diff --git a/DESCRIPTION b/DESCRIPTION index 68546b1..2739987 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -63,7 +63,8 @@ Imports: gvlma, psych, jtools, - Hmisc + Hmisc, + ggstats Suggests: styler, devtools, diff --git a/R/app_version.R b/R/app_version.R index 65bc193..e753e43 100644 --- a/R/app_version.R +++ b/R/app_version.R @@ -1 +1 @@ -app_version <- function()'250130_1152' +app_version <- function()'250207_1622' diff --git a/R/correlations-module.R b/R/correlations-module.R new file mode 100644 index 0000000..0063c78 --- /dev/null +++ b/R/correlations-module.R @@ -0,0 +1,136 @@ +#' Data correlations evaluation module +#' +#' @param id Module id. (Use 'ns("id")') +#' +#' @name data-correlations +#' @returns Shiny ui module +#' @export +data_correlations_ui <- function(id, ...) { + ns <- NS(id) + + shiny::tagList( + shiny::textOutput(outputId = ns("suggest")), + shiny::plotOutput(outputId = ns("correlation_plot"), ...) + ) +} + + +#' +#' @param data data +#' @param color.main main color +#' @param color.sec secondary color +#' @param ... arguments passed to toastui::datagrid +#' +#' @name data-correlations +#' @returns shiny server module +#' @export +data_correlations_server <- function(id, + data, + include.class = NULL, + cutoff = .7, + ...) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + # ns <- session$ns + + rv <- shiny::reactiveValues( + data = NULL + ) + + rv$data <- shiny::reactive({ + shiny::req(data) + if (!is.null(include.class)) { + filter <- sapply(data(), class) %in% include.class + out <- data()[filter] + } else { + out <- data() + } + out + }) + + # rv <- list() + # rv$data <- mtcars + + output$suggest <- shiny::renderPrint({ + shiny::req(rv$data) + shiny::req(cutoff) + pairs <- correlation_pairs(rv$data(), threshold = cutoff()) + + more <- ifelse(nrow(pairs) > 1, "from each pair ", "") + + if (nrow(pairs) == 0) { + out <- glue::glue("No variables have a correlation measure above the threshold.") + } else { + out <- pairs |> + apply(1, \(.x){ + glue::glue("'{.x[1]}'x'{.x[2]}'({round(as.numeric(.x[3]),2)})") + }) |> + (\(.x){ + glue::glue("The following variable pairs are highly correlated: {sentence_paste(.x)}.\nConsider excluding one {more}from the dataset to ensure variables are independent.") + })() + } + out + }) + + output$correlation_plot <- shiny::renderPlot({ + psych::pairs.panels(rv$data()) + }) + } + ) +} + +correlation_pairs <- function(data, threshold = .8) { + data <- data[!sapply(data, is.character)] + data <- data |> dplyr::mutate(dplyr::across(dplyr::where(is.factor), as.numeric)) + cor <- Hmisc::rcorr(as.matrix(data)) + r <- cor$r %>% as.table() + d <- r |> + as.data.frame() |> + dplyr::filter(abs(Freq) > threshold, Freq != 1) + + d[1:2] |> + apply(1, \(.x){ + sort(unname(.x)) + }, + simplify = logical(1) + ) |> + duplicated() |> + (\(.x){ + d[!.x, ] + })() |> + setNames(c("var1", "var2", "cor")) +} + +sentence_paste <- function(data, and.str = "and") { + and.str <- gsub(" ", "", and.str) + if (length(data) < 2) { + data + } else if (length(data) == 2) { + paste(data, collapse = glue::glue(" {and.str} ")) + } else if (length(data) > 2) { + paste(paste(data[-length(data)], collapse = ", "), data[length(data)], collapse = glue::glue(" {and.str} ")) + } +} + + +cor_app <- function() { + ui <- shiny::fluidPage( + shiny::sliderInput( + inputId = "cor_cutoff", + label = "Correlation cut-off", + min = 0, + max = 1, + step = .1, + value = .7, + ticks = FALSE + ), + data_correlations_ui("data", height = 600) + ) + server <- function(input, output, session) { + data_correlations_server("data", data = shiny::reactive(mtcars), cutoff = shiny::reactive(input$cor_cutoff)) + } + shiny::shinyApp(ui, server) +} + +cor_app() diff --git a/R/helpers.R b/R/helpers.R index aecfce7..5051bfd 100644 --- a/R/helpers.R +++ b/R/helpers.R @@ -249,3 +249,20 @@ remove_na_attr <- function(data,attr="label"){ dplyr::bind_cols(out) } + +#' Removes columns with completenes below cutoff +#' +#' @param data data frame +#' @param cutoff numeric +#' +#' @returns data frame +#' @export +#' +#' @examples +#'data.frame(a=1:10,b=NA, c=c(2,NA)) |> remove_empty_cols(cutoff=.5) +remove_empty_cols <- function(data,cutoff=.7){ + filter <- apply(X = data,MARGIN = 2,FUN = \(.x){ + sum(as.numeric(!is.na(.x)))/length(.x) + }) >= cutoff + data[filter] +} diff --git a/R/report.R b/R/report.R index 1061bce..0b2b62f 100644 --- a/R/report.R +++ b/R/report.R @@ -79,3 +79,4 @@ modify_qmd <- function(file, format) { specify_qmd_format(fileformat = "all") |> writeLines(paste0(tools::file_path_sans_ext(file), "_format.", tools::file_ext(file))) } + diff --git a/R/theme.R b/R/theme.R index 43d32db..ea0b3f9 100644 --- a/R/theme.R +++ b/R/theme.R @@ -25,6 +25,7 @@ custom_theme <- function(..., ){ bslib::bs_theme( ..., + "navbar-bg" = primary, version = version, primary = primary, secondary = secondary, diff --git a/R/update-variables-ext.R b/R/update-variables-ext.R index 6d78b97..b319d36 100644 --- a/R/update-variables-ext.R +++ b/R/update-variables-ext.R @@ -461,6 +461,15 @@ update_variables_datagrid <- function(data, height = NULL, selectionId = NULL, b fontStyle = "italic" ) + grid <- toastui::grid_filters( + grid = grid, + column = "name", + # columns = unname(std_names[std_names!="vals"]), + showApplyBtn = FALSE, + showClearBtn = TRUE, + type = "text" + ) + # grid <- toastui::grid_columns( # grid = grid, # columns = "name_toset", @@ -571,6 +580,7 @@ convert_to <- function(data, new_class <- match.arg(new_class, several.ok = TRUE) stopifnot(length(new_class) == length(variable)) args <- list(...) + args$format <- clean_sep(args$format) if (length(variable) > 1) { for (i in seq_along(variable)) { data <- convert_to(data, variable[i], new_class[i], ...) @@ -602,10 +612,10 @@ convert_to <- function(data, setNames(list(expr(as.integer(!!sym(variable)))), variable) ) } else if (identical(new_class, "date")) { - data[[variable]] <- as.Date(x = data[[variable]], ...) + data[[variable]] <- as.Date(x = clean_date(data[[variable]]), ...) attr(data, "code_03_convert") <- c( attr(data, "code_03_convert"), - setNames(list(expr(as.Date(!!sym(variable), origin = !!args$origin))), variable) + setNames(list(expr(as.Date(clean_date(!!sym(variable)), origin = !!args$origin, format=clean_sep(!!args$format)))), variable) ) } else if (identical(new_class, "datetime")) { data[[variable]] <- as.POSIXct(x = data[[variable]], ...) @@ -710,3 +720,39 @@ get_vars_to_convert <- function(vars, classes_input) { } +#' gsub wrapper for piping with default values for separator substituting +#' +#' @param data character vector +#' @param old.sep old separator +#' @param new.sep new separator +#' +#' @returns character vector +#' @export +#' +clean_sep <- function(data,old.sep="[-.,/]",new.sep="-"){ + gsub(old.sep,new.sep,data) +} + +#' Attempts at applying uniform date format +#' +#' @param data character string vector of possible dates +#' +#' @returns character string +#' @export +#' +clean_date <- function(data){ + data |> + clean_sep() |> + sapply(\(.x){ + if (is.na(.x)){ + .x + } else { + strsplit(.x,"-") |> + unlist()|> + lapply(\(.y){ + if (nchar(.y)==1) paste0("0",.y) else .y + }) |> paste(collapse="-") + } + }) |> + unname() +} diff --git a/inst/apps/data_analysis_modules/app.R b/inst/apps/data_analysis_modules/app.R index 0d2e8fb..938bd0a 100644 --- a/inst/apps/data_analysis_modules/app.R +++ b/inst/apps/data_analysis_modules/app.R @@ -10,7 +10,7 @@ #### Current file: R//app_version.R ######## -app_version <- function()'250130_1152' +app_version <- function()'250207_1622' ######## @@ -41,6 +41,148 @@ baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary, +######## +#### Current file: R//correlations-module.R +######## + +#' Data correlations evaluation module +#' +#' @param id Module id. (Use 'ns("id")') +#' +#' @name data-correlations +#' @returns Shiny ui module +#' @export +data_correlations_ui <- function(id, ...) { + ns <- NS(id) + + shiny::tagList( + shiny::textOutput(outputId = ns("suggest")), + shiny::plotOutput(outputId = ns("correlation_plot"), ...) + ) +} + + +#' +#' @param data data +#' @param color.main main color +#' @param color.sec secondary color +#' @param ... arguments passed to toastui::datagrid +#' +#' @name data-correlations +#' @returns shiny server module +#' @export +data_correlations_server <- function(id, + data, + include.class = NULL, + cutoff = .7, + ...) { + shiny::moduleServer( + id = id, + module = function(input, output, session) { + # ns <- session$ns + + rv <- shiny::reactiveValues( + data = NULL + ) + + rv$data <- shiny::reactive({ + shiny::req(data) + if (!is.null(include.class)) { + filter <- sapply(data(), class) %in% include.class + out <- data()[filter] + } else { + out <- data() + } + out + }) + + # rv <- list() + # rv$data <- mtcars + + output$suggest <- shiny::renderPrint({ + shiny::req(rv$data) + shiny::req(cutoff) + pairs <- correlation_pairs(rv$data(), threshold = cutoff()) + + more <- ifelse(nrow(pairs) > 1, "from each pair ", "") + + if (nrow(pairs) == 0) { + out <- glue::glue("No variables have a correlation measure above the threshold.") + } else { + out <- pairs |> + apply(1, \(.x){ + glue::glue("'{.x[1]}'x'{.x[2]}'({round(as.numeric(.x[3]),2)})") + }) |> + (\(.x){ + glue::glue("The following variable pairs are highly correlated: {sentence_paste(.x)}.\nConsider excluding one {more}from the dataset to ensure variables are independent.") + })() + } + out + }) + + output$correlation_plot <- shiny::renderPlot({ + psych::pairs.panels(rv$data()) + }) + } + ) +} + +correlation_pairs <- function(data, threshold = .8) { + data <- data[!sapply(data, is.character)] + data <- data |> dplyr::mutate(dplyr::across(dplyr::where(is.factor), as.numeric)) + cor <- Hmisc::rcorr(as.matrix(data)) + r <- cor$r %>% as.table() + d <- r |> + as.data.frame() |> + dplyr::filter(abs(Freq) > threshold, Freq != 1) + + d[1:2] |> + apply(1, \(.x){ + sort(unname(.x)) + }, + simplify = logical(1) + ) |> + duplicated() |> + (\(.x){ + d[!.x, ] + })() |> + setNames(c("var1", "var2", "cor")) +} + +sentence_paste <- function(data, and.str = "and") { + and.str <- gsub(" ", "", and.str) + if (length(data) < 2) { + data + } else if (length(data) == 2) { + paste(data, collapse = glue::glue(" {and.str} ")) + } else if (length(data) > 2) { + paste(paste(data[-length(data)], collapse = ", "), data[length(data)], collapse = glue::glue(" {and.str} ")) + } +} + + +cor_app <- function() { + ui <- shiny::fluidPage( + shiny::sliderInput( + inputId = "cor_cutoff", + label = "Correlation cut-off", + min = 0, + max = 1, + step = .1, + value = .7, + ticks = FALSE + ), + data_correlations_ui("data", height = 600) + ) + server <- function(input, output, session) { + data_correlations_server("data", data = shiny::reactive(mtcars), cutoff = shiny::reactive(input$cor_cutoff)) + } + shiny::shinyApp(ui, server) +} + +cor_app() + + ######## #### Current file: R//cut-variable-dates.R ######## @@ -1367,6 +1509,23 @@ remove_na_attr <- function(data,attr="label"){ dplyr::bind_cols(out) } +#' Removes columns with completenes below cutoff +#' +#' @param data data frame +#' @param cutoff numeric +#' +#' @returns data frame +#' @export +#' +#' @examples +#'data.frame(a=1:10,b=NA, c=c(2,NA)) |> remove_empty_cols(cutoff=.5) +remove_empty_cols <- function(data,cutoff=.7){ + filter <- apply(X = data,MARGIN = 2,FUN = \(.x){ + sum(as.numeric(!is.na(.x)))/length(.x) + }) >= cutoff + data[filter] +} + ######## #### Current file: R//redcap_read_shiny_module.R @@ -2743,6 +2902,7 @@ modify_qmd <- function(file, format) { } + ######## #### Current file: R//shiny_freesearcheR.R ######## @@ -2805,6 +2965,7 @@ custom_theme <- function(..., ){ bslib::bs_theme( ..., + "navbar-bg" = primary, version = version, primary = primary, secondary = secondary, @@ -3322,6 +3483,15 @@ update_variables_datagrid <- function(data, height = NULL, selectionId = NULL, b fontStyle = "italic" ) + grid <- toastui::grid_filters( + grid = grid, + column = "name", + # columns = unname(std_names[std_names!="vals"]), + showApplyBtn = FALSE, + showClearBtn = TRUE, + type = "text" + ) + # grid <- toastui::grid_columns( # grid = grid, # columns = "name_toset", @@ -3432,6 +3602,7 @@ convert_to <- function(data, new_class <- match.arg(new_class, several.ok = TRUE) stopifnot(length(new_class) == length(variable)) args <- list(...) + args$format <- clean_sep(args$format) if (length(variable) > 1) { for (i in seq_along(variable)) { data <- convert_to(data, variable[i], new_class[i], ...) @@ -3463,10 +3634,10 @@ convert_to <- function(data, setNames(list(expr(as.integer(!!sym(variable)))), variable) ) } else if (identical(new_class, "date")) { - data[[variable]] <- as.Date(x = data[[variable]], ...) + data[[variable]] <- as.Date(x = clean_date(data[[variable]]), ...) attr(data, "code_03_convert") <- c( attr(data, "code_03_convert"), - setNames(list(expr(as.Date(!!sym(variable), origin = !!args$origin))), variable) + setNames(list(expr(as.Date(clean_date(!!sym(variable)), origin = !!args$origin, format=clean_sep(!!args$format)))), variable) ) } else if (identical(new_class, "datetime")) { data[[variable]] <- as.POSIXct(x = data[[variable]], ...) @@ -3571,6 +3742,42 @@ get_vars_to_convert <- function(vars, classes_input) { } +#' gsub wrapper for piping with default values for separator substituting +#' +#' @param data character vector +#' @param old.sep old separator +#' @param new.sep new separator +#' +#' @returns character vector +#' @export +#' +clean_sep <- function(data,old.sep="[-.,/]",new.sep="-"){ + gsub(old.sep,new.sep,data) +} + +#' Attempts at applying uniform date format +#' +#' @param data character string vector of possible dates +#' +#' @returns character string +#' @export +#' +clean_date <- function(data){ + data |> + clean_sep() |> + sapply(\(.x){ + if (is.na(.x)){ + .x + } else { + strsplit(.x,"-") |> + unlist()|> + lapply(\(.y){ + if (nchar(.y)==1) paste0("0",.y) else .y + }) |> paste(collapse="-") + } + }) |> + unname() +} ######## @@ -3597,61 +3804,69 @@ ui_elements <- list( ############################################################################## "import" = bslib::nav_panel( title = "Import", - shiny::tagList( - shiny::h4("Choose your data source"), - # shiny::conditionalPanel( - # condition = "output.has_input=='yes'", - # # Input: Select a file ---- - # shiny::helpText("Analyses are performed on provided data") + shiny::h4("Choose your data source"), + shiny::br(), + shinyWidgets::radioGroupButtons( + inputId = "source", + selected = "env", + # label = "Choice: ", + choices = c( + "File upload" = "file", + "REDCap server" = "redcap", + "Local data" = "env" + ), + # checkIcon = list( + # yes = icon("square-check"), + # no = icon("square") # ), - # shiny::conditionalPanel( - # condition = "output.has_input=='no'", - # Input: Select a file ---- - shinyWidgets::radioGroupButtons( - inputId = "source", - selected = "env", - # label = "Choice: ", - choices = c( - "File upload" = "file", - "REDCap server" = "redcap", - "Local data" = "env" - ), - # checkIcon = list( - # yes = icon("square-check"), - # no = icon("square") - # ), - width = "100%" - ), - shiny::conditionalPanel( - condition = "input.source=='file'", - datamods::import_file_ui("file_import", - title = "Choose a datafile to upload", - file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav", ".ods", ".dta") - ) - ), - shiny::conditionalPanel( - condition = "input.source=='redcap'", - m_redcap_readUI("redcap_import") - ), - shiny::conditionalPanel( - condition = "input.source=='env'", - import_globalenv_ui(id = "env", title = NULL) - ), - shiny::conditionalPanel( - condition = "input.source=='redcap'", - DT::DTOutput(outputId = "redcap_prev") - ), - shiny::br(), - shiny::actionButton( - inputId = "act_start", - label = "Start", - width = "100%", - icon = shiny::icon("play") - ), - shiny::helpText('After importing, hit "Start" or navigate to the desired tab.'), - shiny::br(), - shiny::br() - ) + width = "100%" + ), + shiny::helpText("Upload a file from your device, get data directly from REDCap or select a sample data set for testing from the app."), + shiny::conditionalPanel( + condition = "input.source=='file'", + datamods::import_file_ui("file_import", + title = "Choose a datafile to upload", + file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav", ".ods", ".dta") + ) + ), + shiny::conditionalPanel( + condition = "input.source=='redcap'", + m_redcap_readUI("redcap_import") + ), + shiny::conditionalPanel( + condition = "input.source=='env'", + import_globalenv_ui(id = "env", title = NULL) + ), + shiny::conditionalPanel( + condition = "input.source=='redcap'", + DT::DTOutput(outputId = "redcap_prev") + ), + shiny::br(), + shiny::br(), + shiny::h5("Exclude in-complete variables"), + shiny::p("Before going further, you can exclude variables with a low degree of completeness."), + shiny::br(), + shiny::sliderInput( + inputId = "complete_cutoff", + label = "Choose completeness threshold (%)", + min = 0, + max = 100, + step = 10, + value = 70, + ticks = FALSE + ), + shiny::helpText("Only include variables with completeness above a specified percentage."), + shiny::br(), + shiny::br(), + shiny::actionButton( + inputId = "act_start", + label = "Start", + width = "100%", + icon = shiny::icon("play") + ), + shiny::helpText('After importing, hit "Start" or navigate to the desired tab.'), + shiny::br(), + shiny::br() ), ############################################################################## ######### @@ -3731,7 +3946,7 @@ ui_elements <- list( fluidRow( shiny::column( width = 9, - shiny::tags$p("Below, you can subset the data (by not selecting the variables to exclude on applying changes), rename variables, set new labels (for nicer tables in the analysis report) and change variable classes. + shiny::tags$p("Below, you can subset the data (select variables to include on clicking 'Apply changes'), rename variables, set new labels (for nicer tables in the report) and change variable classes (numeric, factor/categorical etc.). Italic text can be edited/changed. On the right, you can create and modify factor/categorical variables as well as resetting the data to the originally imported data.") ) @@ -3851,15 +4066,13 @@ ui_elements <- list( ), ############################################################################## ######### - ######### Data analyses panel + ######### Descriptive analyses panel ######### ############################################################################## - "analyze" = - # bslib::nav_panel_hidden( + "describe" = bslib::nav_panel( - # value = "analyze", - title = "Analyses", - id = "navanalyses", + title = "Evaluate", + id = "navdescribe", bslib::navset_bar( title = "", # bslib::layout_sidebar( @@ -3889,6 +4102,47 @@ ui_elements <- list( shiny::helpText("Option to perform statistical comparisons between strata in baseline table.") ) ), + bslib::accordion_panel( + title = "Correlations", + shiny::sliderInput( + inputId = "cor_cutoff", + label = "Correlation cut-off", + min = 0, + max = 1, + step = .02, + value = .7, + ticks = FALSE + ) + ) + ) + ), + bslib::nav_panel( + title = "Baseline characteristics", + gt::gt_output(outputId = "table1") + ), + bslib::nav_panel( + title = "Variable correlations", + data_correlations_ui(id = "correlations", height = 600) + ) + ) + ), + ############################################################################## + ######### + ######### Regression analyses panel + ######### + ############################################################################## + "analyze" = + bslib::nav_panel( + title = "Regression", + id = "navanalyses", + bslib::navset_bar( + title = "", + # bslib::layout_sidebar( + # fillable = TRUE, + sidebar = bslib::sidebar( + bslib::accordion( + open = "acc_reg", + multiple = FALSE, bslib::accordion_panel( value = "acc_reg", title = "Regression", @@ -3927,23 +4181,14 @@ ui_elements <- list( type = "secondary", auto_reset = TRUE ), - shiny::helpText("If you change the parameters, press 'Analyse' again to update the regression analysis"), + shiny::helpText("Press 'Analyse' again after changing parameters."), + shiny::tags$br(), shiny::uiOutput("plot_model") ), bslib::accordion_panel( value = "acc_advanced", title = "Advanced", icon = bsicons::bs_icon("gear"), - shiny::sliderInput( - inputId = "complete_cutoff", - label = "Cut-off for column completeness (%)", - min = 0, - max = 100, - step = 10, - value = 70, - ticks = FALSE - ), - shiny::helpText("To improve speed, columns are removed before analysing data, if copleteness is below above value."), shiny::radioButtons( inputId = "all", label = "Specify covariables", @@ -3958,52 +4203,6 @@ ui_elements <- list( condition = "input.all==1", shiny::uiOutput("include_vars") ) - ), - bslib::accordion_panel( - value = "acc_down", - title = "Download", - icon = bsicons::bs_icon("download"), - shiny::h4("Report"), - shiny::helpText("Choose your favourite output file format for further work, and download, when the analyses are done."), - shiny::selectInput( - inputId = "output_type", - label = "Output format", - selected = NULL, - choices = list( - "MS Word" = "docx", - "LibreOffice" = "odt" - # , - # "PDF" = "pdf", - # "All the above" = "all" - ) - ), - shiny::br(), - # Button - shiny::downloadButton( - outputId = "report", - label = "Download report", - icon = shiny::icon("download") - ), - # shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."), - shiny::tags$hr(), - shiny::h4("Data"), - shiny::helpText("Choose your favourite output data format to download the modified data."), - shiny::selectInput( - inputId = "data_type", - label = "Data format", - selected = NULL, - choices = list( - "R" = "rds", - "stata" = "dta" - ) - ), - shiny::br(), - # Button - shiny::downloadButton( - outputId = "data_modified", - label = "Download data", - icon = shiny::icon("download") - ) ) ), # shiny::helpText(em("Please specify relevant settings for your data, and press 'Analyse'")), @@ -4025,10 +4224,6 @@ ui_elements <- list( # condition = "output.ready=='yes'", # shiny::tags$hr(), ), - bslib::nav_panel( - title = "Baseline characteristics", - gt::gt_output(outputId = "table1") - ), bslib::nav_panel( title = "Regression table", gt::gt_output(outputId = "table2") @@ -4046,6 +4241,66 @@ ui_elements <- list( ), ############################################################################## ######### + ######### Download panel + ######### + ############################################################################## + "download" = + bslib::nav_panel( + title = "Download", + id = "navdownload", + shiny::fluidRow( + shiny::column( + width = 6, + shiny::h4("Report"), + shiny::helpText("Choose your favourite output file format for further work, and download, when the analyses are done."), + shiny::selectInput( + inputId = "output_type", + label = "Output format", + selected = NULL, + choices = list( + "MS Word" = "docx", + "LibreOffice" = "odt" + # , + # "PDF" = "pdf", + # "All the above" = "all" + ) + ), + shiny::br(), + # Button + shiny::downloadButton( + outputId = "report", + label = "Download report", + icon = shiny::icon("download") + ) + # shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."), + ), + shiny::column( + width = 6, + shiny::h4("Data"), + shiny::helpText("Choose your favourite output data format to download the modified data."), + shiny::selectInput( + inputId = "data_type", + label = "Data format", + selected = NULL, + choices = list( + "R" = "rds", + "stata" = "dta", + "CSV" = "csv" + ) + ), + shiny::br(), + # Button + shiny::downloadButton( + outputId = "data_modified", + label = "Download data", + icon = shiny::icon("download") + ) + ) + ), + shiny::br() + ), + ############################################################################## + ######### ######### Documentation panel ######### ############################################################################## @@ -4065,7 +4320,6 @@ ui_elements <- list( # shiny::br() # ) ) - # Initial attempt at creating light and dark versions light <- custom_theme() dark <- custom_theme( @@ -4090,17 +4344,15 @@ ui <- bslib::page_fixed( theme = light, shiny::useBusyIndicators(), bslib::page_navbar( - # title = "freesearcheR", id = "main_panel", - # header = shiny::tags$header(shiny::p("Data is only stored temporarily for analysis and deleted immediately afterwards.")), ui_elements$home, ui_elements$import, ui_elements$overview, + ui_elements$describe, ui_elements$analyze, + ui_elements$download, bslib::nav_spacer(), ui_elements$docs, - # bslib::nav_spacer(), - # bslib::nav_item(shinyWidgets::circleButton(inputId = "mode", icon = icon("moon"),status = "primary")), fillable = FALSE, footer = shiny::tags$footer( style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;", @@ -4213,7 +4465,7 @@ server <- function(input, output, session) { ######### ############################################################################## - consider.na <- c("NA", "\"\"", "") + consider.na <- c("NA", "\"\"", "", "\'\'", "na") data_file <- datamods::import_file_server( id = "file_import", @@ -4228,7 +4480,8 @@ server <- function(input, output, session) { haven::read_dta(file = file, .name_repair = "unique_quiet") }, csv = function(file) { - readr::read_csv(file = file, na = consider.na) + readr::read_csv(file = file, na = consider.na, name_repair = "unique_quiet") #|> + # janitor::remove_empty(which = "cols", cutoff = 1, quiet = TRUE) }, # xls = function(file){ # openxlsx2::read_xlsx(file = file, na.strings = consider.na,) @@ -4237,7 +4490,7 @@ server <- function(input, output, session) { # openxlsx2::read_xlsx(file = file, na.strings = consider.na,) # }, rds = function(file) { - readr::read_rds(file = file) + readr::read_rds(file = file, name_repair = "unique_quiet") } ) ) @@ -4284,11 +4537,22 @@ server <- function(input, output, session) { ######### ############################################################################## - shiny::observeEvent(rv$data_original, { - rv$data <- rv$data_original |> - default_parsing() |> - janitor::clean_names() - }) + shiny::observeEvent( + eventExpr = list( + rv$data_original, + input$reset_confirm, + input$complete_cutoff + ), + handlerExpr = { + shiny::req(rv$data_original) + rv$data <- rv$data_original |> + # janitor::clean_names() |> + default_parsing() |> + remove_empty_cols( + cutoff = input$complete_cutoff / 100 + ) + } + ) shiny::observeEvent(input$data_reset, { shinyWidgets::ask_confirmation( @@ -4297,9 +4561,9 @@ server <- function(input, output, session) { ) }) - shiny::observeEvent(input$reset_confirm, { - rv$data <- rv$data_original |> default_parsing() - }) + # shiny::observeEvent(input$reset_confirm, { + # rv$data <- rv$data_original |> default_parsing() + # }) ######### Overview @@ -4366,7 +4630,8 @@ server <- function(input, output, session) { ) ######### Show result - + tryCatch( + { output$table_mod <- toastui::renderDatagrid({ shiny::req(rv$data) # data <- rv$data @@ -4379,6 +4644,13 @@ server <- function(input, output, session) { # striped = TRUE ) }) + }, + warning = function(warn) { + showNotification(paste0(warn), type = "warning") + }, + error = function(err) { + showNotification(paste0(err), type = "err") + }) output$code <- renderPrint({ attr(rv$data, "code") @@ -4422,14 +4694,14 @@ server <- function(input, output, session) { rv$data_filtered <- data_filter() rv$list$data <- data_filter() |> - REDCapCAST::fct_drop.data.frame() |> + REDCapCAST::fct_drop() |> (\(.x){ .x[base_vars()] - })() |> - janitor::remove_empty( - which = "cols", - cutoff = input$complete_cutoff / 100 - ) + })() #|> + # janitor::remove_empty( + # which = "cols", + # cutoff = input$complete_cutoff / 100 + # ) } ) @@ -4488,13 +4760,17 @@ server <- function(input, output, session) { shiny::req(input$outcome_var) shiny::selectizeInput( inputId = "regression_type", - # selected = colnames(rv$data_filtered)[sapply(rv$data_filtered, is.factor)], label = "Choose regression analysis", - choices = possible_functions(data = dplyr::select(rv$data_filtered, - ifelse(input$outcome_var %in% names(rv$data_filtered), - input$outcome_var, - names(rv$data_filtered)[1]) - ), design = "cross-sectional"), + ## The below ifelse statement handles the case of loading a new dataset + choices = possible_functions( + data = dplyr::select( + rv$data_filtered, + ifelse(input$outcome_var %in% names(rv$data_filtered), + input$outcome_var, + names(rv$data_filtered)[1] + ) + ), design = "cross-sectional" + ), multiple = FALSE ) }) @@ -4553,90 +4829,9 @@ server <- function(input, output, session) { }) - - - ## Have a look at column filters at some point - ## There should be a way to use the filtering the filter data for further analyses - ## Disabled for now, as the JS is apparently not isolated - # output$data_table <- - # DT::renderDT( - # { - # DT::datatable(ds()[base_vars()]) - # }, - # server = FALSE - # ) - # - # output$data.classes <- gt::render_gt({ - # shiny::req(input$file) - # data.frame(matrix(sapply(ds(), \(.x){ - # class(.x)[1] - # }), nrow = 1)) |> - # stats::setNames(names(ds())) |> - # gt::gt() - # }) - - - ### Outputs - - # shiny::observeEvent(data_filter(), { - # rv$data_filtered <- data_filter() - # }) - - # shiny::observeEvent( - # shiny::reactive(rv$data_filtered), - # { - # rv$list$data <- rv$data_filtered |> - # # dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |> - # REDCapCAST::fct_drop.data.frame() |> - # # factorize(vars = input$factor_vars) |> - # remove_na_attr() - # - # # rv$list$data <- data - # # rv$list$data <- data[base_vars()] - # } - # ) - - # shiny::observe({ - # if (input$strat_var == "none") { - # by.var <- NULL - # } else { - # by.var <- input$strat_var - # } - # - # rv$list$table1 <- rv$list$data |> - # baseline_table( - # fun.args = - # list( - # by = by.var - # ) - # ) |> - # (\(.x){ - # if (!is.null(by.var)) { - # .x |> gtsummary::add_overall() - # } else { - # .x - # } - # })() |> - # (\(.x){ - # if (input$add_p == "yes") { - # .x |> - # gtsummary::add_p() |> - # gtsummary::bold_p() - # } else { - # .x - # } - # })() - # }) - # - # output$table1 <- gt::render_gt( - # rv$list$table1 |> - # gtsummary::as_gt() |> - # gt::tab_header(shiny::md("**Table 1. Patient Characteristics**")) - # ) - ############################################################################## ######### - ######### Data analyses results + ######### Descriptive evaluations ######### ############################################################################## @@ -4701,6 +4896,18 @@ server <- function(input, output, session) { gt::tab_header(gt::md("**Table 1: Baseline Characteristics**")) }) + + data_correlations_server(id = "correlations", + data = shiny::reactive(rv$list$data), + cutoff = shiny::reactive(input$cor_cutoff)) + + + ############################################################################## + ######### + ######### Regression model analyses + ######### + ############################################################################## + shiny::observeEvent( input$load, { @@ -4779,37 +4986,6 @@ server <- function(input, output, session) { } ) - # plot_check_r <- shiny::reactive({plot(rv$check)}) - # - # output$check_1 <- shiny::renderUI({ - # shiny::req(rv$check) - # list <- lapply(seq_len(length(plot_check_r())), - # function(i) { - # plotname <- paste0("check_plot_", i) - # shiny::htmlOutput(plotname) - # }) - # - # do.call(shiny::tagList,list) - # }) - # - # # Call renderPlot for each one. Plots are only actually generated when they - # # are visible on the web page. - # - # shiny::observe({ - # shiny::req(rv$check) - # # browser() - # for (i in seq_len(length(plot_check_r()))) { - # local({ - # my_i <- i - # plotname <- paste0("check_plot_", my_i) - # - # output[[plotname]] <- shiny::renderPlot({ - # plot_check_r()[[my_i]] + gg_theme_shiny() - # }) - # }) - # } - # }) - output$check <- shiny::renderPlot( { shiny::req(rv$check) @@ -4932,7 +5108,7 @@ server <- function(input, output, session) { ) out + - ggplot2::scale_y_discrete(labels = scales::label_wrap(15))+ + ggplot2::scale_y_discrete(labels = scales::label_wrap(15)) + gg_theme_shiny() # rv$list$regression$tables$Multivariable |> @@ -5044,8 +5220,10 @@ server <- function(input, output, session) { content = function(file, type = input$data_type) { if (type == "rds") { readr::write_rds(rv$list$data, file = file) - } else { + } else if (type == "dta") { haven::write_dta(as.data.frame(rv$list$data), path = file) + } else if (type == "csv"){ + readr::write_csv(rv$list$data, file = file) } } ) diff --git a/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf b/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf index f0c07b2..8d0b399 100644 --- a/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf +++ b/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf @@ -5,6 +5,6 @@ account: agdamsbo server: shinyapps.io hostUrl: https://api.shinyapps.io/v1 appId: 13611288 -bundleId: 9693816 +bundleId: url: https://agdamsbo.shinyapps.io/freesearcheR/ version: 1 diff --git a/inst/apps/data_analysis_modules/server.R b/inst/apps/data_analysis_modules/server.R index 8abaae1..3822782 100644 --- a/inst/apps/data_analysis_modules/server.R +++ b/inst/apps/data_analysis_modules/server.R @@ -90,7 +90,7 @@ server <- function(input, output, session) { ######### ############################################################################## - consider.na <- c("NA", "\"\"", "") + consider.na <- c("NA", "\"\"", "", "\'\'", "na") data_file <- datamods::import_file_server( id = "file_import", @@ -105,7 +105,8 @@ server <- function(input, output, session) { haven::read_dta(file = file, .name_repair = "unique_quiet") }, csv = function(file) { - readr::read_csv(file = file, na = consider.na) + readr::read_csv(file = file, na = consider.na, name_repair = "unique_quiet") #|> + # janitor::remove_empty(which = "cols", cutoff = 1, quiet = TRUE) }, # xls = function(file){ # openxlsx2::read_xlsx(file = file, na.strings = consider.na,) @@ -114,7 +115,7 @@ server <- function(input, output, session) { # openxlsx2::read_xlsx(file = file, na.strings = consider.na,) # }, rds = function(file) { - readr::read_rds(file = file) + readr::read_rds(file = file, name_repair = "unique_quiet") } ) ) @@ -161,11 +162,22 @@ server <- function(input, output, session) { ######### ############################################################################## - shiny::observeEvent(rv$data_original, { - rv$data <- rv$data_original |> - default_parsing() |> - janitor::clean_names() - }) + shiny::observeEvent( + eventExpr = list( + rv$data_original, + input$reset_confirm, + input$complete_cutoff + ), + handlerExpr = { + shiny::req(rv$data_original) + rv$data <- rv$data_original |> + # janitor::clean_names() |> + default_parsing() |> + remove_empty_cols( + cutoff = input$complete_cutoff / 100 + ) + } + ) shiny::observeEvent(input$data_reset, { shinyWidgets::ask_confirmation( @@ -174,9 +186,9 @@ server <- function(input, output, session) { ) }) - shiny::observeEvent(input$reset_confirm, { - rv$data <- rv$data_original |> default_parsing() - }) + # shiny::observeEvent(input$reset_confirm, { + # rv$data <- rv$data_original |> default_parsing() + # }) ######### Overview @@ -243,7 +255,8 @@ server <- function(input, output, session) { ) ######### Show result - + tryCatch( + { output$table_mod <- toastui::renderDatagrid({ shiny::req(rv$data) # data <- rv$data @@ -256,6 +269,13 @@ server <- function(input, output, session) { # striped = TRUE ) }) + }, + warning = function(warn) { + showNotification(paste0(warn), type = "warning") + }, + error = function(err) { + showNotification(paste0(err), type = "err") + }) output$code <- renderPrint({ attr(rv$data, "code") @@ -299,14 +319,14 @@ server <- function(input, output, session) { rv$data_filtered <- data_filter() rv$list$data <- data_filter() |> - REDCapCAST::fct_drop.data.frame() |> + REDCapCAST::fct_drop() |> (\(.x){ .x[base_vars()] - })() |> - janitor::remove_empty( - which = "cols", - cutoff = input$complete_cutoff / 100 - ) + })() #|> + # janitor::remove_empty( + # which = "cols", + # cutoff = input$complete_cutoff / 100 + # ) } ) @@ -434,90 +454,9 @@ server <- function(input, output, session) { }) - - - ## Have a look at column filters at some point - ## There should be a way to use the filtering the filter data for further analyses - ## Disabled for now, as the JS is apparently not isolated - # output$data_table <- - # DT::renderDT( - # { - # DT::datatable(ds()[base_vars()]) - # }, - # server = FALSE - # ) - # - # output$data.classes <- gt::render_gt({ - # shiny::req(input$file) - # data.frame(matrix(sapply(ds(), \(.x){ - # class(.x)[1] - # }), nrow = 1)) |> - # stats::setNames(names(ds())) |> - # gt::gt() - # }) - - - ### Outputs - - # shiny::observeEvent(data_filter(), { - # rv$data_filtered <- data_filter() - # }) - - # shiny::observeEvent( - # shiny::reactive(rv$data_filtered), - # { - # rv$list$data <- rv$data_filtered |> - # # dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |> - # REDCapCAST::fct_drop.data.frame() |> - # # factorize(vars = input$factor_vars) |> - # remove_na_attr() - # - # # rv$list$data <- data - # # rv$list$data <- data[base_vars()] - # } - # ) - - # shiny::observe({ - # if (input$strat_var == "none") { - # by.var <- NULL - # } else { - # by.var <- input$strat_var - # } - # - # rv$list$table1 <- rv$list$data |> - # baseline_table( - # fun.args = - # list( - # by = by.var - # ) - # ) |> - # (\(.x){ - # if (!is.null(by.var)) { - # .x |> gtsummary::add_overall() - # } else { - # .x - # } - # })() |> - # (\(.x){ - # if (input$add_p == "yes") { - # .x |> - # gtsummary::add_p() |> - # gtsummary::bold_p() - # } else { - # .x - # } - # })() - # }) - # - # output$table1 <- gt::render_gt( - # rv$list$table1 |> - # gtsummary::as_gt() |> - # gt::tab_header(shiny::md("**Table 1. Patient Characteristics**")) - # ) - ############################################################################## ######### - ######### Data analyses results + ######### Descriptive evaluations ######### ############################################################################## @@ -582,6 +521,18 @@ server <- function(input, output, session) { gt::tab_header(gt::md("**Table 1: Baseline Characteristics**")) }) + + data_correlations_server(id = "correlations", + data = shiny::reactive(rv$list$data), + cutoff = shiny::reactive(input$cor_cutoff)) + + + ############################################################################## + ######### + ######### Regression model analyses + ######### + ############################################################################## + shiny::observeEvent( input$load, { @@ -660,37 +611,6 @@ server <- function(input, output, session) { } ) - # plot_check_r <- shiny::reactive({plot(rv$check)}) - # - # output$check_1 <- shiny::renderUI({ - # shiny::req(rv$check) - # list <- lapply(seq_len(length(plot_check_r())), - # function(i) { - # plotname <- paste0("check_plot_", i) - # shiny::htmlOutput(plotname) - # }) - # - # do.call(shiny::tagList,list) - # }) - # - # # Call renderPlot for each one. Plots are only actually generated when they - # # are visible on the web page. - # - # shiny::observe({ - # shiny::req(rv$check) - # # browser() - # for (i in seq_len(length(plot_check_r()))) { - # local({ - # my_i <- i - # plotname <- paste0("check_plot_", my_i) - # - # output[[plotname]] <- shiny::renderPlot({ - # plot_check_r()[[my_i]] + gg_theme_shiny() - # }) - # }) - # } - # }) - output$check <- shiny::renderPlot( { shiny::req(rv$check) @@ -925,8 +845,10 @@ server <- function(input, output, session) { content = function(file, type = input$data_type) { if (type == "rds") { readr::write_rds(rv$list$data, file = file) - } else { + } else if (type == "dta") { haven::write_dta(as.data.frame(rv$list$data), path = file) + } else if (type == "csv"){ + readr::write_csv(rv$list$data, file = file) } } ) diff --git a/inst/apps/data_analysis_modules/ui.R b/inst/apps/data_analysis_modules/ui.R index c182f9e..2e2ac4f 100644 --- a/inst/apps/data_analysis_modules/ui.R +++ b/inst/apps/data_analysis_modules/ui.R @@ -18,61 +18,69 @@ ui_elements <- list( ############################################################################## "import" = bslib::nav_panel( title = "Import", - shiny::tagList( - shiny::h4("Choose your data source"), - # shiny::conditionalPanel( - # condition = "output.has_input=='yes'", - # # Input: Select a file ---- - # shiny::helpText("Analyses are performed on provided data") + shiny::h4("Choose your data source"), + shiny::br(), + shinyWidgets::radioGroupButtons( + inputId = "source", + selected = "env", + # label = "Choice: ", + choices = c( + "File upload" = "file", + "REDCap server" = "redcap", + "Local data" = "env" + ), + # checkIcon = list( + # yes = icon("square-check"), + # no = icon("square") # ), - # shiny::conditionalPanel( - # condition = "output.has_input=='no'", - # Input: Select a file ---- - shinyWidgets::radioGroupButtons( - inputId = "source", - selected = "env", - # label = "Choice: ", - choices = c( - "File upload" = "file", - "REDCap server" = "redcap", - "Local data" = "env" - ), - # checkIcon = list( - # yes = icon("square-check"), - # no = icon("square") - # ), - width = "100%" - ), - shiny::conditionalPanel( - condition = "input.source=='file'", - datamods::import_file_ui("file_import", - title = "Choose a datafile to upload", - file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav", ".ods", ".dta") - ) - ), - shiny::conditionalPanel( - condition = "input.source=='redcap'", - m_redcap_readUI("redcap_import") - ), - shiny::conditionalPanel( - condition = "input.source=='env'", - import_globalenv_ui(id = "env", title = NULL) - ), - shiny::conditionalPanel( - condition = "input.source=='redcap'", - DT::DTOutput(outputId = "redcap_prev") - ), - shiny::br(), - shiny::actionButton( - inputId = "act_start", - label = "Start", - width = "100%", - icon = shiny::icon("play") - ), - shiny::helpText('After importing, hit "Start" or navigate to the desired tab.'), - shiny::br(), - shiny::br() - ) + width = "100%" + ), + shiny::helpText("Upload a file from your device, get data directly from REDCap or select a sample data set for testing from the app."), + shiny::conditionalPanel( + condition = "input.source=='file'", + datamods::import_file_ui("file_import", + title = "Choose a datafile to upload", + file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav", ".ods", ".dta") + ) + ), + shiny::conditionalPanel( + condition = "input.source=='redcap'", + m_redcap_readUI("redcap_import") + ), + shiny::conditionalPanel( + condition = "input.source=='env'", + import_globalenv_ui(id = "env", title = NULL) + ), + shiny::conditionalPanel( + condition = "input.source=='redcap'", + DT::DTOutput(outputId = "redcap_prev") + ), + shiny::br(), + shiny::br(), + shiny::h5("Exclude in-complete variables"), + shiny::p("Before going further, you can exclude variables with a low degree of completeness."), + shiny::br(), + shiny::sliderInput( + inputId = "complete_cutoff", + label = "Choose completeness threshold (%)", + min = 0, + max = 100, + step = 10, + value = 70, + ticks = FALSE + ), + shiny::helpText("Only include variables with completeness above a specified percentage."), + shiny::br(), + shiny::br(), + shiny::actionButton( + inputId = "act_start", + label = "Start", + width = "100%", + icon = shiny::icon("play") + ), + shiny::helpText('After importing, hit "Start" or navigate to the desired tab.'), + shiny::br(), + shiny::br() ), ############################################################################## ######### @@ -152,7 +160,7 @@ ui_elements <- list( fluidRow( shiny::column( width = 9, - shiny::tags$p("Below, you can subset the data (by not selecting the variables to exclude on applying changes), rename variables, set new labels (for nicer tables in the analysis report) and change variable classes. + shiny::tags$p("Below, you can subset the data (select variables to include on clicking 'Apply changes'), rename variables, set new labels (for nicer tables in the report) and change variable classes (numeric, factor/categorical etc.). Italic text can be edited/changed. On the right, you can create and modify factor/categorical variables as well as resetting the data to the originally imported data.") ) @@ -272,15 +280,13 @@ ui_elements <- list( ), ############################################################################## ######### - ######### Data analyses panel + ######### Descriptive analyses panel ######### ############################################################################## - "analyze" = - # bslib::nav_panel_hidden( + "describe" = bslib::nav_panel( - # value = "analyze", - title = "Analyses", - id = "navanalyses", + title = "Evaluate", + id = "navdescribe", bslib::navset_bar( title = "", # bslib::layout_sidebar( @@ -310,6 +316,47 @@ ui_elements <- list( shiny::helpText("Option to perform statistical comparisons between strata in baseline table.") ) ), + bslib::accordion_panel( + title = "Correlations", + shiny::sliderInput( + inputId = "cor_cutoff", + label = "Correlation cut-off", + min = 0, + max = 1, + step = .02, + value = .7, + ticks = FALSE + ) + ) + ) + ), + bslib::nav_panel( + title = "Baseline characteristics", + gt::gt_output(outputId = "table1") + ), + bslib::nav_panel( + title = "Variable correlations", + data_correlations_ui(id = "correlations", height = 600) + ) + ) + ), + ############################################################################## + ######### + ######### Regression analyses panel + ######### + ############################################################################## + "analyze" = + bslib::nav_panel( + title = "Regression", + id = "navanalyses", + bslib::navset_bar( + title = "", + # bslib::layout_sidebar( + # fillable = TRUE, + sidebar = bslib::sidebar( + bslib::accordion( + open = "acc_reg", + multiple = FALSE, bslib::accordion_panel( value = "acc_reg", title = "Regression", @@ -348,23 +395,14 @@ ui_elements <- list( type = "secondary", auto_reset = TRUE ), - shiny::helpText("If you change the parameters, press 'Analyse' again to update the regression analysis"), + shiny::helpText("Press 'Analyse' again after changing parameters."), + shiny::tags$br(), shiny::uiOutput("plot_model") ), bslib::accordion_panel( value = "acc_advanced", title = "Advanced", icon = bsicons::bs_icon("gear"), - shiny::sliderInput( - inputId = "complete_cutoff", - label = "Cut-off for column completeness (%)", - min = 0, - max = 100, - step = 10, - value = 70, - ticks = FALSE - ), - shiny::helpText("To improve speed, columns are removed before analysing data, if copleteness is below above value."), shiny::radioButtons( inputId = "all", label = "Specify covariables", @@ -379,52 +417,6 @@ ui_elements <- list( condition = "input.all==1", shiny::uiOutput("include_vars") ) - ), - bslib::accordion_panel( - value = "acc_down", - title = "Download", - icon = bsicons::bs_icon("download"), - shiny::h4("Report"), - shiny::helpText("Choose your favourite output file format for further work, and download, when the analyses are done."), - shiny::selectInput( - inputId = "output_type", - label = "Output format", - selected = NULL, - choices = list( - "MS Word" = "docx", - "LibreOffice" = "odt" - # , - # "PDF" = "pdf", - # "All the above" = "all" - ) - ), - shiny::br(), - # Button - shiny::downloadButton( - outputId = "report", - label = "Download report", - icon = shiny::icon("download") - ), - # shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."), - shiny::tags$hr(), - shiny::h4("Data"), - shiny::helpText("Choose your favourite output data format to download the modified data."), - shiny::selectInput( - inputId = "data_type", - label = "Data format", - selected = NULL, - choices = list( - "R" = "rds", - "stata" = "dta" - ) - ), - shiny::br(), - # Button - shiny::downloadButton( - outputId = "data_modified", - label = "Download data", - icon = shiny::icon("download") - ) ) ), # shiny::helpText(em("Please specify relevant settings for your data, and press 'Analyse'")), @@ -446,10 +438,6 @@ ui_elements <- list( # condition = "output.ready=='yes'", # shiny::tags$hr(), ), - bslib::nav_panel( - title = "Baseline characteristics", - gt::gt_output(outputId = "table1") - ), bslib::nav_panel( title = "Regression table", gt::gt_output(outputId = "table2") @@ -467,6 +455,66 @@ ui_elements <- list( ), ############################################################################## ######### + ######### Download panel + ######### + ############################################################################## + "download" = + bslib::nav_panel( + title = "Download", + id = "navdownload", + shiny::fluidRow( + shiny::column( + width = 6, + shiny::h4("Report"), + shiny::helpText("Choose your favourite output file format for further work, and download, when the analyses are done."), + shiny::selectInput( + inputId = "output_type", + label = "Output format", + selected = NULL, + choices = list( + "MS Word" = "docx", + "LibreOffice" = "odt" + # , + # "PDF" = "pdf", + # "All the above" = "all" + ) + ), + shiny::br(), + # Button + shiny::downloadButton( + outputId = "report", + label = "Download report", + icon = shiny::icon("download") + ) + # shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."), + ), + shiny::column( + width = 6, + shiny::h4("Data"), + shiny::helpText("Choose your favourite output data format to download the modified data."), + shiny::selectInput( + inputId = "data_type", + label = "Data format", + selected = NULL, + choices = list( + "R" = "rds", + "stata" = "dta", + "CSV" = "csv" + ) + ), + shiny::br(), + # Button + shiny::downloadButton( + outputId = "data_modified", + label = "Download data", + icon = shiny::icon("download") + ) + ) + ), + shiny::br() + ), + ############################################################################## + ######### ######### Documentation panel ######### ############################################################################## @@ -486,7 +534,6 @@ ui_elements <- list( # shiny::br() # ) ) - # Initial attempt at creating light and dark versions light <- custom_theme() dark <- custom_theme( @@ -511,17 +558,15 @@ ui <- bslib::page_fixed( theme = light, shiny::useBusyIndicators(), bslib::page_navbar( - # title = "freesearcheR", id = "main_panel", - # header = shiny::tags$header(shiny::p("Data is only stored temporarily for analysis and deleted immediately afterwards.")), ui_elements$home, ui_elements$import, ui_elements$overview, + ui_elements$describe, ui_elements$analyze, + ui_elements$download, bslib::nav_spacer(), ui_elements$docs, - # bslib::nav_spacer(), - # bslib::nav_item(shinyWidgets::circleButton(inputId = "mode", icon = icon("moon"),status = "primary")), fillable = FALSE, footer = shiny::tags$footer( style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;", diff --git a/inst/apps/data_analysis_modules/www/intro.html b/inst/apps/data_analysis_modules/www/intro.html index 3a1299b..f61794b 100644 --- a/inst/apps/data_analysis_modules/www/intro.html +++ b/inst/apps/data_analysis_modules/www/intro.html @@ -354,22 +354,21 @@ display: none;

