctb] (, BASF SE), Indrajeet Patil [ctb], Vincent Arel-Bundock [ctb] (), Bill Denney [ctb], Cory Brunson [ctb], Joe Wasserman [ctb] (), Alexey Stukalov [ctb], Matthieu Bruneaux [ctb]", - "Repository": "CRAN" - }, "bsicons": { "Package": "bsicons", "Version": "0.1.2", @@ -1646,47 +1564,9 @@ "Maintainer": "Winston Chang ", "Repository": "CRAN" }, - "callr": { - "Package": "callr", - "Version": "3.7.6", - "Source": "Repository", - "Title": "Call R from R", - "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0001-7098-9676\")), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Ascent Digital Services\", role = c(\"cph\", \"fnd\")) )", - "Description": "It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.", - "License": "MIT + file LICENSE", - "URL": "https://callr.r-lib.org, https://github.com/r-lib/callr", - "BugReports": "https://github.com/r-lib/callr/issues", - "Depends": [ - "R (>= 3.4)" - ], - "Imports": [ - "processx (>= 3.6.1)", - "R6", - "utils" - ], - "Suggests": [ - "asciicast (>= 2.3.1)", - "cli (>= 1.1.0)", - "mockery", - "ps", - "rprojroot", - "spelling", - "testthat (>= 3.2.0)", - "withr (>= 2.3.0)" - ], - "Config/Needs/website": "r-lib/asciicast, glue, htmlwidgets, igraph, tibble, tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "Language": "en-US", - "RoxygenNote": "7.3.1.9000", - "NeedsCompilation": "no", - "Author": "Gábor Csárdi [aut, cre, cph] (), Winston Chang [aut], Posit Software, PBC [cph, fnd], Ascent Digital Services [cph, fnd]", - "Maintainer": "Gábor Csárdi ", - "Repository": "CRAN" - }, "cards": { "Package": "cards", - "Version": "0.5.1", + "Version": "0.6.0", "Source": "Repository", "Title": "Analysis Results Data", "Authors@R": "c( person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-0862-2018\")), person(\"Becca\", \"Krouse\", , \"becca.z.krouse@gsk.com\", role = \"aut\"), person(\"Emily\", \"de la Rua\", , \"emily.de_la_rua@contractors.roche.com\", role = \"aut\"), person(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")), person(\"GlaxoSmithKline Research & Development Limited\", role = \"cph\") )", @@ -1725,19 +1605,19 @@ }, "cardx": { "Package": "cardx", - "Version": "0.2.3", + "Version": "0.2.4", "Source": "Repository", "Title": "Extra Analysis Results Data Utilities", "Authors@R": "c( person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-0862-2018\")), person(\"Abinaya\", \"Yogasekaram\", , \"abinaya.yogasekaram@contractors.roche.com\", role = \"aut\"), person(\"Emily\", \"de la Rua\", , \"emily.de_la_rua@contractors.roche.com\", role = \"aut\"), person(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")) )", "Description": "Create extra Analysis Results Data (ARD) summary objects. The package supplements the simple ARD functions from the 'cards' package, exporting functions to put statistical results in the ARD format. These objects are used and re-used to construct summary tables, visualizations, and written reports.", "License": "Apache License 2.0", - "URL": "https://insightsengineering.github.io/cardx/, https://github.com/insightsengineering/cardx/", + "URL": "https://github.com/insightsengineering/cardx, https://insightsengineering.github.io/cardx/", "BugReports": "https://github.com/insightsengineering/cardx/issues", "Depends": [ "R (>= 4.2)" ], "Imports": [ - "cards (>= 0.5.0)", + "cards (>= 0.5.1)", "cli (>= 3.6.1)", "dplyr (>= 1.1.2)", "glue (>= 1.6.2)", @@ -1747,7 +1627,7 @@ ], "Suggests": [ "aod (>= 1.3.3)", - "broom (>= 1.0.5)", + "broom (>= 1.0.8)", "broom.helpers (>= 1.17.0)", "broom.mixed (>= 0.2.9)", "car (>= 3.1-2)", @@ -1755,7 +1635,7 @@ "emmeans (>= 1.7.3)", "geepack (>= 1.3.2)", "ggsurvfit (>= 1.1.0)", - "lme4 (>= 1.1-35.3)", + "lme4 (>= 1.1-37)", "parameters (>= 0.20.2)", "smd (>= 0.6.6)", "survey (>= 4.2)", @@ -2030,26 +1910,6 @@ "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", "Repository": "CRAN" }, - "coda": { - "Package": "coda", - "Version": "0.19-4.1", - "Source": "Repository", - "Date": "2020-09-30", - "Title": "Output Analysis and Diagnostics for MCMC", - "Authors@R": "c(person(\"Martyn\", \"Plummer\", role=c(\"aut\",\"cre\",\"trl\"), email=\"martyn.plummer@gmail.com\"), person(\"Nicky\", \"Best\", role=\"aut\"), person(\"Kate\", \"Cowles\", role=\"aut\"), person(\"Karen\", \"Vines\", role=\"aut\"), person(\"Deepayan\", \"Sarkar\", role=\"aut\"), person(\"Douglas\", \"Bates\", role=\"aut\"), person(\"Russell\", \"Almond\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"))", - "Depends": [ - "R (>= 2.14.0)" - ], - "Imports": [ - "lattice" - ], - "Description": "Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.", - "License": "GPL (>= 2)", - "NeedsCompilation": "no", - "Author": "Martyn Plummer [aut, cre, trl], Nicky Best [aut], Kate Cowles [aut], Karen Vines [aut], Deepayan Sarkar [aut], Douglas Bates [aut], Russell Almond [aut], Arni Magnusson [aut]", - "Maintainer": "Martyn Plummer ", - "Repository": "CRAN" - }, "codetools": { "Package": "codetools", "Version": "0.2-20", @@ -3354,7 +3214,7 @@ }, "fs": { "Package": "fs", - "Version": "1.6.5", + "Version": "1.6.6", "Source": "Repository", "Title": "Cross-Platform File System Operations Based on 'libuv'", "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -3394,82 +3254,6 @@ "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" }, - "furrr": { - "Package": "furrr", - "Version": "0.3.1", - "Source": "Repository", - "Title": "Apply Mapping Functions in Parallel using Futures", - "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"Matt\", \"Dancho\", , \"mdancho@business-science.io\", role = \"aut\"), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", - "Description": "Implementations of the family of map() functions from 'purrr' that can be resolved using any 'future'-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/DavisVaughan/furrr, https://furrr.futureverse.org/", - "BugReports": "https://github.com/DavisVaughan/furrr/issues", - "Depends": [ - "future (>= 1.25.0)", - "R (>= 3.4.0)" - ], - "Imports": [ - "globals (>= 0.14.0)", - "lifecycle (>= 1.0.1)", - "purrr (>= 0.3.4)", - "rlang (>= 1.0.2)", - "vctrs (>= 0.4.1)" - ], - "Suggests": [ - "carrier", - "covr", - "dplyr (>= 0.7.4)", - "knitr", - "listenv (>= 0.6.0)", - "magrittr", - "rmarkdown", - "testthat (>= 3.0.0)", - "tidyselect", - "withr" - ], - "Config/Needs/website": "progressr", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "RoxygenNote": "7.2.1", - "NeedsCompilation": "no", - "Author": "Davis Vaughan [aut, cre], Matt Dancho [aut], RStudio [cph, fnd]", - "Maintainer": "Davis Vaughan ", - "Repository": "CRAN" - }, - "future": { - "Package": "future", - "Version": "1.34.0", - "Source": "Repository", - "Title": "Unified Parallel and Distributed Processing in R for Everyone", - "Imports": [ - "digest", - "globals (>= 0.16.1)", - "listenv (>= 0.8.0)", - "parallel", - "parallelly (>= 1.38.0)", - "utils" - ], - "Suggests": [ - "methods", - "RhpcBLASctl", - "R.rsp", - "markdown" - ], - "VignetteBuilder": "R.rsp", - "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role = c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\", comment = c(ORCID = \"0000-0002-7579-5165\")))", - "Description": "The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. The simplest way to evaluate an expression in parallel is to use `x %<-% { expression }` with `plan(multisession)`. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implement additional backends for processing futures via compute cluster schedulers, etc. Because of its unified API, there is no need to modify any code in order switch from sequential on the local machine to, say, distributed processing on a remote compute cluster. Another strength of this package is that global variables and functions are automatically identified and exported as needed, making it straightforward to tweak existing code to make use of futures.", - "License": "LGPL (>= 2.1)", - "LazyLoad": "TRUE", - "ByteCompile": "TRUE", - "URL": "https://future.futureverse.org, https://github.com/HenrikBengtsson/future", - "BugReports": "https://github.com/HenrikBengtsson/future/issues", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "no", - "Author": "Henrik Bengtsson [aut, cre, cph] ()", - "Maintainer": "Henrik Bengtsson ", - "Repository": "CRAN" - }, "gap": { "Package": "gap", "Version": "1.6", @@ -3717,114 +3501,6 @@ "Maintainer": "Alboukadel Kassambara ", "Repository": "CRAN" }, - "ggeffects": { - "Package": "ggeffects", - "Version": "2.2.1", - "Source": "Repository", - "Type": "Package", - "Encoding": "UTF-8", - "Title": "Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs", - "Authors@R": "c( person(\"Daniel\", \"Lüdecke\", role = c(\"aut\", \"cre\"), email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(\"Frederik\", \"Aust\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4900-788X\")), person(\"Sam\", \"Crawley\", role = \"ctb\", email = \"sam@crawley.nz\", comment = c(ORCID = \"0000-0002-7847-0411\")), person(c(\"Mattan\", \"S.\"), \"Ben-Shachar\", role = \"ctb\", email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(c(\"Sean\", \"C.\"), \"Anderson\", role = \"ctb\", email = \"sean@seananderson.ca\", comment = c(ORCID = \"0000-0001-9563-1937\")) )", - "Maintainer": "Daniel Lüdecke ", - "Description": "Compute marginal effects and adjusted predictions from statistical models and returns the result as tidy data frames. These data frames are ready to use with the 'ggplot2'-package. Effects and predictions can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a generic plot()-method to plot the results using 'ggplot2'.", - "Depends": [ - "R (>= 3.6)" - ], - "Imports": [ - "graphics", - "insight (>= 1.0.1)", - "datawizard (>= 1.0.0)", - "stats", - "utils" - ], - "Suggests": [ - "AER", - "afex", - "aod", - "bayestestR", - "betareg", - "brglm", - "brglm2", - "brms", - "broom", - "car", - "carData", - "clubSandwich", - "dfidx", - "effects (>= 4.2-2)", - "effectsize (>= 1.0.0)", - "emmeans (>= 1.8.9)", - "fixest", - "gam", - "gamlss", - "gamm4", - "gee", - "geepack", - "ggplot2", - "ggrepel", - "GLMMadaptive", - "glmmTMB (>= 1.1.7)", - "gridExtra", - "gt", - "haven", - "htmltools", - "httr2", - "jsonlite", - "knitr", - "lme4 (>= 1.1-35)", - "logistf", - "logitr", - "marginaleffects (>= 0.25.0)", - "modelbased (>= 0.9.0)", - "MASS", - "Matrix", - "mice", - "MCMCglmm", - "MuMIn", - "mgcv", - "mclogit", - "mlogit", - "nestedLogit (>= 0.3.0)", - "nlme", - "nnet", - "ordinal", - "parameters", - "parsnip", - "patchwork", - "pscl", - "plm", - "quantreg", - "rmarkdown", - "rms", - "robustbase", - "rstanarm", - "rstantools", - "sandwich", - "sdmTMB (>= 0.4.0)", - "see", - "sjlabelled (>= 1.1.2)", - "sjstats", - "speedglm", - "survey", - "survival", - "testthat", - "tibble", - "tinytable (>= 0.1.0)", - "vdiffr", - "withr", - "VGAM" - ], - "URL": "https://strengejacke.github.io/ggeffects/", - "BugReports": "https://github.com/strengejacke/ggeffects/issues/", - "RoxygenNote": "7.3.2", - "VignetteBuilder": "knitr", - "Config/testthat/edition": "3", - "License": "MIT + file LICENSE", - "LazyData": "true", - "NeedsCompilation": "no", - "Author": "Daniel Lüdecke [aut, cre] (), Frederik Aust [ctb] (), Sam Crawley [ctb] (), Mattan S. Ben-Shachar [ctb] (), Sean C. Anderson [ctb] ()", - "Repository": "CRAN" - }, "ggforce": { "Package": "ggforce", "Version": "0.4.2", @@ -3880,63 +3556,9 @@ "Author": "Thomas Lin Pedersen [cre, aut] (), RStudio [cph]", "Repository": "CRAN" }, - "ggiraph": { - "Package": "ggiraph", - "Version": "0.8.13", - "Source": "Repository", - "Type": "Package", - "Title": "Make 'ggplot2' Graphics Interactive", - "Authors@R": "c( person(\"David\", \"Gohel\", , \"david.gohel@ardata.fr\", role = c(\"aut\", \"cre\")), person(\"Panagiotis\", \"Skintzos\", , \"sigmapi@posteo.net\", role = \"aut\"), person(\"Mike\", \"Bostock\", role = \"cph\", comment = \"d3.js\"), person(\"Speros\", \"Kokenes\", role = \"cph\", comment = \"d3-lasso\"), person(\"Eric\", \"Shull\", role = \"cph\", comment = \"saveSvgAsPng js library\"), person(\"Lee\", \"Thomason\", role = \"cph\", comment = \"TinyXML2\"), person(\"Vladimir\", \"Agafonkin\", role = \"cph\", comment = \"Flatbush\"), person(\"Eric\", \"Book\", role = \"ctb\", comment = \"hline and vline geoms\") )", - "Description": "Create interactive 'ggplot2' graphics using 'htmlwidgets'.", - "License": "GPL-3", - "URL": "https://davidgohel.github.io/ggiraph/", - "BugReports": "https://github.com/davidgohel/ggiraph/issues", - "Imports": [ - "cli", - "ggplot2 (>= 3.5.1)", - "grid", - "htmltools", - "htmlwidgets (>= 1.5)", - "purrr", - "Rcpp (>= 1.0)", - "rlang", - "stats", - "systemfonts", - "uuid", - "vctrs" - ], - "Suggests": [ - "dplyr", - "gdtools (>= 0.3.0)", - "ggrepel (>= 0.9.1)", - "hexbin", - "knitr", - "maps", - "quantreg", - "rmarkdown", - "sf (>= 1.0)", - "shiny", - "tinytest", - "xml2 (>= 1.0)" - ], - "LinkingTo": [ - "Rcpp", - "systemfonts" - ], - "VignetteBuilder": "knitr", - "Copyright": "See file COPYRIGHTS.", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "SystemRequirements": "libpng", - "Collate": "'RcppExports.R' 'ipar.R' 'utils_ggplot2_performance.R' 'utils_ggplot2.R' 'utils.R' 'annotate_interactive.R' 'annotation_raster_interactive.R' 'utils_css.R' 'fonts.R' 'girafe_options.R' 'default.R' 'dsvg.R' 'dsvg_view.R' 'element_interactive.R' 'facet_interactive.R' 'geom_abline_interactive.R' 'geom_path_interactive.R' 'geom_polygon_interactive.R' 'geom_rect_interactive.R' 'geom_bar_interactive.R' 'geom_bin_2d_interactive.R' 'geom_boxplot_interactive.R' 'geom_col_interactive.R' 'geom_contour_interactive.R' 'geom_count_interactive.R' 'geom_crossbar_interactive.R' 'geom_curve_interactive.R' 'geom_density_2d_interactive.R' 'geom_density_interactive.R' 'geom_dotplot_interactive.R' 'geom_errorbar_interactive.R' 'geom_errorbarh_interactive.R' 'geom_freqpoly_interactive.R' 'geom_hex_interactive.R' 'geom_histogram_interactive.R' 'geom_hline_interactive.R' 'geom_jitter_interactive.R' 'geom_label_interactive.R' 'geom_linerange_interactive.R' 'geom_map_interactive.R' 'geom_point_interactive.R' 'geom_pointrange_interactive.R' 'geom_quantile_interactive.R' 'geom_raster_interactive.R' 'geom_ribbon_interactive.R' 'geom_segment_interactive.R' 'geom_sf_interactive.R' 'geom_smooth_interactive.R' 'geom_spoke_interactive.R' 'geom_text_interactive.R' 'geom_text_repel_interactive.R' 'geom_tile_interactive.R' 'geom_violin_interactive.R' 'geom_vline_interactive.R' 'ggiraph.R' 'girafe.R' 'grob_interactive.R' 'guide_bins_interactive.R' 'guide_colourbar_interactive.R' 'guide_coloursteps_interactive.R' 'guide_interactive.R' 'guide_legend_interactive.R' 'interactive_circle_grob.R' 'interactive_curve_grob.R' 'interactive_path_grob.R' 'interactive_points_grob.R' 'interactive_polygon_grob.R' 'interactive_polyline_grob.R' 'interactive_raster_grob.R' 'interactive_rect_grob.R' 'interactive_roundrect_grob.R' 'interactive_segments_grob.R' 'interactive_text_grob.R' 'labeller_interactive.R' 'layer_interactive.R' 'scale_alpha_interactive.R' 'scale_brewer_interactive.R' 'scale_colour_interactive.R' 'scale_gradient_interactive.R' 'scale_interactive.R' 'scale_linetype_interactive.R' 'scale_manual_interactive.R' 'scale_shape_interactive.R' 'scale_size_interactive.R' 'scale_steps_interactive.R' 'scale_viridis_interactive.R' 'tracers.R'", - "NeedsCompilation": "yes", - "Author": "David Gohel [aut, cre], Panagiotis Skintzos [aut], Mike Bostock [cph] (d3.js), Speros Kokenes [cph] (d3-lasso), Eric Shull [cph] (saveSvgAsPng js library), Lee Thomason [cph] (TinyXML2), Vladimir Agafonkin [cph] (Flatbush), Eric Book [ctb] (hline and vline geoms)", - "Maintainer": "David Gohel ", - "Repository": "CRAN" - }, "ggplot2": { "Package": "ggplot2", - "Version": "3.5.1", + "Version": "3.5.2", "Source": "Repository", "Title": "Create Elegant Data Visualisations Using the Grammar of Graphics", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Winston\", \"Chang\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Kohske\", \"Takahashi\", role = \"aut\"), person(\"Claus\", \"Wilke\", role = \"aut\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(\"Kara\", \"Woo\", role = \"aut\", comment = c(ORCID = \"0000-0002-5125-4188\")), person(\"Hiroaki\", \"Yutani\", role = \"aut\", comment = c(ORCID = \"0000-0002-3385-7233\")), person(\"Dewey\", \"Dunnington\", role = \"aut\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(\"Teun\", \"van den Brand\", role = \"aut\", comment = c(ORCID = \"0000-0002-9335-7468\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -3996,7 +3618,7 @@ "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "Collate": "'ggproto.R' 'ggplot-global.R' 'aaa-.R' 'aes-colour-fill-alpha.R' 'aes-evaluation.R' 'aes-group-order.R' 'aes-linetype-size-shape.R' 'aes-position.R' 'compat-plyr.R' 'utilities.R' 'aes.R' 'utilities-checks.R' 'legend-draw.R' 'geom-.R' 'annotation-custom.R' 'annotation-logticks.R' 'geom-polygon.R' 'geom-map.R' 'annotation-map.R' 'geom-raster.R' 'annotation-raster.R' 'annotation.R' 'autolayer.R' 'autoplot.R' 'axis-secondary.R' 'backports.R' 'bench.R' 'bin.R' 'coord-.R' 'coord-cartesian-.R' 'coord-fixed.R' 'coord-flip.R' 'coord-map.R' 'coord-munch.R' 'coord-polar.R' 'coord-quickmap.R' 'coord-radial.R' 'coord-sf.R' 'coord-transform.R' 'data.R' 'docs_layer.R' 'facet-.R' 'facet-grid-.R' 'facet-null.R' 'facet-wrap.R' 'fortify-lm.R' 'fortify-map.R' 'fortify-multcomp.R' 'fortify-spatial.R' 'fortify.R' 'stat-.R' 'geom-abline.R' 'geom-rect.R' 'geom-bar.R' 'geom-bin2d.R' 'geom-blank.R' 'geom-boxplot.R' 'geom-col.R' 'geom-path.R' 'geom-contour.R' 'geom-count.R' 'geom-crossbar.R' 'geom-segment.R' 'geom-curve.R' 'geom-defaults.R' 'geom-ribbon.R' 'geom-density.R' 'geom-density2d.R' 'geom-dotplot.R' 'geom-errorbar.R' 'geom-errorbarh.R' 'geom-freqpoly.R' 'geom-function.R' 'geom-hex.R' 'geom-histogram.R' 'geom-hline.R' 'geom-jitter.R' 'geom-label.R' 'geom-linerange.R' 'geom-point.R' 'geom-pointrange.R' 'geom-quantile.R' 'geom-rug.R' 'geom-sf.R' 'geom-smooth.R' 'geom-spoke.R' 'geom-text.R' 'geom-tile.R' 'geom-violin.R' 'geom-vline.R' 'ggplot2-package.R' 'grob-absolute.R' 'grob-dotstack.R' 'grob-null.R' 'grouping.R' 'theme-elements.R' 'guide-.R' 'guide-axis.R' 'guide-axis-logticks.R' 'guide-axis-stack.R' 'guide-axis-theta.R' 'guide-legend.R' 'guide-bins.R' 'guide-colorbar.R' 'guide-colorsteps.R' 'guide-custom.R' 'layer.R' 'guide-none.R' 'guide-old.R' 'guides-.R' 'guides-grid.R' 'hexbin.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'labeller.R' 'labels.R' 'layer-sf.R' 'layout.R' 'limits.R' 'margins.R' 'performance.R' 'plot-build.R' 'plot-construction.R' 'plot-last.R' 'plot.R' 'position-.R' 'position-collide.R' 'position-dodge.R' 'position-dodge2.R' 'position-identity.R' 'position-jitter.R' 'position-jitterdodge.R' 'position-nudge.R' 'position-stack.R' 'quick-plot.R' 'reshape-add-margins.R' 'save.R' 'scale-.R' 'scale-alpha.R' 'scale-binned.R' 'scale-brewer.R' 'scale-colour.R' 'scale-continuous.R' 'scale-date.R' 'scale-discrete-.R' 'scale-expansion.R' 'scale-gradient.R' 'scale-grey.R' 'scale-hue.R' 'scale-identity.R' 'scale-linetype.R' 'scale-linewidth.R' 'scale-manual.R' 'scale-shape.R' 'scale-size.R' 'scale-steps.R' 'scale-type.R' 'scale-view.R' 'scale-viridis.R' 'scales-.R' 'stat-align.R' 'stat-bin.R' 'stat-bin2d.R' 'stat-bindot.R' 'stat-binhex.R' 'stat-boxplot.R' 'stat-contour.R' 'stat-count.R' 'stat-density-2d.R' 'stat-density.R' 'stat-ecdf.R' 'stat-ellipse.R' 'stat-function.R' 'stat-identity.R' 'stat-qq-line.R' 'stat-qq.R' 'stat-quantilemethods.R' 'stat-sf-coordinates.R' 'stat-sf.R' 'stat-smooth-methods.R' 'stat-smooth.R' 'stat-sum.R' 'stat-summary-2d.R' 'stat-summary-bin.R' 'stat-summary-hex.R' 'stat-summary.R' 'stat-unique.R' 'stat-ydensity.R' 'summarise-plot.R' 'summary.R' 'theme.R' 'theme-defaults.R' 'theme-current.R' 'utilities-break.R' 'utilities-grid.R' 'utilities-help.R' 'utilities-matrix.R' 'utilities-patterns.R' 'utilities-resolution.R' 'utilities-tidy-eval.R' 'zxx.R' 'zzz.R'", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut] (), Winston Chang [aut] (), Lionel Henry [aut], Thomas Lin Pedersen [aut, cre] (), Kohske Takahashi [aut], Claus Wilke [aut] (), Kara Woo [aut] (), Hiroaki Yutani [aut] (), Dewey Dunnington [aut] (), Teun van den Brand [aut] (), Posit, PBC [cph, fnd]", @@ -4103,30 +3725,6 @@ "Maintainer": "Joseph Larmarange ", "Repository": "CRAN" }, - "globals": { - "Package": "globals", - "Version": "0.16.3", - "Source": "Repository", - "Depends": [ - "R (>= 3.1.2)" - ], - "Imports": [ - "codetools" - ], - "Title": "Identify Global Objects in R Expressions", - "Authors@R": "c( person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email=\"henrikb@braju.com\"), person(\"Davis\",\"Vaughan\", role=\"ctb\", email=\"davis@rstudio.com\"))", - "Description": "Identifies global (\"unknown\" or \"free\") objects in R expressions by code inspection using various strategies (ordered, liberal, or conservative). The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in parallel, distributed compute environments.", - "License": "LGPL (>= 2.1)", - "LazyLoad": "TRUE", - "ByteCompile": "TRUE", - "URL": "https://globals.futureverse.org, https://github.com/HenrikBengtsson/globals", - "BugReports": "https://github.com/HenrikBengtsson/globals/issues", - "RoxygenNote": "7.3.1", - "NeedsCompilation": "no", - "Author": "Henrik Bengtsson [aut, cre, cph], Davis Vaughan [ctb]", - "Maintainer": "Henrik Bengtsson ", - "Repository": "CRAN" - }, "glue": { "Package": "glue", "Version": "1.8.0", @@ -4309,10 +3907,10 @@ }, "gtsummary": { "Package": "gtsummary", - "Version": "2.1.0", + "Version": "2.2.0", "Source": "Repository", "Title": "Presentation-Ready Data Summary and Analytic Result Tables", - "Authors@R": "c( person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-0862-2018\")), person(\"Joseph\", \"Larmarange\", role = \"aut\", comment = c(ORCID = \"0000-0001-7097-700X\")), person(\"Michael\", \"Curry\", role = \"aut\", comment = c(ORCID = \"0000-0002-0261-4044\")), person(\"Jessica\", \"Lavery\", role = \"aut\", comment = c(ORCID = \"0000-0002-2746-5647\")), person(\"Karissa\", \"Whiting\", role = \"aut\", comment = c(ORCID = \"0000-0002-4683-1868\")), person(\"Emily C.\", \"Zabor\", role = \"aut\", comment = c(ORCID = \"0000-0002-1402-4498\")), person(\"Xing\", \"Bai\", role = \"ctb\"), person(\"Esther\", \"Drill\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3315-4538\")), person(\"Jessica\", \"Flynn\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8310-6684\")), person(\"Margie\", \"Hannum\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2953-0449\")), person(\"Stephanie\", \"Lobaugh\", role = \"ctb\"), person(\"Shannon\", \"Pileggi\", role = \"ctb\", comment = c(ORCID = \"0000-0002-7732-4164\")), person(\"Amy\", \"Tin\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8005-0694\")), person(\"Gustavo\", \"Zapata Wainberg\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2524-3637\")) )", + "Authors@R": "c( person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-0862-2018\")), person(\"Joseph\", \"Larmarange\", role = \"aut\", comment = c(ORCID = \"0000-0001-7097-700X\")), person(\"Michael\", \"Curry\", role = \"aut\", comment = c(ORCID = \"0000-0002-0261-4044\")), person(\"Emily\", \"de la Rua\", , role = \"aut\", comment = c(ORCID = \"0009-0000-8738-5561\")), person(\"Jessica\", \"Lavery\", role = \"aut\", comment = c(ORCID = \"0000-0002-2746-5647\")), person(\"Karissa\", \"Whiting\", role = \"aut\", comment = c(ORCID = \"0000-0002-4683-1868\")), person(\"Emily C.