Welcome

-

This is the freesearcheR web data analysis +

This is the freesearcheR data analysis tool. We intend the freesearcheR to be a powerful and free tool for easy data evaluation and analysis at the hands of the clinician.

By intention, this tool has been designed to be simple to use with a minimum of mandatory options to keep the workflow streamlined, while also including a few options to go even further.

-

There are four simple steps to go through (see corresponding tabs in +

There are some simple steps to go through (see corresponding tabs in the top):

  1. Import data (a spreadsheet/file on your machine, direct export from a REDCap server, or a local file provided with a package) to get started.

    2. -

  2. An optional step of data modification (change variable -classes and creating categorical variables (factors) from numeric or -time data)

    3. +

  3. Inspec of data modification (change variable classes and creating +categorical variables (factors) from numeric or time data)

  4. Data analysis of cross-sectionally designed studies (more study designs are planned to be included)

      @@ -382,10 +381,9 @@ depending on specified outcome variable

    • Export the the analyses results for MS Word or LibreOffice as well as the data with preserved metadata.

-

Have a look at the documentations page for further -project description. If you’re interested in the source code, then go -on, have a -look!

+

Have a look at the documentations page +for further project description. If you’re interested in the source +code, then go on, have a look!

If you encounter anything strange or the app doesn’t act as expected. Please report on Github.

diff --git a/inst/apps/data_analysis_modules/www/intro.md b/inst/apps/data_analysis_modules/www/intro.md index 4b5e9f6..56cc8e3 100644 --- a/inst/apps/data_analysis_modules/www/intro.md +++ b/inst/apps/data_analysis_modules/www/intro.md @@ -1,24 +1,26 @@ # Welcome -This is the ***freesearcheR*** web data analysis tool. We intend the ***freesearcheR*** to be a powerful and free tool for easy data evaluation and analysis at the hands of the clinician. +This is the ***freesearcheR*** data analysis tool. We intend the ***freesearcheR*** to be a powerful and free tool for easy data evaluation and analysis at the hands of the clinician. By intention, this tool has been designed to be simple to use with a minimum of mandatory options to keep the workflow streamlined, while also including a few options to go even further. -There are four simple steps to go through (see corresponding tabs in the top): +There are some simple steps to go through (see corresponding tabs in the top): 1. Import data (a spreadsheet/file on your machine, direct export from a REDCap server, or a local file provided with a package) to get started. -2. An *optional* step of data modification (change variable classes and creating categorical variables (factors) from numeric or time data) +1. Data inspection and modification (change variable classes, create new variables (categorical from numeric or time data, or completely new variables from the data) -3. Data analysis of cross-sectionally designed studies (more study designs are planned to be included) +1. Evaluate data using descriptive analyses methods and inspect cross-correlations - - Classic baseline charactieristics (options to stratify and compare variables) +1. Create regression models for even more advanced data analyses - Linear, dichotomous or ordinal logistic regression will be used depending on specified outcome variable + + - Plot regression analysis coefficients - Evaluation of model assumptions -4. Export the the analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/) as well as the data with preserved metadata. +1. Export the the analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/) as well as the data with preserved metadata. Have a look at the [documentations page](https://agdamsbo.github.io/freesearcheR/) for further project description. If you're interested in the source code, then go on, [have a look](https://github.com/agdamsbo/freesearcheR)! diff --git a/inst/apps/data_analysis_modules/www/report.qmd b/inst/apps/data_analysis_modules/www/report.qmd deleted file mode 100644 index 7715c24..0000000 --- a/inst/apps/data_analysis_modules/www/report.qmd +++ /dev/null @@ -1,55 +0,0 @@ ---- -title: "freesearcheR analysis results" -date: today -format: docx -author: freesearcheR Tool -toc: false -execute: - echo: false -params: - data.file: NA ---- - -```{r} -#| message: false -#| warning: false -web_data <- readr::read_rds(file = params$data.file) -library(gtsummary) -library(gt) - -tbl_merge <- function(data) { - if (is.null(names(data))) { - data |> gtsummary::tbl_merge() - } else { - data |> gtsummary::tbl_merge(tab_spanner = names(data)) - } -} -``` - -## Introduction - -Research should be free and open with easy access for all. The freesearcheR tool attempts to help lower the bar to participate in contributing to science by making guided data analysis easily accessible in the web-browser. - -## Methods - -Analyses were conducted in the *freesearcheR* data analysis web-tool based on R version 4.4.1. - -## Results - -Below are the baseline characteristics. - -```{r, results = 'asis'} -tbl <- gtsummary::as_gt(web_data$table1) -knitr::knit_print(tbl) -``` - -Below are the results from the - -```{r, results = 'asis'} -reg_tbl <- web_data$regression$tables -knitr::knit_print(tbl_merge(reg_tbl)) -``` - -## Discussion - -Good luck on your further work! diff --git a/inst/apps/data_analysis_modules/www/report.rmd b/inst/apps/data_analysis_modules/www/report.rmd index f314587..aacd48c 100644 --- a/inst/apps/data_analysis_modules/www/report.rmd +++ b/inst/apps/data_analysis_modules/www/report.rmd @@ -1,8 +1,8 @@ --- -title: "freesearcheR analysis results" -date: today +title: "freesearcheR data report" +date: "Report generated `r gsub('(\\D)0', '\\1', format(Sys.time(), '%A, %d.%m.%Y'))`" format: docx -author: freesearcheR Tool +author: freesearcheR data analysis tool toc: false params: data.file: NA @@ -10,6 +10,7 @@ params: ```{r setup, echo = FALSE} knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE) +# glue::glue("{format(lubridate::today(),'%A')}, {lubridate::day(lubridate::today())}.{lubridate::month(lubridate::today())}.{lubridate::year(lubridate::today())}") ``` @@ -52,15 +53,18 @@ Analyses were conducted in the *freesearcheR* data analysis web-tool based on R Below are the baseline characteristics. ```{r, results = 'asis'} +if ("table1" %in% names(web_data)){ tbl <- gtsummary::as_gt(web_data$table1) -knitr::knit_print(tbl) +knitr::knit_print(tbl)} ``` -Below are the results from the `r tolower(vec2sentence(names(web_data$regression$tables)))` `r web_data$regression$params$descr`. +`r if ("regression" %in% names(web_data)) glue::glue("Below are the results from the { tolower(vec2sentence(names(web_data$regression$tables)))} {web_data$regression$params$descr}.")` ```{r, results = 'asis'} +if ("regression" %in% names(web_data)){ reg_tbl <- web_data$regression$tables knitr::knit_print(tbl_merge(reg_tbl)) +} ``` ## Discussion diff --git a/renv.lock b/renv.lock index 309f851..135b316 100644 --- a/renv.lock +++ b/renv.lock @@ -13,883 +13,2586 @@ "Package": "DEoptimR", "Version": "1.1-3-1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Date": "2024-11-23", + "Title": "Differential Evolution Optimization in Pure R", + "Authors@R": "c( person(c(\"Eduardo\", \"L. T.\"), \"Conceicao\", role = c(\"aut\", \"cre\"), email = \"mail@eduardoconceicao.org\"), person(\"Martin\", \"Maechler\", role = \"ctb\", email = \"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) )", + "URL": "svn://svn.r-forge.r-project.org/svnroot/robustbase/pkg/DEoptimR", + "Description": "Differential Evolution (DE) stochastic heuristic algorithms for global optimization of problems with and without general constraints. The aim is to curate a collection of its variants that (1) do not sacrifice simplicity of design, (2) are essentially tuning-free, and (3) can be efficiently implemented directly in the R language. Currently, it provides implementations of the algorithms 'jDE' by Brest et al. (2006) for single-objective optimization and 'NCDE' by Qu et al. (2012) for multimodal optimization (single-objective problems with multiple solutions).", + "Imports": [ "stats" ], - "Hash": "53a0299b56b4cbe418b12e3b65587211" + "Enhances": [ + "robustbase" + ], + "License": "GPL (>= 2)", + "Author": "Eduardo L. T. Conceicao [aut, cre], Martin Maechler [ctb] ()", + "Maintainer": "Eduardo L. T. Conceicao ", + "Repository": "CRAN", + "Repository/R-Forge/Project": "robustbase", + "Repository/R-Forge/Revision": "1008", + "Repository/R-Forge/DateTimeStamp": "2024-11-23 19:13:45", + "NeedsCompilation": "no" }, "DHARMa": { "Package": "DHARMa", "Version": "0.4.7", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "Matrix", - "R", - "ape", - "gap", - "grDevices", - "graphics", - "lme4", - "lmtest", - "parallel", - "qgam", - "stats", - "utils" + "Title": "Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models", + "Date": "2024-10-16", + "Authors@R": "c(person(\"Florian\", \"Hartig\", email = \"florian.hartig@biologie.uni-regensburg.de\", role = c(\"aut\", \"cre\"), comment=c(ORCID=\"0000-0002-6255-9059\")), person(\"Lukas\", \"Lohse\", role = \"ctb\"), person(\"Melina\", \"de Souza leite\", role = \"ctb\"))", + "Description": "The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Currently supported are linear and generalized linear (mixed) models from 'lme4' (classes 'lmerMod', 'glmerMod'), 'glmmTMB', 'GLMMadaptive', and 'spaMM'; phylogenetic linear models from 'phylolm' (classes 'phylolm' and 'phyloglm'); generalized additive models ('gam' from 'mgcv'); 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model classes. Moreover, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problems, such as over/underdispersion, zero-inflation, and residual spatial, phylogenetic and temporal autocorrelation.", + "Depends": [ + "R (>= 3.0.2)" ], - "Hash": "1ce015f138dd74b3695fc60a86fcce98" + "Imports": [ + "stats", + "graphics", + "utils", + "grDevices", + "Matrix", + "parallel", + "gap", + "lmtest", + "ape", + "qgam (>= 1.3.2)", + "lme4" + ], + "Suggests": [ + "knitr", + "testthat (>= 3.0.0)", + "rmarkdown", + "KernSmooth", + "sfsmisc", + "MASS", + "mgcv", + "mgcViz (>= 0.1.9)", + "spaMM (>= 3.2.0)", + "GLMMadaptive", + "glmmTMB (>= 1.1.2.3)", + "phylolm (>= 2.6.5)" + ], + "Enhances": [ + "phyr", + "rstan", + "rjags", + "BayesianTools" + ], + "License": "GPL (>= 3)", + "URL": "http://florianhartig.github.io/DHARMa/", + "LazyData": "TRUE", + "BugReports": "https://github.com/florianhartig/DHARMa/issues", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Florian Hartig [aut, cre] (), Lukas Lohse [ctb], Melina de Souza leite [ctb]", + "Maintainer": "Florian Hartig ", + "Repository": "CRAN" }, "DT": { "Package": "DT", "Version": "0.33", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "crosstalk", - "htmltools", - "htmlwidgets", + "Type": "Package", + "Title": "A Wrapper of the JavaScript Library 'DataTables'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"Joe\", \"Cheng\", email = \"joe@posit.co\", role = c(\"aut\", \"cre\")), person(\"Xianying\", \"Tan\", role = \"aut\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Maximilian\", \"Girlich\", role = \"ctb\"), person(\"Greg\", \"Freedman Ellis\", role = \"ctb\"), person(\"Johannes\", \"Rauh\", role = \"ctb\"), person(\"SpryMedia Limited\", role = c(\"ctb\", \"cph\"), comment = \"DataTables in htmlwidgets/lib\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js in htmlwidgets/lib\"), person(\"Leon\", \"Gersen\", role = c(\"ctb\", \"cph\"), comment = \"noUiSlider in htmlwidgets/lib\"), person(\"Bartek\", \"Szopka\", role = c(\"ctb\", \"cph\"), comment = \"jquery.highlight.js in htmlwidgets/lib\"), person(\"Alex\", \"Pickering\", role = c(\"ctb\")), person(\"William\", \"Holmes\", role = c(\"ctb\")), person(\"Mikko\", \"Marttila\", role = c(\"ctb\")), person(\"Andres\", \"Quintero\", role = c(\"ctb\")), person(\"Stéphane\", \"Laurent\", role = c(\"ctb\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.", + "URL": "https://github.com/rstudio/DT", + "BugReports": "https://github.com/rstudio/DT/issues", + "License": "GPL-3 | file LICENSE", + "Imports": [ + "htmltools (>= 0.3.6)", + "htmlwidgets (>= 1.3)", "httpuv", - "jquerylib", - "jsonlite", + "jsonlite (>= 0.9.16)", "magrittr", + "crosstalk", + "jquerylib", "promises" ], - "Hash": "64ff3427f559ce3f2597a4fe13255cb6" + "Suggests": [ + "knitr (>= 1.8)", + "rmarkdown", + "shiny (>= 1.6)", + "bslib", + "future", + "testit", + "tibble" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "7.3.1", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut], Joe Cheng [aut, cre], Xianying Tan [aut], JJ Allaire [ctb], Maximilian Girlich [ctb], Greg Freedman Ellis [ctb], Johannes Rauh [ctb], SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib), Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib), Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib), Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib), Alex Pickering [ctb], William Holmes [ctb], Mikko Marttila [ctb], Andres Quintero [ctb], Stéphane Laurent [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Joe Cheng ", + "Repository": "CRAN" }, "Deriv": { "Package": "Deriv", "Version": "4.1.6", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Type": "Package", + "Title": "Symbolic Differentiation", + "Date": "2024-09-12", + "Authors@R": "c(person(given=\"Andrew\", family=\"Clausen\", role=\"aut\"), person(given=\"Serguei\", family=\"Sokol\", role=c(\"aut\", \"cre\"), email=\"sokol@insa-toulouse.fr\", comment = c(ORCID = \"0000-0002-5674-3327\")), person(given=\"Andreas\", family=\"Rappold\", role=\"ctb\", email=\"arappold@gmx.at\"))", + "Description": "R-based solution for symbolic differentiation. It admits user-defined function as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.", + "License": "GPL (>= 3)", + "Suggests": [ + "testthat (>= 0.11.0)" + ], + "BugReports": "https://github.com/sgsokol/Deriv/issues", + "RoxygenNote": "7.3.1", + "Imports": [ "methods" ], - "Hash": "cd52c065c9e687c60c56b51f10f7bcd3" + "NeedsCompilation": "no", + "Author": "Andrew Clausen [aut], Serguei Sokol [aut, cre] (), Andreas Rappold [ctb]", + "Maintainer": "Serguei Sokol ", + "Repository": "CRAN" }, "Formula": { "Package": "Formula", "Version": "1.2-5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Date": "2023-02-23", + "Title": "Extended Model Formulas", + "Description": "Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side (see ).", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Yves\", family = \"Croissant\", role = \"aut\", email = \"Yves.Croissant@univ-reunion.fr\"))", + "Depends": [ + "R (>= 2.0.0)", "stats" ], - "Hash": "7a29697b75e027767a53fde6c903eca7" + "License": "GPL-2 | GPL-3", + "NeedsCompilation": "no", + "Author": "Achim Zeileis [aut, cre] (), Yves Croissant [aut]", + "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. 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REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.", + "Authors@R": "c(person(\"Will\", \"Beasley\", role = c(\"aut\", \"cre\"), email = \"wibeasley@hotmail.com\", comment = c(ORCID = \"0000-0002-5613-5006\")), person(\"David\", \"Bard\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3922-8489\")), person(\"Thomas\", \"Wilson\", role = \"ctb\"), person(given=\"John J\", family=\"Aponte\", role = \"ctb\", email=\"john.aponte@isglobal.org\"), person(\"Rollie\", \"Parrish\", role = \"ctb\", email = \"rparrish@flightweb.com\", comment = c(ORCID = \"0000-0001-8858-6381\")), person(\"Benjamin\", \"Nutter\", role = \"ctb\"), person(\"Andrew\", \"Peters\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2487-1268\")), person(\"Hao\", \"Zhu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3386-6076\")), person(\"Janosch\", \"Linkersdörfer\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1577-1233\")), person(\"Jonathan\", \"Mang\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0518-4710\")), person(\"Felix\", \"Torres\", role = \"ctb\", email = \"fetorres@ucsd.edu\"), person(\"Philip\", \"Chase\", role = \"ctb\", email = \"pbc@ufl.edu\", comment = c(ORCID = \"0000-0002-5318-9420\")), person(\"Victor\", \"Castro\", role = \"ctb\", email = \"vcastro@mgh.harvard.edu\", comment = c(ORCID = \"0000-0001-7390-6354\")), person(\"Greg\", \"Botwin\", role = \"ctb\"), person(\"Stephan\", \"Kadauke\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2996-8034\")), person(\"Ezra\", \"Porter\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4690-8343\")), person(\"Matthew\", \"Schuelke\", role = \"ctb\", email=\"matt@themadstatter.com\", comment = c(ORCID = \"0000-0001-5755-1725\")))", + "URL": "https://ouhscbbmc.github.io/REDCapR/, https://github.com/OuhscBbmc/REDCapR, https://www.ouhsc.edu/bbmc/, https://projectredcap.org", + "BugReports": "https://github.com/OuhscBbmc/REDCapR/issues", + "Depends": [ + "R(>= 3.5.0)" ], - "Hash": "de630e9e6168aae0a178eaa3198dbe54" + "Imports": [ + "checkmate (>= 2.0)", + "dplyr (>= 1.0)", + "httr (>= 1.4.0)", + "jsonlite", + "magrittr (>= 1.5)", + "methods", + "readr (>= 2.0)", + "rlang (>= 0.4)", + "tibble (>= 2.0)", + "tidyr (>= 1.0)" + ], + "Suggests": [ + "spelling", + "covr (>= 3.4)", + "DBI (>= 1.1)", + "kableExtra (>= 1.0)", + "knitr", + "odbc (>= 1.1.1)", + "purrr (>= 0.3.4)", + "rmarkdown", + "sessioninfo (>= 1.1.1)", + "testthat (>= 3.0)", + "tidyselect", + "yaml" + ], + "License": "MIT + file LICENSE", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Language": "en-US", + "NeedsCompilation": "no", + "Author": "Will Beasley [aut, cre] (), David Bard [ctb] (), Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb] (), Benjamin Nutter [ctb], Andrew Peters [ctb] (), Hao Zhu [ctb] (), Janosch Linkersdörfer [ctb] (), Jonathan Mang [ctb] (), Felix Torres [ctb], Philip Chase [ctb] (), Victor Castro [ctb] (), Greg Botwin [ctb], Stephan Kadauke [ctb] (), Ezra Porter [ctb] (), Matthew Schuelke [ctb] ()", + "Maintainer": "Will Beasley ", + "Repository": "CRAN" }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.13-1", + "Version": "1.0.14", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "Seamless R and C++ Integration", + "Date": "2025-01-11", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))", + "Description": "The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. 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'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library. Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", + "License": "GPL (>= 2) | file LICENSE", + "LazyLoad": "yes", + "Depends": [ + "R (>= 3.6.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp (>= 0.11.0)", "stats", "utils" ], - "Hash": "4ac8e423216b8b70cb9653d1b3f71eb9" + "Suggests": [ + "Matrix", + "inline", + "tinytest", + "pkgKitten", + "microbenchmark" + ], + "URL": "https://github.com/RcppCore/RcppEigen, https://dirk.eddelbuettel.com/code/rcpp.eigen.html", + "BugReports": "https://github.com/RcppCore/RcppEigen/issues", + "NeedsCompilation": "yes", + "Author": "Doug Bates [aut] (), Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), Yixuan Qiu [aut] (), Authors of Eigen [cph] (Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS)", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" }, "Rdpack": { "Package": "Rdpack", "Version": "2.6.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods", - "rbibutils", - "tools", - "utils" + "Type": "Package", + "Title": "Update and Manipulate Rd Documentation Objects", + "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), email = \"georgi.boshnakov@manchester.ac.uk\"), person(given = \"Duncan\", family = \"Murdoch\", role = \"ctb\", email = \"murdoch.duncan@gmail.com\") )", + "Description": "Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.", + "URL": "https://geobosh.github.io/Rdpack/ (doc), https://github.com/GeoBosh/Rdpack (devel)", + "BugReports": "https://github.com/GeoBosh/Rdpack/issues", + "Depends": [ + "R (>= 2.15.0)", + "methods" ], - "Hash": "a9e2118c664c2cd694f03de074e8d4b3" + "Imports": [ + "tools", + "utils", + "rbibutils (>= 1.3)" + ], + "Suggests": [ + "grDevices", + "testthat", + "rstudioapi", + "rprojroot", + "gbRd" + ], + "License": "GPL (>= 2)", + "LazyLoad": "yes", + "RoxygenNote": "7.1.1", + "NeedsCompilation": "no", + "Author": "Georgi N. 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This package can be compiled either with V8 version 6 and up or NodeJS when built as a shared library.", + "License": "MIT + file LICENSE", + "URL": "https://jeroen.r-universe.dev/V8", + "BugReports": "https://github.com/jeroen/v8/issues", + "SystemRequirements": "V8 engine version 6+ is needed for ES6 and WASM support. On Linux you can build against libv8-dev (Debian) or v8-devel (Fedora). 