\", \"Zabor\", role = \"aut\", comment = c(ORCID = \"0000-0002-1402-4498\")), person(\"Xing\", \"Bai\", role = \"ctb\"), person(\"Esther\", \"Drill\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3315-4538\")), person(\"Jessica\", \"Flynn\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8310-6684\")), person(\"Margie\", \"Hannum\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2953-0449\")), person(\"Stephanie\", \"Lobaugh\", role = \"ctb\"), person(\"Shannon\", \"Pileggi\", role = \"ctb\", comment = c(ORCID = \"0000-0002-7732-4164\")), person(\"Amy\", \"Tin\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8005-0694\")), person(\"Gustavo\", \"Zapata Wainberg\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2524-3637\")) )", "Description": "Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers.", "License": "MIT + file LICENSE", "URL": "https://github.com/ddsjoberg/gtsummary, https://www.danieldsjoberg.com/gtsummary/", @@ -4321,7 +3919,7 @@ "R (>= 4.2)" ], "Imports": [ - "cards (>= 0.5.0)", + "cards (>= 0.6.0)", "cli (>= 3.6.3)", "dplyr (>= 1.1.3)", "glue (>= 1.8.0)", @@ -4337,7 +3935,7 @@ "broom.helpers (>= 1.17.0)", "broom.mixed (>= 0.2.9)", "car (>= 3.0-11)", - "cardx (>= 0.2.3)", + "cardx (>= 0.2.4)", "cmprsk", "effectsize (>= 0.6.0)", "emmeans (>= 1.7.3)", @@ -4374,26 +3972,10 @@ "LazyData": "true", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", - "Author": "Daniel D. Sjoberg [aut, cre] (), Joseph Larmarange [aut] (), Michael Curry [aut] (), Jessica Lavery [aut] (), Karissa Whiting [aut] (), Emily C. Zabor [aut] (), Xing Bai [ctb], Esther Drill [ctb] (), Jessica Flynn [ctb] (), Margie Hannum [ctb] (), Stephanie Lobaugh [ctb], Shannon Pileggi [ctb] (), Amy Tin [ctb] (), Gustavo Zapata Wainberg [ctb] ()", + "Author": "Daniel D. Sjoberg [aut, cre] (), Joseph Larmarange [aut] (), Michael Curry [aut] (), Emily de la Rua [aut] (), Jessica Lavery [aut] (), Karissa Whiting [aut] (), Emily C. Zabor [aut] (), Xing Bai [ctb], Esther Drill [ctb] (), Jessica Flynn [ctb] (), Margie Hannum [ctb] (), Stephanie Lobaugh [ctb], Shannon Pileggi [ctb] (), Amy Tin [ctb] (), Gustavo Zapata Wainberg [ctb] ()", "Maintainer": "Daniel D. Sjoberg ", "Repository": "CRAN" }, - "gvlma": { - "Package": "gvlma", - "Version": "1.0.0.3", - "Source": "Repository", - "Type": "Package", - "Title": "Global Validation of Linear Models Assumptions", - "Author": "Edsel A. Pena and Elizabeth H. Slate ", - "Maintainer": "Elizabeth Slate ", - "Description": "Methods from the paper: Pena, EA and Slate, EH, \"Global Validation of Linear Model Assumptions,\" J. American Statistical Association, 101(473):341-354, 2006.", - "Depends": [ - "R (>= 2.1.1)" - ], - "License": "GPL", - "NeedsCompilation": "no", - "Repository": "CRAN" - }, "haven": { "Package": "haven", "Version": "2.5.4", @@ -4672,7 +4254,7 @@ }, "httpuv": { "Package": "httpuv", - "Version": "1.6.15", + "Version": "1.6.16", "Source": "Repository", "Type": "Package", "Title": "HTTP and WebSocket Server Library", @@ -4694,6 +4276,7 @@ "Suggests": [ "callr", "curl", + "jsonlite", "testthat", "websocket" ], @@ -4702,7 +4285,7 @@ "Rcpp" ], "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "SystemRequirements": "GNU make, zlib", "Collate": "'RcppExports.R' 'httpuv.R' 'random_port.R' 'server.R' 'staticServer.R' 'static_paths.R' 'utils.R'", "NeedsCompilation": "yes", @@ -4752,12 +4335,12 @@ }, "insight": { "Package": "insight", - "Version": "1.1.0", + "Version": "1.2.0", "Source": "Repository", "Type": "Package", "Title": "Easy Access to Model Information for Various Model Objects", - "Authors@R": "c(person(given = \"Daniel\", family = \"Lüdecke\", role = c(\"aut\", \"cre\"), email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Dominique\", family = \"Makowski\", role = c(\"aut\", \"ctb\"), email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Indrajeet\", family = \"Patil\", role = c(\"aut\", \"ctb\"), email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Philip\", family = \"Waggoner\", role = c(\"aut\", \"ctb\"), email = \"philip.waggoner@gmail.com\", comment = c(ORCID = \"0000-0002-7825-7573\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = c(\"aut\", \"ctb\"), email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = c(\"aut\", \"ctb\"), email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Vincent\", family = \"Arel-Bundock\", email = \"vincent.arel-bundock@umontreal.ca\", role = c(\"aut\", \"ctb\"), comment = c(ORCID = \"0000-0003-2042-7063\")), person(given = \"Etienne\", family = \"Bacher\", email = \"etienne.bacher@protonmail.com\", role = c(\"aut\", \"ctb\"), comment = c(ORCID = \"0000-0002-9271-5075\")), person(given = \"Alex\", family = \"Hayes\", role = c(\"rev\"), email = \"alexpghayes@gmail.com\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(given = \"Grant\", family = \"McDermott\", role = c(\"ctb\"), email = \"grantmcd@uoregon.edu\", comment = c(ORCID = \"0000-0001-7883-8573\")), person(given = \"Rémi\", family = \"Thériault\", role = \"ctb\", email = \"remi.theriault@mail.mcgill.ca\", comment = c(ORCID = \"0000-0003-4315-6788\")), person(given = \"Alex\", family = \"Reinhart\", role = \"ctb\", email = \"areinhar@stat.cmu.edu\", comment = c(ORCID = \"0000-0002-6658-514X\")))", - "Maintainer": "Daniel Lüdecke ", + "Authors@R": "c(person(given = \"Daniel\", family = \"Lüdecke\", role = c(\"aut\", \"cre\"), email = \"officialeasystats@gmail.com\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Dominique\", family = \"Makowski\", role = c(\"aut\", \"ctb\"), email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Indrajeet\", family = \"Patil\", role = c(\"aut\", \"ctb\"), email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Philip\", family = \"Waggoner\", role = c(\"aut\", \"ctb\"), email = \"philip.waggoner@gmail.com\", comment = c(ORCID = \"0000-0002-7825-7573\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = c(\"aut\", \"ctb\"), email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = c(\"aut\", \"ctb\"), email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Vincent\", family = \"Arel-Bundock\", email = \"vincent.arel-bundock@umontreal.ca\", role = c(\"aut\", \"ctb\"), comment = c(ORCID = \"0000-0003-2042-7063\")), person(given = \"Etienne\", family = \"Bacher\", email = \"etienne.bacher@protonmail.com\", role = c(\"aut\", \"ctb\"), comment = c(ORCID = \"0000-0002-9271-5075\")), person(given = \"Alex\", family = \"Hayes\", role = c(\"rev\"), email = \"alexpghayes@gmail.com\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(given = \"Grant\", family = \"McDermott\", role = c(\"ctb\"), email = \"grantmcd@uoregon.edu\", comment = c(ORCID = \"0000-0001-7883-8573\")), person(given = \"Rémi\", family = \"Thériault\", role = \"ctb\", email = \"remi.theriault@mail.mcgill.ca\", comment = c(ORCID = \"0000-0003-4315-6788\")), person(given = \"Alex\", family = \"Reinhart\", role = \"ctb\", email = \"areinhar@stat.cmu.edu\", comment = c(ORCID = \"0000-0002-6658-514X\")))", + "Maintainer": "Daniel Lüdecke ", "Description": "A tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. 'insight' mainly revolves around two types of functions: Functions that find (the names of) information, starting with 'find_', and functions that get the underlying data, starting with 'get_'. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.", "License": "GPL-3", "URL": "https://easystats.github.io/insight/", @@ -4815,7 +4398,6 @@ "gee", "geepack", "geoR", - "ggeffects (>= 2.2.0)", "GLMMadaptive", "glmmTMB (>= 1.1.10)", "glmtoolbox", @@ -4881,6 +4463,7 @@ "rstanarm (>= 2.21.1)", "rstantools (>= 2.1.0)", "rstudioapi", + "RWiener", "sandwich", "serp", "speedglm", @@ -4890,7 +4473,7 @@ "survival", "svylme", "testthat", - "tinytable (>= 0.1.0)", + "tinytable (>= 0.8.0)", "TMB", "truncreg", "tune", @@ -4970,52 +4553,6 @@ "Maintainer": "Folashade Daniel ", "Repository": "CRAN" }, - "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", @@ -5068,65 +4605,6 @@ "Author": "Jeroen Ooms [aut, cre] (), Duncan Temple Lang [ctb], Lloyd Hilaiel [cph] (author of bundled libyajl)", "Repository": "CRAN" }, - "jtools": { - "Package": "jtools", - "Version": "2.3.0", - "Source": "Repository", - "Type": "Package", - "Title": "Analysis and Presentation of Social Scientific Data", - "Authors@R": "person(c(\"Jacob\",\"A.\"), \"Long\", email = \"jacob.long@sc.