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It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 ) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors). References: Makowski et al. (2021) .", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "insight (>= 1.0.1)", + "datawizard (>= 1.0.0)", "graphics", - "insight", "methods", "stats", "utils" ], - "Hash": "d7c05ccb9d60d87dbbe8b4042c385f01" + "Suggests": [ + "BayesFactor (>= 0.9.12-4.4)", + "bayesQR", + "bayesplot", + "betareg", + "BH", + "blavaan", + "bridgesampling", + "brms", + "collapse", + "curl", + "effectsize", + "emmeans", + "gamm4", + "ggdist", + "ggplot2", + "glmmTMB", + "httr2", + "KernSmooth", + "knitr", + "lavaan", + "lme4", + "logspline (>= 2.1.21)", + "marginaleffects (>= 0.24.0)", + "MASS", + "mclust", + "mediation", + "modelbased", + "ordbetareg", + "parameters", + "patchwork", + "performance", + "quadprog", + "posterior", + "RcppEigen", + "rmarkdown", + "rstan", + "rstanarm", + "see (>= 0.8.5)", + "testthat", + "tweedie", + "withr" + ], + "License": "GPL-3", + "URL": "https://easystats.github.io/bayestestR/", + "BugReports": "https://github.com/easystats/bayestestR/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/rcmdcheck/ignore-inconsequential-notes": "true", + "Config/Needs/website": "easystats/easystatstemplate", + "Config/Needs/check": "stan-dev/cmdstanr", + "NeedsCompilation": "no", + "Author": "Dominique Makowski [aut, cre] (), Daniel Lüdecke [aut] (), Mattan S. 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Several of the provided helper functions allow for automatic generation of locale-aware formatting patterns based on date/time skeleton formats and standardized date/time formats with varying specificity.", + "Authors@R": "c( person(\"Richard\", \"Iannone\", , \"rich@posit.co\", c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "License": "MIT + file LICENSE", + "URL": "https://rstudio.github.io/bigD/, https://github.com/rstudio/bigD", + "BugReports": "https://github.com/rstudio/bigD/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Depends": [ + "R (>= 3.3.0)" ], - "Hash": "78dfe2b21e523358871eea1601b04b56" + "Suggests": [ + "covr", + "testthat (>= 3.0.0)", + "tibble (>= 3.2.1)" + ], + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "NeedsCompilation": "no", + "Author": "Richard Iannone [aut, cre] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Richard Iannone ", + "Repository": "CRAN" }, "bit": { "Package": "bit", "Version": "4.5.0.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Type": "Package", + "Title": "Classes and Methods for Fast Memory-Efficient Boolean Selections", + "Date": "2024-09-17", + "Authors@R": "c(person(given = \"Jens\", family = \"Oehlschlägel\", role = c(\"aut\", \"cre\"), email = \"Jens.Oehlschlaegel@truecluster.com\"), person(given = \"Brian\", family = \"Ripley\", role = \"ctb\"))", + "Author": "Jens Oehlschlägel [aut, cre], Brian Ripley [ctb]", + "Maintainer": "Jens Oehlschlägel ", + "Depends": [ + "R (>= 3.4.0)" ], - "Hash": "f89f074e0e49bf1dbe3eba0a15a91476" + "Suggests": [ + "testthat (>= 0.11.0)", + "roxygen2", + "knitr", + "markdown", + "rmarkdown", + "microbenchmark", + "bit64 (>= 4.0.0)", + "ff (>= 4.0.0)" + ], + "Description": "Provided are classes for boolean and skewed boolean vectors, fast boolean methods, fast unique and non-unique integer sorting, fast set operations on sorted and unsorted sets of integers, and foundations for ff (range index, compression, chunked processing).", + "License": "GPL-2 | GPL-3", + "LazyLoad": "yes", + "ByteCompile": "yes", + "Encoding": "UTF-8", + "URL": "https://github.com/truecluster/bit", + "VignetteBuilder": "knitr, rmarkdown", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Repository": "CRAN" }, "bit64": { "Package": "bit64", - "Version": "4.5.2", + "Version": "4.6.0-1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bit", + "Title": "A S3 Class for Vectors of 64bit Integers", + "Authors@R": "c( person(\"Michael\", \"Chirico\", email = \"michaelchirico4@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Jens\", \"Oehlschlägel\", role = \"aut\"), person(\"Leonardo\", \"Silvestri\", role = \"ctb\"), person(\"Ofek\", \"Shilon\", role = \"ctb\") )", + "Depends": [ + "R (>= 3.4.0)", + "bit (>= 4.0.0)" + ], + "Description": "Package 'bit64' provides serializable S3 atomic 64bit (signed) integers. These are useful for handling database keys and exact counting in +-2^63. WARNING: do not use them as replacement for 32bit integers, integer64 are not supported for subscripting by R-core and they have different semantics when combined with double, e.g. integer64 + double => integer64. Class integer64 can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support inter- active data exploration and manipulation and optionally leverage caching.", + "License": "GPL-2 | GPL-3", + "LazyLoad": "yes", + "ByteCompile": "yes", + "URL": "https://github.com/r-lib/bit64", + "Encoding": "UTF-8", + "Imports": [ + "graphics", "methods", "stats", "utils" ], - "Hash": "e84984bf5f12a18628d9a02322128dfd" + "Suggests": [ + "testthat (>= 3.0.3)", + "withr" + ], + "Config/testthat/edition": "3", + "Config/needs/development": "testthat", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Michael Chirico [aut, cre], Jens Oehlschlägel [aut], Leonardo Silvestri [ctb], Ofek Shilon [ctb]", + "Maintainer": "Michael Chirico ", + "Repository": "CRAN" }, "bitops": { "Package": "bitops", "Version": "1.0-9", "Source": "Repository", - "Repository": "CRAN", - "Hash": "d972ef991d58c19e6efa71b21f5e144b" + "Date": "2024-10-03", + "Authors@R": "c( person(\"Steve\", \"Dutky\", role = \"aut\", email = \"sdutky@terpalum.umd.edu\", comment = \"S original; then (after MM's port) revised and modified\"), person(\"Martin\", \"Maechler\", role = c(\"cre\", \"aut\"), email = \"maechler@stat.math.ethz.ch\", comment = c(\"Initial R port; tweaks\", ORCID = \"0000-0002-8685-9910\")))", + "Title": "Bitwise Operations", + "Description": "Functions for bitwise operations on integer vectors.", + "License": "GPL (>= 2)", + "URL": "https://github.com/mmaechler/R-bitops", + "BugReports": "https://github.com/mmaechler/R-bitops/issues", + "NeedsCompilation": "yes", + "Author": "Steve Dutky [aut] (S original; then (after MM's port) revised and modified), Martin Maechler [cre, aut] (Initial R port; tweaks, )", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" }, "boot": { "Package": "boot", "Version": "1.3-31", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Priority": "recommended", + "Date": "2024-08-28", + "Authors@R": "c(person(\"Angelo\", \"Canty\", role = \"aut\", email = \"cantya@mcmaster.ca\", comment = \"author of original code for S\"), person(\"Brian\", \"Ripley\", role = c(\"aut\", \"trl\"), email = \"ripley@stats.ox.ac.uk\", comment = \"conversion to R, maintainer 1999--2022, author of parallel support\"), person(\"Alessandra R.\", \"Brazzale\", role = c(\"ctb\", \"cre\"), email = \"brazzale@stat.unipd.it\", comment = \"minor bug fixes\"))", + "Maintainer": "Alessandra R. Brazzale ", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Description": "Functions and datasets for bootstrapping from the book \"Bootstrap Methods and Their Application\" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.", + "Title": "Bootstrap Functions (Originally by Angelo Canty for S)", + "Depends": [ + "R (>= 3.0.0)", "graphics", "stats" ], - "Hash": "de2a4646c18661d6a0a08ec67f40b7ed" + "Suggests": [ + "MASS", + "survival" + ], + "LazyData": "yes", + "ByteCompile": "yes", + "License": "Unlimited", + "NeedsCompilation": "no", + "Author": "Angelo Canty [aut] (author of original code for S), Brian Ripley [aut, trl] (conversion to R, maintainer 1999--2022, author of parallel support), Alessandra R. Brazzale [ctb, cre] (minor bug fixes)", + "Repository": "CRAN" }, "brio": { "Package": "brio", "Version": "1.1.5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "Basic R Input Output", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Functions to handle basic input output, these functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.", + "License": "MIT + file LICENSE", + "URL": "https://brio.r-lib.org, https://github.com/r-lib/brio", + "BugReports": "https://github.com/r-lib/brio/issues", + "Depends": [ + "R (>= 3.6)" ], - "Hash": "c1ee497a6d999947c2c224ae46799b1a" + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + 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Willem\", family = \"Vervoort\", role = \"ctb\", email = \"Willemvervoort@gmail.com\"), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"ctb\", email = \"brenton@wiernik.org\"), person(given = \"Josh\", family = \"Yamamoto\", role = \"ctb\", email = \"joshuayamamoto5@gmail.com\"), person(given = \"Jasme\", family = \"Lee\", role = \"ctb\"), person(given = \"Taren\", family = \"Sanders\", role = \"ctb\", email = \"taren.sanders@acu.edu.au\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(given = \"Ilaria\", family = \"Prosdocimi\", role = \"ctb\", email = \"prosdocimi.ilaria@gmail.com\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(given = \"Daniel D.\", family = \"Sjoberg\", role = \"ctb\", email = \"danield.sjoberg@gmail.com\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(given = \"Alex\", family = \"Reinhart\", role = \"ctb\", email = \"areinhar@stat.cmu.edu\", comment = c(ORCID = \"0000-0002-6658-514X\")))", + "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. 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It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.", + "License": "MIT + file LICENSE", + "URL": "https://cli.r-lib.org, https://github.com/r-lib/cli", + "BugReports": "https://github.com/r-lib/cli/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ "utils" ], - "Hash": "b21916dd77a27642b447374a5d30ecf3" + "Suggests": [ + "callr", + "covr", + "crayon", + "digest", + "glue (>= 1.6.0)", + "grDevices", + "htmltools", + "htmlwidgets", + "knitr", + "methods", + "mockery", + "processx", + "ps (>= 1.3.4.9000)", + "rlang (>= 1.0.2.9003)", + "rmarkdown", + "rprojroot", + "rstudioapi", + "testthat", + "tibble", + "whoami", + "withr" + ], + "Config/Needs/website": "r-lib/asciicast, bench, brio, cpp11, decor, desc, fansi, prettyunits, sessioninfo, tidyverse/tidytemplate, usethis, vctrs", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], Salim Brüggemann [ctb] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" }, "clipr": { "Package": "clipr", "Version": "0.8.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Type": "Package", + "Title": "Read and Write from the System Clipboard", + "Authors@R": "c( person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4387-3384\")), person(\"Louis\", \"Maddox\", role = \"ctb\"), person(\"Steve\", \"Simpson\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\") )", + "Description": "Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.", + "License": "GPL-3", + "URL": "https://github.com/mdlincoln/clipr, http://matthewlincoln.net/clipr/", + "BugReports": "https://github.com/mdlincoln/clipr/issues", + "Imports": [ "utils" ], - "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "rstudioapi (>= 0.5)", + "testthat (>= 2.0.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.1.2", + "SystemRequirements": "xclip (https://github.com/astrand/xclip) or xsel (http://www.vergenet.net/~conrad/software/xsel/) for accessing the X11 clipboard, or wl-clipboard (https://github.com/bugaevc/wl-clipboard) for systems using Wayland.", + "NeedsCompilation": "no", + "Author": "Matthew Lincoln [aut, cre] (), Louis Maddox [ctb], Steve Simpson [ctb], Jennifer Bryan [ctb]", + "Maintainer": "Matthew Lincoln ", + "Repository": "CRAN" + }, + "cluster": { + "Package": "cluster", + "Version": "2.1.8", + "Source": "Repository", + "VersionNote": "Last CRAN: 2.1.7 on 2024-12-06; 2.1.6 on 2023-11-30; 2.1.5 on 2023-11-27", + "Date": "2024-12-10", + "Priority": "recommended", + "Title": "\"Finding Groups in Data\": Cluster Analysis Extended Rousseeuw et al.", + "Description": "Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".", + "Maintainer": "Martin Maechler ", + "Authors@R": "c(person(\"Martin\",\"Maechler\", role = c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) ,person(\"Peter\", \"Rousseeuw\", role=\"aut\", email=\"peter.rousseeuw@kuleuven.be\", comment = c(\"Fortran original\", ORCID = \"0000-0002-3807-5353\")) ,person(\"Anja\", \"Struyf\", role=\"aut\", comment= \"S original\") ,person(\"Mia\", \"Hubert\", role=\"aut\", email= \"Mia.Hubert@uia.ua.ac.be\", comment = c(\"S original\", ORCID = \"0000-0001-6398-4850\")) ,person(\"Kurt\", \"Hornik\", role=c(\"trl\", \"ctb\"), email=\"Kurt.Hornik@R-project.org\", comment=c(\"port to R; maintenance(1999-2000)\", ORCID=\"0000-0003-4198-9911\")) ,person(\"Matthias\", \"Studer\", role=\"ctb\") ,person(\"Pierre\", \"Roudier\", role=\"ctb\") ,person(\"Juan\", \"Gonzalez\", role=\"ctb\") ,person(\"Kamil\", \"Kozlowski\", role=\"ctb\") ,person(\"Erich\", \"Schubert\", role=\"ctb\", comment = c(\"fastpam options for pam()\", ORCID = \"0000-0001-9143-4880\")) ,person(\"Keefe\", \"Murphy\", role=\"ctb\", comment = \"volume.ellipsoid({d >= 3})\") #not yet ,person(\"Fischer-Rasmussen\", \"Kasper\", role = \"ctb\", comment = \"Gower distance for CLARA\") )", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "graphics", + "grDevices", + "stats", + "utils" + ], + "Suggests": [ + "MASS", + "Matrix" + ], + "SuggestsNote": "MASS: two examples using cov.rob() and mvrnorm(); Matrix tools for testing", + "Enhances": [ + "mvoutlier", + "fpc", + "ellipse", + "sfsmisc" + ], + "EnhancesNote": "xref-ed in man/*.Rd", + "LazyLoad": "yes", + "LazyData": "yes", + "ByteCompile": "yes", + "BuildResaveData": "no", + "License": "GPL (>= 2)", + "URL": "https://svn.r-project.org/R-packages/trunk/cluster/", + "NeedsCompilation": "yes", + "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", + "Repository": "CRAN" + }, + "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", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Priority": "recommended", + "Author": "Luke Tierney ", + "Description": "Code analysis tools for R.", + "Title": "Code Analysis Tools for R", + "Depends": [ + "R (>= 2.1)" ], - "Hash": "61e097f35917d342622f21cdc79c256e" + "Maintainer": "Luke Tierney ", + "URL": "https://gitlab.com/luke-tierney/codetools", + "License": "GPL", + "NeedsCompilation": "no", + "Repository": "CRAN" }, "colorspace": { "Package": "colorspace", "Version": "2.1-1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", + "Date": "2024-07-26", + "Title": "A Toolbox for Manipulating and Assessing Colors and Palettes", + "Authors@R": "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"), person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\", comment = c(ORCID = \"0000-0002-3224-8858\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\", comment = c(ORCID = \"0000-0001-9032-8912\")), person(given = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\", comment = c(ORCID = \"0000-0002-3798-5507\")), person(given = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(given = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\", comment = c(ORCID = \"0000-0001-7346-3047\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")))", + "Description": "Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, ).", + "Depends": [ + "R (>= 3.0.0)", + "methods" + ], + "Imports": [ "graphics", - "methods", + "grDevices", "stats" ], - "Hash": "d954cb1c57e8d8b756165d7ba18aa55a" + "Suggests": [ + "datasets", + "utils", + "KernSmooth", + "MASS", + "kernlab", + "mvtnorm", + "vcd", + "tcltk", + "shiny", + "shinyjs", + "ggplot2", + "dplyr", + "scales", + "grid", + "png", + "jpeg", + "knitr", + "rmarkdown", + "RColorBrewer", + "rcartocolor", + "scico", + "viridis", + "wesanderson" + ], + "VignetteBuilder": "knitr", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", + "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", + "LazyData": "yes", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Ross Ihaka [aut], Paul Murrell [aut] (), Kurt Hornik [aut] (), Jason C. Fisher [aut] (), Reto Stauffer [aut] (), Claus O. Wilke [aut] (), Claire D. McWhite [aut] (), Achim Zeileis [aut, cre] ()", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" }, "commonmark": { "Package": "commonmark", "Version": "1.9.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "14eb0596f987c71535d07c3aff814742" + "Type": "Package", + "Title": "High Performance CommonMark and Github Markdown Rendering in R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", ,\"jeroenooms@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"John MacFarlane\", role = \"cph\", comment = \"Author of cmark\"))", + "Description": "The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. Also includes opt-in support for GFM extensions including tables, autolinks, and strikethrough text.", + "License": "BSD_2_clause + file LICENSE", + "URL": "https://docs.ropensci.org/commonmark/ https://ropensci.r-universe.dev/commonmark", + "BugReports": "https://github.com/r-lib/commonmark/issues", + "Suggests": [ + "curl", + "testthat", + "xml2" + ], + "RoxygenNote": "7.2.3", + "Language": "en-US", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), John MacFarlane [cph] (Author of cmark)", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" }, "correlation": { "Package": "correlation", "Version": "0.8.6", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bayestestR", + "Type": "Package", + "Title": "Methods for Correlation Analysis", + "Authors@R": "c(person(given = \"Dominique\", family = \"Makowski\", role = c(\"aut\", \"inv\"), email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = c(\"aut\", \"cre\"), email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Daniel\", family = \"Lüdecke\", role = \"aut\", email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = \"aut\", email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Rémi\", family = \"Thériault\", role = c(\"aut\"), email = \"remi.theriault@mail.mcgill.ca\", comment = c(ORCID = \"0000-0003-4315-6788\")), person(given = \"Mark\", family = \"White\", email = \"markhwhiteii@gmail.com\", role = \"rev\"), person(given = \"Maximilian M.\", family = \"Rabe\", email = \"maximilian.rabe@uni-potsdam.de\", role = \"rev\", comment = c(ORCID = \"0000-0002-2556-5644\")))", + "Maintainer": "Brenton M. Wiernik ", + "Description": "Lightweight package for computing different kinds of correlations, such as partial correlations, Bayesian correlations, multilevel correlations, polychoric correlations, biweight correlations, distance correlations and more. Part of the 'easystats' ecosystem. References: Makowski et al. (2020) .", + "License": "MIT + file LICENSE", + "URL": "https://easystats.github.io/correlation/", + "BugReports": "https://github.com/easystats/correlation/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "bayestestR (>= 0.15.0)", "datasets", - "datawizard", - "insight", - "parameters", + "datawizard (>= 0.13.0)", + "insight (>= 0.20.5)", + "parameters (>= 0.22.2)", "stats" ], - "Hash": "8b6512d8f60685736ee3bafdc292190d" + "Suggests": [ + "BayesFactor", + "energy", + "ggplot2", + "ggraph", + "gt", + "Hmisc", + "knitr", + "lme4", + "MASS", + "mbend", + "polycor", + "poorman", + "ppcor", + "psych", + "rmarkdown", + "rmcorr", + "rstanarm", + "see (>= 0.8.1)", + "testthat (>= 3.2.1)", + "tidygraph", + "wdm", + "WRS2", + "openxlsx2 (>= 1.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/Needs/website": "rstudio/bslib, r-lib/pkgdown, easystats/easystatstemplate", + "NeedsCompilation": "no", + "Author": "Dominique Makowski [aut, inv] (), Brenton M. Wiernik [aut, cre] (), Indrajeet Patil [aut] (), Daniel Lüdecke [aut] (), Mattan S. Ben-Shachar [aut] (), Rémi Thériault [aut] (), Mark White [rev], Maximilian M. Rabe [rev] ()", + "Repository": "CRAN" }, "cowplot": { "Package": "cowplot", "Version": "1.1.3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "ggplot2", - "grDevices", + "Title": "Streamlined Plot Theme and Plot Annotations for 'ggplot2'", + "Authors@R": "person( given = \"Claus O.