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1582-6214\"))", - "Description": "This is a collection of tools for more efficiently understanding and sharing the results of (primarily) regression analyses. There are also a number of miscellaneous functions for statistical and programming purposes. Support for models produced by the survey and lme4 packages are points of emphasis.", - "URL": "https://jtools.jacob-long.com", - "BugReports": "https://github.com/jacob-long/jtools/issues", - "License": "GPL (>= 3)", - "Encoding": "UTF-8", - "LazyData": "true", - "Imports": [ - "cli", - "generics", - "broom", - "broom.mixed", - "ggplot2 (>= 3.4.0)", - "magrittr", - "pander", - "pkgconfig", - "rlang", - "sandwich", - "tibble" - ], - "Suggests": [ - "boot", - "huxtable", - "kableExtra", - "lme4", - "lmerTest", - "MASS", - "methods", - "pbkrtest", - "RColorBrewer", - "scales", - "survey", - "weights", - "knitr", - "rmarkdown", - "testthat", - "vdiffr" - ], - "Enhances": [ - "brms", - "quantreg", - "rstanarm" - ], - "RoxygenNote": "7.3.2", - "VignetteBuilder": "knitr", - "Depends": [ - "R (>= 3.6.0)" - ], - "NeedsCompilation": "no", - "Author": "Jacob A. Long [aut, cre] ()", - "Maintainer": "Jacob A. Long ", - "Repository": "CRAN" - }, "juicyjuice": { "Package": "juicyjuice", "Version": "0.1.0", @@ -5151,55 +4629,6 @@ "Maintainer": "Richard Iannone ", "Repository": "CRAN" }, - "kableExtra": { - "Package": "kableExtra", - "Version": "1.4.0", - "Source": "Repository", - "Type": "Package", - "Title": "Construct Complex Table with 'kable' and Pipe Syntax", - "Authors@R": "c( person('Hao', 'Zhu', email = 'haozhu233@gmail.com', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-3386-6076')), person('Thomas', 'Travison', role = 'ctb'), person('Timothy', 'Tsai', role = 'ctb'), person('Will', 'Beasley', email = 'wibeasley@hotmail.com', role = 'ctb'), person('Yihui', 'Xie', email = 'xie@yihui.name', role = 'ctb'), person('GuangChuang', 'Yu', email = 'guangchuangyu@gmail.com', role = 'ctb'), person('Stéphane', 'Laurent', role = 'ctb'), person('Rob', 'Shepherd', role = 'ctb'), person('Yoni', 'Sidi', role = 'ctb'), person('Brian', 'Salzer', role = 'ctb'), person('George', 'Gui', role = 'ctb'), person('Yeliang', 'Fan', role = 'ctb'), person('Duncan', 'Murdoch', role = 'ctb'), person('Vincent', 'Arel-Bundock', role = 'ctb'), person('Bill', 'Evans', role = 'ctb') )", - "Description": "Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.", - "License": "MIT + file LICENSE", - "URL": "http://haozhu233.github.io/kableExtra/, https://github.com/haozhu233/kableExtra", - "BugReports": "https://github.com/haozhu233/kableExtra/issues", - "Depends": [ - "R (>= 3.1.0)" - ], - "Imports": [ - "knitr (>= 1.33)", - "magrittr", - "stringr (>= 1.0)", - "xml2 (>= 1.1.1)", - "rmarkdown (>= 1.6.0)", - "scales", - "viridisLite", - "stats", - "grDevices", - "htmltools", - "rstudioapi", - "tools", - "digest", - "graphics", - "svglite" - ], - "Suggests": [ - "testthat", - "magick", - "tinytex", - "formattable", - "sparkline", - "webshot2" - ], - "Config/testthat/edition": "3", - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", - "Language": "en-US", - "NeedsCompilation": "no", - "Author": "Hao Zhu [aut, cre] (), Thomas Travison [ctb], Timothy Tsai [ctb], Will Beasley [ctb], Yihui Xie [ctb], GuangChuang Yu [ctb], Stéphane Laurent [ctb], Rob Shepherd [ctb], Yoni Sidi [ctb], Brian Salzer [ctb], George Gui [ctb], Yeliang Fan [ctb], Duncan Murdoch [ctb], Vincent Arel-Bundock [ctb], Bill Evans [ctb]", - "Maintainer": "Hao Zhu ", - "Repository": "CRAN" - }, "keyring": { "Package": "keyring", "Version": "1.3.2", @@ -5512,32 +4941,6 @@ "Maintainer": "Lionel Henry ", "Repository": "CRAN" }, - "listenv": { - "Package": "listenv", - "Version": "0.9.1", - "Source": "Repository", - "Depends": [ - "R (>= 3.1.2)" - ], - "Suggests": [ - "R.utils", - "R.rsp", - "markdown" - ], - "VignetteBuilder": "R.rsp", - "Title": "Environments Behaving (Almost) as Lists", - "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\"))", - "Description": "List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting, e.g. 'x <- listenv(a = 1, b = 2); for (i in seq_along(x)) x[[i]] <- x[[i]] ^ 2; y <- as.list(x)'.", - "License": "LGPL (>= 2.1)", - "LazyLoad": "TRUE", - "URL": "https://listenv.futureverse.org, https://github.com/HenrikBengtsson/listenv", - "BugReports": "https://github.com/HenrikBengtsson/listenv/issues", - "RoxygenNote": "7.3.1", - "NeedsCompilation": "no", - "Author": "Henrik Bengtsson [aut, cre, cph]", - "Maintainer": "Henrik Bengtsson ", - "Repository": "CRAN" - }, "litedown": { "Package": "litedown", "Version": "0.7", @@ -5920,24 +5323,6 @@ "Maintainer": "Chung-hong Chan ", "Repository": "CRAN" }, - "mnormt": { - "Package": "mnormt", - "Version": "2.1.1", - "Source": "Repository", - "Date": "2022-09-26", - "Title": "The Multivariate Normal and t Distributions, and Their Truncated Versions", - "Author": "Adelchi Azzalini [aut, cre], Alan Genz [aut] (most Fortran code), Alan Miller [ctb] (Fortran routine PHI), Michael J. Wichura [ctb] (Fortran routine PHINV), G. W. Hill [ctb] (Fortran routine STDINV), Yihong Ge [ctb] (Fortran routines BNVU and MVBVU).", - "Maintainer": "Adelchi Azzalini ", - "Depends": [ - "R (>= 2.2.0)" - ], - "Description": "Functions are provided for computing the density and the distribution function of d-dimensional normal and \"t\" random variables, possibly truncated (on one side or two sides), and for generating random vectors sampled from these distributions, except sampling from the truncated \"t\". Moments of arbitrary order of a multivariate truncated normal are computed, and converted to cumulants up to order 4. Probabilities are computed via non-Monte Carlo methods; different routines are used in the case d=1, d=2, d=3, d>3, if d denotes the dimensionality.", - "License": "GPL-2 | GPL-3", - "URL": "http://azzalini.stat.unipd.it/SW/Pkg-mnormt/", - "NeedsCompilation": "yes", - "Encoding": "UTF-8", - "Repository": "CRAN" - }, "modelbased": { "Package": "modelbased", "Version": "0.10.0", @@ -6289,98 +5674,6 @@ "Maintainer": "Jan Marvin Garbuszus ", "Repository": "CRAN" }, - "pander": { - "Package": "pander", - "Version": "0.6.6", - "Source": "Repository", - "Authors@R": "c( person(\"Gergely\", \"Daróczi\", , \"daroczig@rapporter.net\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3149-8537\")), person(\"Roman\", \"Tsegelskyi\", , \"roman.tsegelskyi@gmail.com\", role = c(\"aut\")))", - "Title": "An R 'Pandoc' Writer", - "Type": "Package", - "Encoding": "UTF-8", - "Description": "Contains some functions catching all messages, 'stdout' and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in 'pandoc' markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex 'pandoc' documents to e.g. HTML, 'PDF', 'docx' or 'odt'. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching 'backend'.", - "Date": "2025-03-01", - "URL": "https://rapporter.github.io/pander/", - "BugReports": "https://github.com/rapporter/pander/issues", - "License": "AGPL-3 | file LICENSE", - "Depends": [ - "R (>= 2.15.0)" - ], - "Imports": [ - "grDevices", - "graphics", - "methods", - "utils", - "stats", - "digest", - "tools", - "Rcpp" - ], - "Suggests": [ - "grid", - "lattice", - "ggplot2 (>= 0.9.2)", - "sylly", - "sylly.en", - "logger", - "survival", - "microbenchmark", - "zoo", - "nlme", - "descr", - "MASS", - "knitr", - "rmarkdown", - "tables", - "reshape", - "memisc", - "Epi", - "randomForest", - "tseries", - "gtable", - "rms", - "forecast", - "data.table" - ], - "SystemRequirements": "pandoc (https://johnmacfarlane.net/pandoc) for exporting markdown files to other formats.", - "LinkingTo": [ - "Rcpp" - ], - "VignetteBuilder": "knitr", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "yes", - "Author": "Gergely Daróczi [aut, cre] (), Roman Tsegelskyi [aut]", - "Maintainer": "Gergely Daróczi ", - "Repository": "CRAN" - }, - "parallelly": { - "Package": "parallelly", - "Version": "1.43.0", - "Source": "Repository", - "Title": "Enhancing the 'parallel' Package", - "Imports": [ - "parallel", - "tools", - "utils" - ], - "Suggests": [ - "commonmark", - "base64enc" - ], - "VignetteBuilder": "parallelly", - "Authors@R": "c( person(\"Henrik\", \"Bengtsson\", role = c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Mike\", \"Cheng\", role = c(\"ctb\"), email = \"mikefc@coolbutuseless.com\") )", - "Description": "Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.", - "License": "LGPL (>= 2.1)", - "LazyLoad": "TRUE", - "ByteCompile": "TRUE", - "URL": "https://parallelly.futureverse.org, https://github.com/futureverse/parallelly", - "BugReports": "https://github.com/futureverse/parallelly/issues", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "yes", - "Author": "Henrik Bengtsson [aut, cre, cph] (), Mike Cheng [ctb]", - "Maintainer": "Henrik Bengtsson ", - "Repository": "CRAN" - }, "parameters": { "Package": "parameters", "Version": "0.24.2", @@ -7194,7 +6487,7 @@ }, "ps": { "Package": "ps", - "Version": "1.9.0", + "Version": "1.9.1", "Source": "Repository", "Title": "List, Query, Manipulate System Processes", "Authors@R": "c( person(\"Jay\", \"Loden\", role = \"aut\"), person(\"Dave\", \"Daeschler\", role = \"aut\"), person(\"Giampaolo\", \"Rodola'\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -7231,44 +6524,6 @@ "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" }, - "psych": { - "Package": "psych", - "Version": "2.5.3", - "Source": "Repository", - "Date": "2025-03-18", - "Title": "Procedures for Psychological, Psychometric, and Personality Research", - "Authors@R": "person(\"William\", \"Revelle\", role =c(\"aut\",\"cre\"), email=\"revelle@northwestern.edu\", comment=c(ORCID = \"0000-0003-4880-9610\") )", - "Description": "A general purpose toolbox developed originally for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Validation and cross validation of scales developed using basic machine learning algorithms are provided, as are functions for simulating and testing particular item and test structures. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, including mediation models, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the web page.", - "License": "GPL (>= 2)", - "Imports": [ - "mnormt", - "parallel", - "stats", - "graphics", - "grDevices", - "methods", - "lattice", - "nlme", - "GPArotation" - ], - "Suggests": [ - "psychTools", - "lavaan", - "lme4", - "Rcsdp", - "graph", - "knitr", - "Rgraphviz" - ], - "LazyData": "yes", - "ByteCompile": "true", - "VignetteBuilder": "knitr", - "URL": "https://personality-project.org/r/psych/ https://personality-project.org/r/psych-manual.pdf", - "NeedsCompilation": "no", - "Author": "William Revelle [aut, cre] ()", - "Maintainer": "William Revelle ", - "Repository": "CRAN" - }, "purrr": { "Package": "purrr", "Version": "1.0.4", @@ -7318,18 +6573,18 @@ }, "qgam": { "Package": "qgam", - "Version": "1.3.4", + "Version": "2.0.0", "Source": "Repository", "Type": "Package", "Title": "Smooth Additive Quantile Regression Models", - "Date": "2021-11-21", - "Authors@R": "c(person(\"Matteo\", \"Fasiolo\", email = \"matteo.fasiolo@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Simon\", \"N. Wood\", role = c(\"ctb\")), person(\"Margaux\", \"Zaffran\", role = c(\"ctb\")), person(\"Yannig\", \"Goude\", role = c(\"ctb\")), person(\"Raphael\", \"Nedellec\", role = c(\"ctb\")))", + "Date": "2025-04-10", + "Authors@R": "c(person(\"Matteo\", \"Fasiolo\", email = \"matteo.fasiolo@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Ben\", \"Griffiths\", role = c(\"aut\")), person(\"Simon\", \"N. Wood\", role = c(\"ctb\")), person(\"Margaux\", \"Zaffran\", role = c(\"ctb\")), person(\"Yannig\", \"Goude\", role = c(\"ctb\")), person(\"Raphael\", \"Nedellec\", role = c(\"ctb\")))", "Maintainer": "Matteo Fasiolo ", "Description": "Smooth additive quantile regression models, fitted using the methods of Fasiolo et al. (2020) . See Fasiolo at al. (2021) for an introduction to the package. Differently from 'quantreg', the smoothing parameters are estimated automatically by marginal loss minimization, while the regression coefficients are estimated using either PIRLS or Newton algorithm. The learning rate is determined so that the Bayesian credible intervals of the estimated effects have approximately the correct coverage. The main function is qgam() which is similar to gam() in 'mgcv', but fits non-parametric quantile regression models.", "License": "GPL (>= 2)", "Depends": [ - "R (>= 3.5.0)", - "mgcv (>= 1.8-28)" + "R (>= 4.0)", + "mgcv (>= 1.9)" ], "Imports": [ "shiny", @@ -7346,9 +6601,10 @@ "testthat" ], "VignetteBuilder": "knitr", - "RoxygenNote": "7.1.1", + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", "NeedsCompilation": "yes", - "Author": "Matteo Fasiolo [aut, cre], Simon N. Wood [ctb], Margaux Zaffran [ctb], Yannig Goude [ctb], Raphael Nedellec [ctb]", + "Author": "Matteo Fasiolo [aut, cre], Ben Griffiths [aut], Simon N. Wood [ctb], Margaux Zaffran [ctb], Yannig Goude [ctb], Raphael Nedellec [ctb]", "Repository": "CRAN" }, "qqconf": { @@ -7473,7 +6729,7 @@ }, "ragg": { "Package": "ragg", - "Version": "1.3.3", + "Version": "1.4.0", "Source": "Repository", "Type": "Package", "Title": "Graphic Devices Based on AGG", @@ -7499,9 +6755,10 @@ ], "Config/Needs/website": "ggplot2, devoid, magick, bench, tidyr, ggridges, hexbin, sessioninfo, pkgdown, tidyverse/tidytemplate", "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "SystemRequirements": "freetype2, libpng, libtiff, libjpeg", "Config/testthat/edition": "3", + "Config/build/compilation-database": "true", "NeedsCompilation": "yes", "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" @@ -8119,11 +7376,11 @@ }, "rlang": { "Package": "rlang", - "Version": "1.1.5", + "Version": "1.1.6", "Source": "Repository", "Title": "Functions for Base Types and Core R and 'Tidyverse' Features", "Description": "A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.", - "Authors@R": "c( person(\"Lionel\", \"Henry\", ,\"lionel@posit.co\", c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", ,\"hadley@posit.co\", \"aut\"), person(given = \"mikefc\", email = \"mikefc@coolbutuseless.com\", role = \"cph\", comment = \"Hash implementation based on Mike's xxhashlite\"), person(given = \"Yann\", family = \"Collet\", role = \"cph\", comment = \"Author of the embedded xxHash library\"), person(given = \"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Lionel\", \"Henry\", ,\"lionel@posit.co\", c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", ,\"hadley@posit.co\", \"aut\"), person(given = \"mikefc\", email = \"mikefc@coolbutuseless.com\", role = \"cph\", comment = \"Hash implementation based on Mike's xxhashlite\"), person(given = \"Yann\", family = \"Collet\", role = \"cph\", comment = \"Author of the embedded xxHash library\"), person(given = \"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", "License": "MIT + file LICENSE", "ByteCompile": "true", "Biarch": "true", @@ -8137,15 +7394,17 @@ "cli (>= 3.1.0)", "covr", "crayon", + "desc", "fs", "glue", "knitr", "magrittr", "methods", "pillar", + "pkgload", "rmarkdown", "stats", - "testthat (>= 3.0.0)", + "testthat (>= 3.2.0)", "tibble", "usethis", "vctrs (>= 0.2.3)", @@ -8158,6 +7417,7 @@ "RoxygenNote": "7.3.2", "URL": "https://rlang.r-lib.org, https://github.com/r-lib/rlang", "BugReports": "https://github.com/r-lib/rlang/issues", + "Config/build/compilation-database": "true", "Config/testthat/edition": "3", "Config/Needs/website": "dplyr, tidyverse/tidytemplate", "NeedsCompilation": "yes", @@ -8364,51 +7624,9 @@ "Author": "Kevin Ushey [aut, cre], JJ Allaire [aut], Hadley Wickham [aut], Gary Ritchie [aut], RStudio [cph]", "Repository": "CRAN" }, - "sandwich": { - "Package": "sandwich", - "Version": "3.1-1", - "Source": "Repository", - "Date": "2024-09-16", - "Title": "Robust Covariance Matrix Estimators", - "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 = \"Thomas\", family = \"Lumley\", role = \"aut\", email = \"t.lumley@auckland.ac.nz\", comment = c(ORCID = \"0000-0003-4255-5437\")), person(given = \"Nathaniel\", family = \"Graham\", role = \"ctb\", email = \"npgraham1@gmail.com\", comment = c(ORCID = \"0009-0002-1215-5256\")), person(given = \"Susanne\", family = \"Koell\", role = \"ctb\"))", - "Description": "Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods. Details can be found in Zeileis et al. (2020) , Zeileis (2004) and Zeileis (2006) .", - "Depends": [ - "R (>= 3.0.0)" - ], - "Imports": [ - "stats", - "utils", - "zoo" - ], - "Suggests": [ - "AER", - "car", - "geepack", - "lattice", - "lme4", - "lmtest", - "MASS", - "multiwayvcov", - "parallel", - "pcse", - "plm", - "pscl", - "scatterplot3d", - "stats4", - "strucchange", - "survival" - ], - "License": "GPL-2 | GPL-3", - "URL": "https://sandwich.R-Forge.R-project.org/", - "BugReports": "https://sandwich.R-Forge.R-project.org/contact.html", - "NeedsCompilation": "no", - "Author": "Achim Zeileis [aut, cre] (), Thomas Lumley [aut] (), Nathaniel Graham [ctb] (), Susanne Koell [ctb]", - "Maintainer": "Achim Zeileis ", - "Repository": "CRAN" - }, "sass": { "Package": "sass", - "Version": "0.4.9", + "Version": "0.4.10", "Source": "Repository", "Type": "Package", "Title": "Syntactically Awesome Style Sheets ('Sass')", @@ -8418,7 +7636,7 @@ "URL": "https://rstudio.github.io/sass/, https://github.com/rstudio/sass", "BugReports": "https://github.com/rstudio/sass/issues", "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "SystemRequirements": "GNU make", "Imports": [ "fs (>= 1.2.4)", @@ -8736,246 +7954,6 @@ "Maintainer": "Victor Perrier ", "Repository": "CRAN" }, - "sjPlot": { - "Package": "sjPlot", - "Version": "2.8.17", - "Source": "Repository", - "Type": "Package", - "Encoding": "UTF-8", - "Title": "Data Visualization for Statistics in Social Science", - "Authors@R": "c( person(\"Daniel\", \"Lüdecke\", email = \"d.luedecke@uke.de\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-8895-3206\")), person(\"Alexander\", \"Bartel\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1280-6138\")), person(\"Carsten\", \"Schwemmer\", email = \"carsten.schwemmer@uni-bamberg.de\", role = \"ctb\"), person(given = \"Chuck\", family = \"Powell\", role = \"ctb\", email = \"ibecav@gmail.com\", comment = c(ORCID = \"0000-0002-3606-2188\")), person(given = \"Amir\", family = \"Djalovski\", role = \"ctb\", email = \"Amir.DJV@gmail.com\"), person(given = \"Johannes\", family = \"Titz\", role = \"ctb\", email = \"johannes@titz.science\", comment = c(ORCID = \"0000-0002-1102-5719\")))", - "Maintainer": "Daniel Lüdecke ", - "Description": "Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.", - "License": "GPL-3", - "Depends": [ - "R (>= 3.6)" - ], - "Imports": [ - "graphics", - "grDevices", - "stats", - "utils", - "bayestestR", - "datawizard", - "dplyr", - "ggeffects", - "ggplot2 (>= 3.2.0)", - "knitr", - "insight", - "MASS", - "parameters", - "performance", - "purrr", - "rlang", - "scales", - "sjlabelled (>= 1.1.2)", - "sjmisc (>= 2.8.2)", - "sjstats (>= 0.17.8)", - "tidyr (>= 1.0.0)" - ], - "Suggests": [ - "brms", - "car", - "clubSandwich", - "cluster", - "cowplot", - "effects", - "haven", - "GPArotation", - "ggrepel", - "glmmTMB", - "gridExtra", - "ggridges", - "httr", - "lme4", - "nFactors", - "pscl", - "psych", - "rmarkdown", - "rstanarm", - "sandwich", - "splines", - "survey", - "TMB", - "testthat" - ], - "URL": "https://strengejacke.github.io/sjPlot/", - "BugReports": "https://github.com/strengejacke/sjPlot/issues", - "RoxygenNote": "7.3.2", - "VignetteBuilder": "knitr", - "NeedsCompilation": "no", - "Author": "Daniel Lüdecke [aut, cre] (), Alexander Bartel [ctb] (), Carsten Schwemmer [ctb], Chuck Powell [ctb] (), Amir Djalovski [ctb], Johannes Titz [ctb] ()", - "Repository": "CRAN" - }, - "sjlabelled": { - "Package": "sjlabelled", - "Version": "1.2.0", - "Source": "Repository", - "Type": "Package", - "Encoding": "UTF-8", - "Title": "Labelled Data Utility Functions", - "Authors@R": "c( person(\"Daniel\", \"Lüdecke\", role = c(\"aut\", \"cre\"), email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(\"avid\", \"Ranzolin\", role = \"ctb\", email = \"daranzolin@gmail.com\"), person(\"Jonathan\", \"De Troye\", role = \"ctb\", email = \"detroyejr@outlook.com\") )", - "Maintainer": "Daniel Lüdecke ", - "Description": "Collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata', and working with labelled data. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.", - "License": "GPL-3", - "Depends": [ - "R (>= 3.4)" - ], - "Imports": [ - "insight", - "datawizard", - "stats", - "tools", - "utils" - ], - "Suggests": [ - "dplyr", - "haven (>= 1.1.2)", - "magrittr", - "sjmisc", - "sjPlot", - "knitr", - "rlang", - "rmarkdown", - "snakecase", - "testthat" - ], - "URL": "https://strengejacke.github.io/sjlabelled/", - "BugReports": "https://github.com/strengejacke/sjlabelled/issues", - "RoxygenNote": "7.1.2", - "VignetteBuilder": "knitr", - "NeedsCompilation": "no", - "Author": "Daniel Lüdecke [aut, cre] (), avid Ranzolin [ctb], Jonathan De Troye [ctb]", - "Repository": "CRAN" - }, - "sjmisc": { - "Package": "sjmisc", - "Version": "2.8.10", - "Source": "Repository", - "Type": "Package", - "Encoding": "UTF-8", - "Title": "Data and Variable Transformation Functions", - "Authors@R": "c(person(\"Daniel\", \"Lüdecke\", role = c(\"aut\", \"cre\"), email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(\"Iago\", \"Giné-Vázquez\", role = c(\"ctb\"), email = \"i.gine@pssjd.org\"), person(\"Alexander\", \"Bartel\", role = \"ctb\", email = \"alexander.bartel@fu-berlin.de\", comment = c(ORCID = \"0000-0002-1280-6138\")))", - "Maintainer": "Daniel Lüdecke ", - "Description": "Collection of miscellaneous utility functions, supporting data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. The data transformation functions also support labelled data, and all integrate seamlessly into a 'tidyverse'-workflow.", - "License": "GPL-3", - "Depends": [ - "R (>= 3.4)" - ], - "Imports": [ - "dplyr", - "insight", - "datawizard", - "magrittr", - "methods", - "purrr", - "rlang", - "sjlabelled (>= 1.1.1)", - "stats", - "tidyselect", - "utils" - ], - "Suggests": [ - "ggplot2", - "graphics", - "haven (>= 2.0.0)", - "mice", - "nnet", - "sjPlot", - "sjstats", - "knitr", - "rmarkdown", - "stringdist", - "testthat", - "tidyr" - ], - "URL": "https://strengejacke.github.io/sjmisc/", - "BugReports": "https://github.com/strengejacke/sjmisc/issues", - "RoxygenNote": "7.3.1", - "VignetteBuilder": "knitr", - "NeedsCompilation": "no", - "Author": "Daniel Lüdecke [aut, cre] (), Iago Giné-Vázquez [ctb], Alexander Bartel [ctb] ()", - "Repository": "CRAN" - }, - "sjstats": { - "Package": "sjstats", - "Version": "0.19.0", - "Source": "Repository", - "Type": "Package", - "Encoding": "UTF-8", - "Title": "Collection of Convenient Functions for Common Statistical Computations", - "Authors@R": "person(\"Daniel\", \"Lüdecke\", role = c(\"aut\", \"cre\"), email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\"))", - "Maintainer": "Daniel Lüdecke ", - "Description": "Collection of convenient functions for common statistical computations, which are not directly provided by R's base or stats packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort (like Cramer's V, Phi, or effect size statistics like Eta or Omega squared), or for which currently no functions available. Second, another focus lies on weighted variants of common statistical measures and tests like weighted standard error, mean, t-test, correlation, and more.", - "License": "GPL-3", - "Depends": [ - "R (>= 3.4)", - "utils" - ], - "Imports": [ - "datawizard", - "effectsize (>= 0.8.8)", - "insight", - "parameters", - "performance", - "stats" - ], - "Suggests": [ - "brms", - "car", - "coin", - "ggplot2", - "lme4", - "MASS", - "pscl", - "pwr", - "survey", - "testthat" - ], - "URL": "https://strengejacke.github.io/sjstats/", - "BugReports": "https://github.com/strengejacke/sjstats/issues", - "RoxygenNote": "7.3.1", - "Config/testthat/edition": "3", - "Config/testthat/parallel": "true", - "NeedsCompilation": "no", - "Author": "Daniel