\", family = \"Wilke\", role = c(\"aut\", \"cre\"), email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\") )", + "Description": "Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.", + "URL": "https://wilkelab.org/cowplot/", + "BugReports": "https://github.com/wilkelab/cowplot/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "ggplot2 (>= 3.4.0)", "grid", "gtable", + "grDevices", "methods", "rlang", "scales" ], - "Hash": "8ef2084dd7d28847b374e55440e4f8cb" + "License": "GPL-2", + "Suggests": [ + "Cairo", + "covr", + "dplyr", + "forcats", + "gridGraphics (>= 0.4-0)", + "knitr", + "lattice", + "magick", + "maps", + "PASWR", + "patchwork", + "rmarkdown", + "ragg", + "testthat (>= 1.0.0)", + "tidyr", + "vdiffr (>= 0.3.0)", + "VennDiagram" + ], + "VignetteBuilder": "knitr", + "Collate": "'add_sub.R' 'align_plots.R' 'as_grob.R' 'as_gtable.R' 'axis_canvas.R' 'cowplot.R' 'draw.R' 'get_plot_component.R' 'get_axes.R' 'get_titles.R' 'get_legend.R' 'get_panel.R' 'gtable.R' 'key_glyph.R' 'plot_grid.R' 'save.R' 'set_null_device.R' 'setup.R' 'stamp.R' 'themes.R' 'utils_ggplot2.R'", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Claus O. 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Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" ], - "Hash": "9df43854f1c84685d095ed6270b52387" + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" }, "crayon": { "Package": "crayon", "Version": "1.5.3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ "grDevices", "methods", "utils" ], - "Hash": "859d96e65ef198fd43e82b9628d593ef" + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" }, "crosstalk": { "Package": "crosstalk", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "htmltools", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). 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Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.62): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" ], - "Hash": "e8ba62486230951fcd2b881c5be23f96" + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" }, "data.table": { "Package": "data.table", "Version": "1.16.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ "methods" ], - "Hash": "38bbf05fc2503143db4c734a7e5cab66" + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\"), person(\"Michael\",\"Chirico\", role=\"aut\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), 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Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb], @marc-outins [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Leonardo Silvestri [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb], Dirk Eddelbuettel [ctb], Tony Fischetti [ctb], Ofek Shilon [ctb], Vadim Khotilovich [ctb], Hadley Wickham [ctb], Bennet Becker [ctb], Kyle Haynes [ctb], Boniface Christian Kamgang [ctb], Olivier Delmarcell [ctb], Josh O'Brien [ctb], Dereck de Mezquita [ctb], Michael Czekanski [ctb], Dmitry Shemetov [ctb], Nitish Jha [ctb], Joshua Wu [ctb], Iago Giné-Vázquez [ctb], Anirban Chetia [ctb], Doris Amoakohene [ctb], Ivan Krylov [ctb]", + "Maintainer": "Tyson Barrett ", + "Repository": "CRAN" }, "datamods": { "Package": "datamods", "Version": "1.5.3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Modules to Import and Manipulate Data in 'Shiny'", + "Authors@R": "c(person(given = \"Victor\", family = \"Perrier\", role = c(\"aut\", \"cre\", \"cph\"), email = \"victor.perrier@dreamrs.fr\"), person(given = \"Fanny\", family = \"Meyer\", role = \"aut\"), person(given = \"Samra\", family = \"Goumri\", role = \"aut\"), person(given = \"Zauad Shahreer\", family = \"Abeer\", role = \"aut\", email = \"shahreyar.abeer@gmail.com\"), person(given = \"Eduard\", family = \"Szöcs\", role = \"ctb\", email = \"eduardszoecs@gmail.com\") )", + "Description": "'Shiny' modules to import data into an application or 'addin' from various sources, and to manipulate them after that.", + "License": "GPL-3", + "URL": "https://github.com/dreamRs/datamods, 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"Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "insight", + "Type": "Package", + "Title": "Easy Data Wrangling and Statistical Transformations", + "Authors@R": "c( person(\"Indrajeet\", \"Patil\", , \"patilindrajeet.science@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(\"Etienne\", \"Bacher\", , \"etienne.bacher@protonmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9271-5075\")), person(\"Dominique\", \"Makowski\", , \"dom.makowski@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(\"Daniel\", \"Lüdecke\", , \"d.luedecke@uke.de\", role = \"aut\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(\"Mattan S.\", \"Ben-Shachar\", , \"matanshm@post.bgu.ac.il\", role = \"aut\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(\"Brenton M.\", \"Wiernik\", , \"brenton@wiernik.org\", role = \"aut\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(\"Rémi\", 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It is also the data wrangling backend for packages in 'easystats' ecosystem. References: Patil et al. 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Ben-Shachar ", + "Description": "Provide utilities to work with indices of effect size for a wide variety of models and hypothesis tests (see list of supported models using the function 'insight::supported_models()'), allowing computation of and conversion between indices such as Cohen's d, r, odds, etc. References: Ben-Shachar et al. (2020) .", + "License": "MIT + file LICENSE", + "URL": "https://easystats.github.io/effectsize/", + "BugReports": "https://github.com/easystats/effectsize/issues/", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "bayestestR (>= 0.15.0)", + "insight (>= 1.0.0)", + "parameters (>= 0.24.0)", + "performance (>= 0.12.4)", + "datawizard (>= 0.13.0)", "stats", "utils" ], - "Hash": "b289af101f62cb7b46c53d1a45ed5198" + "Suggests": [ + "correlation (>= 0.8.4)", + "see (>= 0.8.0)", + "afex", + "BayesFactor", + "boot", + "brms", + "car", + "emmeans", + "gt", + "knitr", + "lavaan", + "lme4", + "lmerTest", + "mgcv", + "parsnip", + "pwr", + "rmarkdown", + "rms", + "rstanarm", + "rstantools", + "testthat (>= 3.1.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/Needs/website": "rstudio/bslib, r-lib/pkgdown, easystats/easystatstemplate", + "NeedsCompilation": "no", + "Author": "Mattan S. 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Further the package makes it easy to manipulate and combine 'gtable' objects so that complex compositions can be built up sequentially.", + "License": "MIT + file LICENSE", + "URL": "https://gtable.r-lib.org, https://github.com/r-lib/gtable", + "BugReports": "https://github.com/r-lib/gtable/issues", + "Depends": [ + "R (>= 4.0)" + ], + "Imports": [ "cli", "glue", "grid", "lifecycle", - "rlang", + "rlang (>= 1.1.0)", "stats" ], - "Hash": "de949855009e2d4d0e52a844e30617ae" + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "profvis", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2024-10-25", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" }, "gtsummary": { "Package": "gtsummary", "Version": "2.0.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cards", - "cli", - "dplyr", - "glue", - "gt", - "lifecycle", - "rlang", - "tidyr", - "vctrs" + "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\")) )", + "Description": "Creates presentation-ready tables summarizing data sets, regression models, and more. 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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/", + "BugReports": "https://github.com/ddsjoberg/gtsummary/issues", + "Depends": [ + "R (>= 4.2)" ], - "Hash": "a6cb3a1251d2a86c14ccc3e9977437dc" + "Imports": [ + "cards (>= 0.4.0)", + "cli (>= 3.6.3)", + "dplyr (>= 1.1.3)", + "glue (>= 1.8.0)", + "gt (>= 0.11.1)", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.1.1)", + "tidyr (>= 1.3.0)", + "vctrs (>= 0.6.4)" + ], + "Suggests": [ + "aod (>= 1.3.3)", + "broom (>= 1.0.5)", + "broom.helpers (>= 1.17.0)", + "broom.mixed (>= 0.2.9)", + "car (>= 3.0-11)", + "cardx (>= 0.2.2)", + "cmprsk", + "effectsize (>= 0.6.0)", + "emmeans (>= 1.7.3)", + "flextable (>= 0.8.1)", + "geepack (>= 1.3.10)", + "ggstats (>= 0.2.1)", + "huxtable (>= 5.4.0)", + "insight (>= 0.15.0)", + "kableExtra (>= 1.3.4)", + "knitr (>= 1.37)", + "lme4 (>= 1.1-31)", + "mice (>= 3.10.0)", + "nnet", + "officer", + "openxlsx", + "parameters (>= 0.20.2)", + "parsnip (>= 0.1.7)", + "rmarkdown", + "smd (>= 0.6.6)", + "spelling", + "survey (>= 4.2)", + "survival (>= 3.6-4)", + "testthat (>= 3.2.0)", + "withr (>= 2.5.0)", + "workflows (>= 0.2.4)" + ], + "VignetteBuilder": "knitr", + "RdMacros": "lifecycle", + "Config/Needs/check": "hms", + "Config/Needs/website": "forcats, scales", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Encoding": "UTF-8", + "Language": "en-US", + "LazyData": "true", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Daniel D. 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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", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "cpp11", - "forcats", + "Title": "Import and Export 'SPSS', 'Stata' and 'SAS' Files", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Evan\", \"Miller\", role = c(\"aut\", \"cph\"), comment = \"Author of included ReadStat code\"), person(\"Danny\", \"Smith\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Import foreign statistical formats into R via the embedded 'ReadStat' C library, .", + "License": "MIT + file LICENSE", + "URL": "https://haven.tidyverse.org, https://github.com/tidyverse/haven, https://github.com/WizardMac/ReadStat", + "BugReports": "https://github.com/tidyverse/haven/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.0.0)", + "forcats (>= 0.2.0)", "hms", "lifecycle", "methods", - "readr", - "rlang", + "readr (>= 0.1.0)", + "rlang (>= 0.4.0)", "tibble", "tidyselect", - "vctrs" + "vctrs (>= 0.3.0)" ], - "Hash": "9171f898db9d9c4c1b2c745adc2c1ef1" + "Suggests": [ + "covr", + "crayon", + "fs", + "knitr", + "pillar (>= 1.4.0)", + "rmarkdown", + "testthat (>= 3.0.0)", + "utf8" + ], + "LinkingTo": [ + "cpp11" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "GNU make, zlib: zlib1g-dev (deb), zlib-devel (rpm)", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Evan Miller [aut, cph] (Author of included ReadStat code), Danny Smith [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" }, "here": { "Package": "here", "Version": "1.0.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "rprojroot" + "Title": "A Simpler Way to Find Your Files", + "Date": "2020-12-13", + "Authors@R": "c(person(given = \"Kirill\", family = \"M\\u00fcller\", role = c(\"aut\", \"cre\"), email = \"krlmlr+r@mailbox.org\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Jennifer\", family = \"Bryan\", role = \"ctb\", email = \"jenny@rstudio.com\", comment = c(ORCID = \"0000-0002-6983-2759\")))", + "Description": "Constructs paths to your project's files. Declare the relative path of a file within your project with 'i_am()'. Use the 'here()' function as a drop-in replacement for 'file.path()', it will always locate the files relative to your project root.", + "License": "MIT + file LICENSE", + "URL": "https://here.r-lib.org/, https://github.com/r-lib/here", + "BugReports": "https://github.com/r-lib/here/issues", + "Imports": [ + "rprojroot (>= 2.0.2)" ], - "Hash": "24b224366f9c2e7534d2344d10d59211" + "Suggests": [ + "conflicted", + "covr", + "fs", + "knitr", + "palmerpenguins", + "plyr", + "readr", + "rlang", + "rmarkdown", + "testthat", + "uuid", + "withr" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.1.1.9000", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Kirill Müller [aut, cre] (), Jennifer Bryan [ctb] ()", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" }, "highr": { "Package": "highr", "Version": "0.11", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "xfun" + "Type": "Package", + "Title": "Syntax Highlighting for R Source Code", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Yixuan\", \"Qiu\", role = \"aut\"), person(\"Christopher\", \"Gandrud\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\") )", + "Description": "Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package ().", + "Depends": [ + "R (>= 3.3.0)" ], - "Hash": "d65ba49117ca223614f71b60d85b8ab7" + "Imports": [ + "xfun (>= 0.18)" + ], + "Suggests": [ + "knitr", + "markdown", + "testit" + ], + "License": "GPL", + "URL": "https://github.com/yihui/highr", + "BugReports": "https://github.com/yihui/highr/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "hms": { "Package": "hms", "Version": "1.1.3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "Pretty Time of Day", + "Date": "2023-03-21", + "Authors@R": "c( person(\"Kirill\", \"Müller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\"), person(\"RStudio\", role = \"fnd\") )", + "Description": "Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.", + "Imports": [ "lifecycle", "methods", "pkgconfig", - "rlang", - "vctrs" + "rlang (>= 1.0.2)", + "vctrs (>= 0.3.8)" ], - "Hash": "b59377caa7ed00fa41808342002138f9" + "Suggests": [ + "crayon", + "lubridate", + "pillar (>= 1.1.0)", + "testthat (>= 3.0.0)" + ], + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "URL": "https://hms.tidyverse.org/, https://github.com/tidyverse/hms", + "BugReports": "https://github.com/tidyverse/hms/issues", + "RoxygenNote": "7.2.3", + "Config/testthat/edition": "3", + "Config/autostyle/scope": "line_breaks", + "Config/autostyle/strict": "false", + "Config/Needs/website": "tidyverse/tidytemplate", + "NeedsCompilation": "no", + "Author": "Kirill Müller [aut, cre] (), R Consortium [fnd], RStudio [fnd]", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" + }, + "htmlTable": { + "Package": "htmlTable", + "Version": "2.4.3", + "Source": "Repository", + "Title": "Advanced Tables for Markdown/HTML", + "Authors@R": "c( person(\"Max\", \"Gordon\", email = \"max@gforge.se\", role = c(\"aut\", \"cre\")), person(\"Stephen\", \"Gragg\", role=c(\"aut\")), person(\"Peter\", \"Konings\", role=c(\"aut\")))", + "Maintainer": "Max Gordon ", + "Description": "Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with common word processors. The package also contains a few text formatting functions that help outputting text compatible with HTML/LaTeX.", + "License": "GPL (>= 3)", + "URL": "https://gforge.se/packages/", + "BugReports": "https://github.com/gforge/htmlTable/issues", + "Biarch": "yes", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "stringr", + "knitr (>= 1.6)", + "magrittr (>= 1.5)", + "methods", + "checkmate", + "htmlwidgets", + "htmltools", + "rstudioapi (>= 0.6)" + ], + "Suggests": [ + "testthat", + "XML", + "xml2", + "Hmisc", + "rmarkdown", + "chron", + "lubridate", + "tibble", + "purrr", + "tidyselect", + "glue", + "rlang", + "tidyr (>= 0.7.2)", + "dplyr (>= 0.7.4)" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "VignetteBuilder": "knitr", + "RoxygenNote": "7.2.2", + "Author": "Max Gordon [aut, cre], Stephen Gragg [aut], Peter Konings [aut]", + "Repository": "CRAN" }, "htmltools": { "Package": "htmltools", "Version": "0.5.8.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - 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It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)", + "License": "GPL (>= 2) | file LICENSE", + "URL": "https://github.com/rstudio/httpuv", + "BugReports": "https://github.com/rstudio/httpuv/issues", + "Depends": [ + "R (>= 2.15.1)" + ], + "Imports": [ + "later (>= 0.8.0)", "promises", + "R6", + "Rcpp (>= 1.0.7)", "utils" ], - "Hash": "d55aa087c47a63ead0f6fc10f8fa1ee0" + "Suggests": [ + "callr", + "curl", + "testthat", + "websocket" + ], + "LinkingTo": [ + "later", + "Rcpp" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "SystemRequirements": "GNU make, zlib", + "Collate": "'RcppExports.R' 'httpuv.R' 'random_port.R' 'server.R' 'staticServer.R' 'static_paths.R' 'utils.R'", + "NeedsCompilation": "yes", + "Author": "Joe Cheng [aut], Winston Chang [aut, cre], Posit, PBC fnd [cph], Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Andrzej Krzemienski [cph] (optional.hpp), libuv project contributors [cph] (libuv library, see src/libuv/AUTHORS file), Joyent, Inc. and other Node contributors [cph] (libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file), Niels Provos [cph] (libuv subcomponent: tree.h), Internet Systems Consortium, Inc. [cph] (libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c), Alexander Chemeris [cph] (libuv subcomponent: stdint-msvc2008.h (from msinttypes)), Google, Inc. [cph] (libuv subcomponent: pthread-fixes.c), Sony Mobile Communcations AB [cph] (libuv subcomponent: pthread-fixes.c), Berkeley Software Design Inc. [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Kenneth MacKay [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016) [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Steve Reid [aut] (SHA-1 implementation), James Brown [aut] (SHA-1 implementation), Bob Trower [aut] (base64 implementation), Alexander Peslyak [aut] (MD5 implementation), Trantor Standard Systems [cph] (base64 implementation), Igor Sysoev [cph] (http-parser)", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" }, "httr": { "Package": "httr", "Version": "1.4.7", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "curl", + "Title": "Tools for Working with URLs and HTTP", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).", + "License": "MIT + file LICENSE", + "URL": "https://httr.r-lib.org/, https://github.com/r-lib/httr", + "BugReports": "https://github.com/r-lib/httr/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "curl (>= 5.0.2)", "jsonlite", "mime", - "openssl" + "openssl (>= 0.8)", + "R6" ], - "Hash": "ac107251d9d9fd72f0ca8049988f1d7f" + "Suggests": [ + "covr", + "httpuv", + "jpeg", + "knitr", + "png", + "readr", + "rmarkdown", + "testthat (>= 0.8.0)", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" }, "insight": { "Package": "insight", - "Version": "1.0.0", + "Version": "1.0.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "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 ", + "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/", + "BugReports": "https://github.com/easystats/insight/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ "methods", "stats", "utils" ], - "Hash": "bee0c3abb5eea6c4170ea2a7c334893f" + "Suggests": [ + "AER", + "afex", + "aod", + "ape", + "BayesFactor", + "bayestestR", + "bbmle", + "bdsmatrix", + "betareg", + "bife", + "biglm", + "BH", + "blavaan (>= 0.5-5)", + "blme", + "boot", + "brms", + "broom", + "car", + "carData", + "censReg", + "cgam", + "clubSandwich", + "cobalt", + "coxme", + "cplm", + "crch", + "curl", + "datawizard", + "effectsize", + "emmeans", + "epiR", + "estimatr", + "feisr", + "fixest (>= 0.11.2)", + "fungible", + "fwb", + "gam", + "gamlss", + "gamlss.data", + "gamm4", + "gbm", + "gee", + "geepack", + "geoR", + "ggeffects (>= 2.2.0)", + "GLMMadaptive", + "glmmTMB (>= 1.1.10)", + "glmtoolbox", + "gmnl", + "grDevices", + "gt", + "httptest2", + "httr2", + "interp", + "ivreg", + "JM", + "knitr", + "lavaan", + "lavaSearch2", + "lfe", + "lme4", + "lmerTest", + "lmtest", + "logistf", + "logitr", + "marginaleffects (>= 0.25.0)", + "MASS", + "Matrix", + "mclogit", + "mclust", + "MCMCglmm", + "merTools", + "metaBMA", + "metadat", + "metafor", + "metaplus", + "mgcv", + "mice (>= 3.17.0)", + "mlogit", + "mmrm", + "modelbased (>= 0.9.0)", + "multgee", + "MuMIn", + "nestedLogit", + "nlme", + "nnet", + "nonnest2", + "ordinal", + "panelr", + "parameters", + "parsnip", + "pbkrtest", + "performance", + "phylolm", + "plm", + "poorman", + "PROreg (>= 1.3.0)", + "pscl", + "psych", + "quantreg", + "Rcpp", + "RcppEigen", + "rmarkdown", + "rms", + "robustbase", + "robustlmm", + "rpart", + "rstanarm (>= 2.21.1)", + "rstantools (>= 2.1.0)", + "rstudioapi", + "sandwich", + "serp", + "speedglm", + "splines", + "statmod", + "survey", + "survival", + "svylme", + "testthat", + "tinytable (>= 0.1.0)", + "TMB", + "truncreg", + "tweedie", + "VGAM", + "WeightIt", + "withr" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/Needs/website": "easystats/easystatstemplate", + "Config/Needs/check": "stan-dev/cmdstanr", + "NeedsCompilation": "no", + "Author": "Daniel Lüdecke [aut, cre] (), Dominique Makowski [aut, ctb] (), Indrajeet Patil [aut, ctb] (), Philip Waggoner [aut, ctb] (), Mattan S. Ben-Shachar [aut, ctb] (), Brenton M. Wiernik [aut, ctb] (), Vincent Arel-Bundock [aut, ctb] (), Etienne Bacher [aut, ctb] (), Alex Hayes [rev] (), Grant McDermott [ctb] (), Rémi Thériault [ctb] (), Alex Reinhart [ctb] ()", + "Repository": "CRAN" }, "isoband": { "Package": "isoband", "Version": "0.2.7", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "Generate Isolines and Isobands from Regularly Spaced Elevation Grids", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Claus O.