Lüdecke [aut, cre] ()", - "Repository": "CRAN" - }, - "snakecase": { - "Package": "snakecase", - "Version": "0.11.1", - "Source": "Repository", - "Date": "2023-08-27", - "Title": "Convert Strings into any Case", - "Description": "A consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others.", - "Authors@R": "c( person(\"Malte\", \"Grosser\", , \"malte.grosser@gmail.com\", role = c(\"aut\", \"cre\")))", - "Maintainer": "Malte Grosser ", - "Depends": [ - "R (>= 3.2)" - ], - "Imports": [ - "stringr", - "stringi" - ], - "Suggests": [ - "testthat", - "covr", - "tibble", - "purrrlyr", - "knitr", - "rmarkdown", - "magrittr" - ], - "URL": "https://github.com/Tazinho/snakecase", - "BugReports": "https://github.com/Tazinho/snakecase/issues", - "Encoding": "UTF-8", - "License": "GPL-3", - "RoxygenNote": "6.1.1", - "VignetteBuilder": "knitr", - "NeedsCompilation": "no", - "Author": "Malte Grosser [aut, cre]", - "Repository": "CRAN" - }, "sodium": { "Package": "sodium", "Version": "1.4.0", @@ -9021,33 +7999,6 @@ "NeedsCompilation": "yes", "Repository": "CRAN" }, - "sparkline": { - "Package": "sparkline", - "Version": "2.0", - "Source": "Repository", - "Type": "Package", - "Title": "'jQuery' Sparkline 'htmlwidget'", - "Date": "2016-11-10", - "Authors@R": "c( person(\"Ramnath\", \"Vaidyanathan\", email = \"ramnath.vaidya@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kent\", \"Russell\", email = \"kent.russell@timelyportfolio.com\", role = c(\"aut\", \"ctb\")), person(\"Gareth\", \"Watts\", role = c(\"aut\", \"cph\"), comment = \"jquery.sparkline library in htmlwidgets/lib, https://github.com/gwatts/jquery.sparkline\"), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/htmlwidgets/lib/jquery/jquery-AUTHORS.txt\" ) )", - "Maintainer": "Ramnath Vaidyanathan ", - "Description": "Include interactive sparkline charts in all R contexts with the convenience of 'htmlwidgets'.", - "Imports": [ - "htmltools", - "htmlwidgets (>= 0.8)" - ], - "Suggests": [ - "formattable", - "knitr", - "rmarkdown", - "shiny" - ], - "License": "MIT + file LICENSE", - "RoxygenNote": "5.0.1", - "VignetteBuilder": "knitr", - "NeedsCompilation": "no", - "Author": "Ramnath Vaidyanathan [aut, cre], Kent Russell [aut, ctb], Gareth Watts [aut, cph] (jquery.sparkline library in htmlwidgets/lib, https://github.com/gwatts/jquery.sparkline), jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/htmlwidgets/lib/jquery/jquery-AUTHORS.txt)", - "Repository": "CRAN" - }, "stringi": { "Package": "stringi", "Version": "1.8.7", @@ -9122,46 +8073,6 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "svglite": { - "Package": "svglite", - "Version": "2.1.3", - "Source": "Repository", - "Title": "An 'SVG' Graphics Device", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"T Jake\", \"Luciani\", , \"jake@apache.org\", role = \"aut\"), person(\"Matthieu\", \"Decorde\", , \"matthieu.decorde@ens-lyon.fr\", role = \"aut\"), person(\"Vaudor\", \"Lise\", , \"lise.vaudor@ens-lyon.fr\", role = \"aut\"), person(\"Tony\", \"Plate\", role = \"ctb\", comment = \"Early line dashing code\"), person(\"David\", \"Gohel\", role = \"ctb\", comment = \"Line dashing code and early raster code\"), person(\"Yixuan\", \"Qiu\", role = \"ctb\", comment = \"Improved styles; polypath implementation\"), person(\"Håkon\", \"Malmedal\", role = \"ctb\", comment = \"Opacity code\"), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "A graphics device for R that produces 'Scalable Vector Graphics'. 'svglite' is a fork of the older 'RSvgDevice' package.", - "License": "GPL (>= 2)", - "URL": "https://svglite.r-lib.org, https://github.com/r-lib/svglite", - "BugReports": "https://github.com/r-lib/svglite/issues", - "Depends": [ - "R (>= 3.5.0)" - ], - "Imports": [ - "systemfonts (>= 1.0.0)" - ], - "Suggests": [ - "covr", - "fontquiver (>= 0.2.0)", - "htmltools", - "knitr", - "rmarkdown", - "testthat (>= 3.0.0)", - "xml2 (>= 1.0.0)" - ], - "LinkingTo": [ - "cpp11", - "systemfonts" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate", - "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", - "SystemRequirements": "libpng", - "Config/testthat/edition": "3", - "NeedsCompilation": "yes", - "Author": "Hadley Wickham [aut], Lionel Henry [aut], Thomas Lin Pedersen [cre, aut] (), T Jake Luciani [aut], Matthieu Decorde [aut], Vaudor Lise [aut], Tony Plate [ctb] (Early line dashing code), David Gohel [ctb] (Line dashing code and early raster code), Yixuan Qiu [ctb] (Improved styles; polypath implementation), Håkon Malmedal [ctb] (Opacity code), Posit, PBC [cph, fnd]", - "Maintainer": "Thomas Lin Pedersen ", - "Repository": "CRAN" - }, "sys": { "Package": "sys", "Version": "3.4.3", @@ -9522,7 +8433,7 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.56", + "Version": "0.57", "Source": "Repository", "Type": "Package", "Title": "Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents", @@ -9914,40 +8825,6 @@ "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, - "webshot": { - "Package": "webshot", - "Version": "0.5.5", - "Source": "Repository", - "Title": "Take Screenshots of Web Pages", - "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"Yihui\", \"Xie\", role = \"ctb\"), person(\"Francois\", \"Guillem\", role = \"ctb\"), person(\"Barret\", \"Schloerke\", role = \"ctb\"), person(\"Nicolas\", \"Perriault\", role = \"ctb\", comment = \"The CasperJS library\") )", - "Description": "Takes screenshots of web pages, including Shiny applications and R Markdown documents.", - "Depends": [ - "R (>= 3.0)" - ], - "Imports": [ - "magrittr", - "jsonlite", - "callr" - ], - "Suggests": [ - "httpuv", - "knitr", - "rmarkdown", - "shiny", - "testthat (>= 3.0.0)" - ], - "License": "GPL-2", - "SystemRequirements": "PhantomJS for taking screenshots, ImageMagick or GraphicsMagick and OptiPNG for manipulating images.", - "RoxygenNote": "7.2.3", - "Encoding": "UTF-8", - "URL": "https://wch.github.io/webshot/, https://github.com/wch/webshot/", - "BugReports": "https://github.com/wch/webshot/issues", - "Config/testthat/edition": "3", - "NeedsCompilation": "no", - "Author": "Winston Chang [aut, cre], Yihui Xie [ctb], Francois Guillem [ctb], Barret Schloerke [ctb], Nicolas Perriault [ctb] (The CasperJS library)", - "Maintainer": "Winston Chang ", - "Repository": "CRAN" - }, "withr": { "Package": "withr", "Version": "3.0.2", @@ -9988,7 +8865,7 @@ }, "writexl": { "Package": "writexl", - "Version": "1.5.3", + "Version": "1.5.4", "Source": "Repository", "Type": "Package", "Title": "Export Data Frames to Excel 'xlsx' Format", @@ -10178,9 +9055,9 @@ }, "zoo": { "Package": "zoo", - "Version": "1.8-13", + "Version": "1.8-14", "Source": "Repository", - "Date": "2025-02-20", + "Date": "2025-04-09", "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", @@ -10192,7 +9069,7 @@ "AER", "coda", "chron", - "ggplot2 (>= 3.0.0)", + "ggplot2 (>= 3.5.0)", "mondate", "scales", "stinepack", diff --git a/tests/testthat/test-data_plots.R b/tests/testthat/test-data_plots.R index a173d37..9ac771a 100644 --- a/tests/testthat/test-data_plots.R +++ b/tests/testthat/test-data_plots.R @@ -46,7 +46,7 @@ test_that("create_plot works", { p <- p_list[[1]] + ggplot2::labs(title = "Test plot") expect_equal(length(p_list), 2) - expect_true(ggplot2::is.ggplot(p)) + expect_true(ggplot2::is_ggplot(p)) # Includes helper functions # wrap_plot_list @@ -60,7 +60,7 @@ test_that("create_plot works", { ) lapply(p_list, \(.x){ - expect_true(ggplot2::is.ggplot(.x)) + expect_true(ggplot2::is_ggplot(.x)) }) purrr::map2(p_list, list(11, 11), \(.x, .y){ diff --git a/vignettes/data-types.Rmd b/vignettes/data-types.Rmd index c7852cf..2c23895 100644 --- a/vignettes/data-types.Rmd +++ b/vignettes/data-types.Rmd @@ -12,6 +12,7 @@ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) +options(rmarkdown.html_vignette.check_title = FALSE) ``` ```{r setup}