\", \"Wilke\", , \"wilke@austin.utexas.edu\", role = \"aut\", comment = c(\"Original author\", ORCID = \"0000-0002-7470-9261\")), person(\"Thomas Lin\", \"Pedersen\", , \"thomasp85@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-5147-4711\")) )", + "Description": "A fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.", + "License": "MIT + file LICENSE", + "URL": "https://isoband.r-lib.org", + "BugReports": "https://github.com/r-lib/isoband/issues", + "Imports": [ "grid", "utils" ], - "Hash": "0080607b4a1a7b28979aecef976d8bc2" + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "magick", + "microbenchmark", + "rmarkdown", + "sf", + "testthat", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "C++11", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre] (), Claus O. Wilke [aut] (Original author, ), Thomas Lin Pedersen [aut] ()", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" }, "iterators": { "Package": "iterators", "Version": "1.0.14", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Type": "Package", + "Title": "Provides Iterator Construct", + "Authors@R": "c(person(\"Folashade\", \"Daniel\", role=\"cre\", email=\"fdaniel@microsoft.com\"), person(\"Revolution\", \"Analytics\", role=c(\"aut\", \"cph\")), person(\"Steve\", \"Weston\", role=\"aut\"))", + "Description": "Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.", + "URL": "https://github.com/RevolutionAnalytics/iterators", + "Depends": [ + "R (>= 2.5.0)", "utils" ], - "Hash": "8954069286b4b2b0d023d1b288dce978" + "Suggests": [ + "RUnit", + "foreach" + ], + "License": "Apache License (== 2.0)", + "NeedsCompilation": "no", + "Author": "Folashade Daniel [cre], Revolution Analytics [aut, cph], Steve Weston [aut]", + "Maintainer": "Folashade Daniel ", + "Repository": "CRAN" }, "janitor": { "Package": "janitor", "Version": "2.2.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "dplyr", + "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", - "snakecase", "stringi", "stringr", - "tidyr", - "tidyselect" + "snakecase (>= 0.9.2)", + "tidyselect (>= 1.0.0)", + "tidyr (>= 0.7.0)" ], - "Hash": "64f308bf1fbf5f856cdf4b4c7c0ce51b" + "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", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "Obtain 'jQuery' as an HTML Dependency Object", + "Authors@R": "c( person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@rstudio.com\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@rstudio.com\"), person(family = \"RStudio\", role = \"cph\"), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt\") )", + "Description": "Obtain any major version of 'jQuery' () and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown'). Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "RoxygenNote": "7.0.2", + "Imports": [ "htmltools" ], - "Hash": "5aab57a3bd297eee1c1d862735972182" + "Suggests": [ + "testthat" + ], + "NeedsCompilation": "no", + "Author": "Carson Sievert [aut, cre] (), Joe Cheng [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt)", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" }, "jsonlite": { "Package": "jsonlite", "Version": "1.8.9", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "A Simple and Robust JSON Parser and Generator for R", + "License": "MIT + file LICENSE", + "Depends": [ "methods" ], - "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b" + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Duncan\", \"Temple Lang\", role = \"ctb\"), person(\"Lloyd\", \"Hilaiel\", role = \"cph\", comment=\"author of bundled libyajl\"))", + "URL": "https://jeroen.r-universe.dev/jsonlite https://arxiv.org/abs/1403.2805", + "BugReports": "https://github.com/jeroen/jsonlite/issues", + "Maintainer": "Jeroen Ooms ", + "VignetteBuilder": "knitr, R.rsp", + "Description": "A reasonably fast JSON parser and generator, optimized for statistical data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.", + "Suggests": [ + "httr", + "vctrs", + "testthat", + "knitr", + "rmarkdown", + "R.rsp", + "sf" + ], + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "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", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "V8" + "Title": "Inline CSS Properties into HTML Tags Using 'juice'", + "Authors@R": "c( person(\"Richard\", \"Iannone\", , \"riannone@me.com\", c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Automattic\", role = c(\"cph\"), comment = \"juice library\"), person(\"juice contributors\", role = c(\"ctb\"), comment = \"juice library\") )", + "Description": "There are occasions where you need a piece of HTML with integrated styles. A prime example of this is HTML email. This transformation involves moving the CSS and associated formatting instructions from the style block in the head of your document into the body of the HTML. Many prominent email clients require integrated styles in HTML email; otherwise a received HTML email will be displayed without any styling. This package will quickly and precisely perform these CSS transformations when given HTML text and it does so by using the JavaScript 'juice' library.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/rich-iannone/juicyjuice", + "BugReports": "https://github.com/rich-iannone/juicyjuice/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.1", + "Imports": [ + "V8 (>= 4.2.0)" ], - "Hash": "3bcd11943da509341838da9399e18bce" + "Suggests": [ + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Richard Iannone [aut, cre, cph] (), Automattic [cph] (juice library), juice contributors [ctb] (juice library)", + "Maintainer": "Richard Iannone ", + "Repository": "CRAN" }, "kableExtra": { "Package": "kableExtra", "Version": "1.4.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "digest", - "grDevices", - "graphics", - "htmltools", - "knitr", - "magrittr", - "rmarkdown", - "rstudioapi", - "scales", - "stats", - "stringr", - "svglite", - "tools", - "viridisLite", - "xml2" + "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)" ], - "Hash": "532d16304274c23c8563f94b79351c86" + "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", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", + "Title": "Access the System Credential Store from R", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Alec\", \"Wong\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Platform independent 'API' to access the operating system's credential store. Currently supports: 'Keychain' on 'macOS', Credential Store on 'Windows', the Secret Service 'API' on 'Linux', and simple, platform independent stores implemented with environment variables or encrypted files. Additional storage back-ends can be added easily.", + "License": "MIT + file LICENSE", + "URL": "https://keyring.r-lib.org/, https://github.com/r-lib/keyring", + "BugReports": "https://github.com/r-lib/keyring/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ "askpass", "assertthat", "filelock", "openssl", + "R6", "rappdirs", "sodium", "tools", "utils", "yaml" ], - "Hash": "5cd8cfb2e90c57110b7dd1785c599aba" + "Suggests": [ + "callr", + "covr", + "mockery", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "Optional: libsecret on Linux (libsecret-1-dev on Debian/Ubuntu, libsecret-devel on Fedora/CentOS)", + "Collate": "'api.R' 'assertions.R' 'backend-class.R' 'backend-env.R' 'backend-file.R' 'backend-macos.R' 'backend-secret-service.R' 'backend-wincred.R' 'default_backend.R' 'keyring-package.R' 'package.R' 'pass.R' 'utils.R'", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Alec Wong [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" }, "knitr": { "Package": "knitr", "Version": "1.49", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "evaluate", - "highr", + "Type": "Package", + "Title": "A General-Purpose Package for Dynamic Report Generation in R", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Abhraneel\", \"Sarma\", role = \"ctb\"), person(\"Adam\", \"Vogt\", role = \"ctb\"), person(\"Alastair\", \"Andrew\", role = \"ctb\"), person(\"Alex\", \"Zvoleff\", role = \"ctb\"), person(\"Amar\", \"Al-Zubaidi\", role = \"ctb\"), person(\"Andre\", \"Simon\", role = \"ctb\", comment = \"the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de\"), person(\"Aron\", \"Atkins\", role = \"ctb\"), person(\"Aaron\", \"Wolen\", role = \"ctb\"), person(\"Ashley\", \"Manton\", role = \"ctb\"), person(\"Atsushi\", \"Yasumoto\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8335-495X\")), person(\"Ben\", \"Baumer\", role = \"ctb\"), person(\"Brian\", \"Diggs\", role = \"ctb\"), person(\"Brian\", \"Zhang\", role = \"ctb\"), person(\"Bulat\", \"Yapparov\", role = \"ctb\"), person(\"Cassio\", \"Pereira\", role = \"ctb\"), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person(\"David\", \"Hall\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", role = \"ctb\"), person(\"David\", \"Robinson\", role = \"ctb\"), person(\"Doug\", \"Hemken\", role = \"ctb\"), person(\"Duncan\", \"Murdoch\", role = \"ctb\"), person(\"Elio\", \"Campitelli\", role = \"ctb\"), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Emily\", \"Riederer\", role = \"ctb\"), person(\"Fabian\", \"Hirschmann\", role = \"ctb\"), person(\"Fitch\", \"Simeon\", role = \"ctb\"), person(\"Forest\", 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c(\"ctb\", \"cph\"), comment = \"the CSS file at inst/misc/docco-classic.css\"), person(\"Jeremy\", \"Stephens\", role = \"ctb\"), person(\"Jim\", \"Hester\", role = \"ctb\"), person(\"Joe\", \"Cheng\", role = \"ctb\"), person(\"Johannes\", \"Ranke\", role = \"ctb\"), person(\"John\", \"Honaker\", role = \"ctb\"), person(\"John\", \"Muschelli\", role = \"ctb\"), person(\"Jonathan\", \"Keane\", role = \"ctb\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Johan\", \"Toloe\", role = \"ctb\"), person(\"Jonathan\", \"Sidi\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Julien\", \"Barnier\", role = \"ctb\"), person(\"Kaiyin\", \"Zhong\", role = \"ctb\"), person(\"Kamil\", \"Slowikowski\", role = \"ctb\"), person(\"Karl\", \"Forner\", role = \"ctb\"), person(c(\"Kevin\", \"K.\"), \"Smith\", role = \"ctb\"), person(\"Kirill\", \"Mueller\", role = \"ctb\"), person(\"Kohske\", \"Takahashi\", role = \"ctb\"), person(\"Lorenz\", \"Walthert\", role = \"ctb\"), person(\"Lucas\", \"Gallindo\", role = \"ctb\"), person(\"Marius\", \"Hofert\", role = \"ctb\"), person(\"Martin\", \"Modrák\", role = \"ctb\"), person(\"Michael\", \"Chirico\", role = \"ctb\"), person(\"Michael\", \"Friendly\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", role = \"ctb\"), person(\"Michel\", \"Kuhlmann\", role = \"ctb\"), person(\"Miller\", \"Patrick\", role = \"ctb\"), person(\"Nacho\", \"Caballero\", role = \"ctb\"), person(\"Nick\", \"Salkowski\", role = \"ctb\"), person(\"Niels Richard\", \"Hansen\", role = \"ctb\"), person(\"Noam\", \"Ross\", role = \"ctb\"), person(\"Obada\", \"Mahdi\", role = \"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role = \"ctb\", comment=c(ORCID = \"0000-0002-9101-3362\")), person(\"Pedro\", \"Faria\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\"), person(\"Ramnath\", \"Vaidyanathan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Robert\", \"Krzyzanowski\", role = \"ctb\"), 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\"Foster\", role = \"ctb\"), person(\"Zhian N.\", \"Kamvar\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1458-7108\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "evaluate (>= 0.15)", + "highr (>= 0.11)", "methods", "tools", - "xfun", - "yaml" + "xfun (>= 0.48)", + "yaml (>= 2.1.19)" ], - "Hash": "9fcb189926d93c636dea94fbe4f44480" + "Suggests": [ + "bslib", + "codetools", + "DBI (>= 0.4-1)", + "digest", + "formatR", + "gifski", + "gridSVG", + "htmlwidgets (>= 0.7)", + "jpeg", + "JuliaCall (>= 0.11.1)", + "magick", + "litedown", + "markdown (>= 1.3)", + "png", + "ragg", + "reticulate (>= 1.4)", + "rgl (>= 0.95.1201)", + "rlang", + "rmarkdown", + "sass", + "showtext", + "styler (>= 1.2.0)", + "targets (>= 0.6.0)", + "testit", + "tibble", + "tikzDevice (>= 0.10)", + "tinytex (>= 0.46)", + "webshot", + "rstudioapi", + "svglite" + ], + "License": "GPL", + "URL": "https://yihui.org/knitr/", + "BugReports": "https://github.com/yihui/knitr/issues", + "Encoding": "UTF-8", + "VignetteBuilder": "litedown, knitr", + "SystemRequirements": "Package vignettes based on R Markdown v2 or reStructuredText require Pandoc (http://pandoc.org). The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).", + "Collate": "'block.R' 'cache.R' 'utils.R' 'citation.R' 'hooks-html.R' 'plot.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. Kamvar [ctb] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "labeling": { "Package": "labeling", "Version": "0.4.3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "graphics", - "stats" + "Type": "Package", + "Title": "Axis Labeling", + "Date": "2023-08-29", + "Author": "Justin Talbot,", + "Maintainer": "Nuno Sempere ", + "Description": "Functions which provide a range of axis labeling algorithms.", + "License": "MIT + file LICENSE | Unlimited", + "Collate": "'labeling.R'", + "NeedsCompilation": "no", + "Imports": [ + "stats", + "graphics" ], - "Hash": "b64ec208ac5bc1852b285f665d6368b3" + "Repository": "CRAN" }, "labelled": { "Package": "labelled", - "Version": "2.13.0", + "Version": "2.14.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "dplyr", - "haven", + "Type": "Package", + "Title": "Manipulating Labelled Data", + "Maintainer": "Joseph Larmarange ", + "Authors@R": "c( person(\"Joseph\", \"Larmarange\", email = \"joseph@larmarange.net\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7097-700X\")), person(\"Daniel\", \"Ludecke\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", role = \"ctb\"), person(\"François\", \"Briatte\", role = \"ctb\") )", + "Description": "Work with labelled data imported from 'SPSS' or 'Stata' with 'haven' or 'foreign'. This package provides useful functions to deal with \"haven_labelled\" and \"haven_labelled_spss\" classes introduced by 'haven' package.", + "License": "GPL (>= 3)", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 3.2)" + ], + "Imports": [ + "haven (>= 2.4.1)", + "cli", + "dplyr (>= 1.1.0)", "lifecycle", - "rlang", + "rlang (>= 1.1.0)", + "vctrs", "stringr", "tidyr", - "tidyselect", - "vctrs" + "tidyselect" ], - "Hash": "ad4b6d757624221aec6220b8c78defeb" + "Suggests": [ + "testthat (>= 3.2.0)", + "knitr", + "rmarkdown", + "questionr", + "snakecase", + "spelling" + ], + "Enhances": [ + "memisc" + ], + "URL": "https://larmarange.github.io/labelled/, https://github.com/larmarange/labelled", + "BugReports": "https://github.com/larmarange/labelled/issues", + "VignetteBuilder": "knitr", + "LazyData": "true", + "RoxygenNote": "7.3.2", + "Language": "en-US", + "Config/testthat/edition": "3", + "Config/Needs/check": "memisc", + "NeedsCompilation": "no", + "Author": "Joseph Larmarange [aut, cre] (), Daniel Ludecke [ctb], Hadley Wickham [ctb], Michal Bojanowski [ctb], François Briatte [ctb]", + "Repository": "CRAN" }, "later": { "Package": "later", "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "Rcpp", + "Type": "Package", + "Title": "Utilities for Scheduling Functions to Execute Later with Event Loops", + "Authors@R": "c( person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@posit.co\"), person(\"Joe\", \"Cheng\", role = c(\"aut\"), email = \"joe@posit.co\"), person(\"Charlie\", \"Gao\", role = c(\"aut\"), email = \"charlie.gao@shikokuchuo.net\", comment = c(ORCID = \"0000-0002-0750-061X\")), person(family = \"Posit Software, PBC\", role = \"cph\"), person(\"Marcus\", \"Geelnard\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\"), person(\"Evan\", \"Nemerson\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\") )", + "Description": "Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. The functions are scheduled in an event loop.", + "URL": "https://r-lib.github.io/later/, https://github.com/r-lib/later", + "BugReports": "https://github.com/r-lib/later/issues", + "License": "MIT + file LICENSE", + "Imports": [ + "Rcpp (>= 0.12.9)", "rlang" ], - "Hash": "501744395cac0bab0fbcfab9375ae92c" + "LinkingTo": [ + "Rcpp" + ], + "RoxygenNote": "7.3.2", + "Suggests": [ + "knitr", + "nanonext", + "R6", + "rmarkdown", + "testthat (>= 2.1.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Winston Chang [aut, cre], Joe Cheng [aut], Charlie Gao [aut] (), Posit Software, PBC [cph], Marcus Geelnard [ctb, cph] (TinyCThread library, https://tinycthread.github.io/), Evan Nemerson [ctb, cph] (TinyCThread library, https://tinycthread.github.io/)", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" }, "lattice": { "Package": "lattice", "Version": "0.22-6", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Date": "2024-03-20", + "Priority": "recommended", + "Title": "Trellis Graphics for R", + "Authors@R": "c(person(\"Deepayan\", \"Sarkar\", role = c(\"aut\", \"cre\"), email = \"deepayan.sarkar@r-project.org\", comment = c(ORCID = \"0000-0003-4107-1553\")), person(\"Felix\", \"Andrews\", role = \"ctb\"), person(\"Kevin\", \"Wright\", role = \"ctb\", comment = \"documentation\"), person(\"Neil\", \"Klepeis\", role = \"ctb\"), person(\"Johan\", \"Larsson\", role = \"ctb\", comment = \"miscellaneous improvements\"), person(\"Zhijian (Jason)\", \"Wen\", role = \"cph\", comment = \"filled contour code\"), person(\"Paul\", \"Murrell\", role = \"ctb\", email = \"paul@stat.auckland.ac.nz\"), person(\"Stefan\", \"Eng\", role = \"ctb\", comment = \"violin plot improvements\"), person(\"Achim\", \"Zeileis\", role = \"ctb\", comment = \"modern colors\"), person(\"Alexandre\", \"Courtiol\", role = \"ctb\", comment = \"generics for larrows, lpolygon, lrect and lsegments\") )", + "Description": "A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. 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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": "0.8.9", + "Version": "0.9.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bayestestR", - "datawizard", - "effectsize", + "Type": "Package", + "Title": "Estimation of Model-Based Predictions, Contrasts and Means", + "Authors@R": "c(person(given = \"Dominique\", family = \"Makowski\", role = c(\"aut\", \"cre\"), email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Daniel\", family = \"Lüdecke\", role = \"aut\", email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = \"aut\", email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")))", + "Maintainer": "Dominique Makowski ", + "Description": "Implements a general interface for model-based estimations for a wide variety of models, used in the computation of marginal means, contrast analysis and predictions. 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Users can easily customize color and theme settings before using the reset of NEST packages to ensure consistent settings in both static and interactive output at the downstream.", + "License": "Apache License 2.0", + "URL": "https://insightsengineering.github.io/nestcolor/, https://github.com/insightsengineering/nestcolor/", + "BugReports": "https://github.com/insightsengineering/nestcolor/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "checkmate (>= 2.1.0)", + "ggplot2 (>= 3.5.0)", + "lifecycle (>= 1.0.3)" + ], + "Suggests": [ + "knitr (>= 1.42)", + "rmarkdown (>= 2.19)", + "testthat (>= 3.0.4)" + ], + "VignetteBuilder": "knitr, rmarkdown", + "RdMacros": "lifecycle", + "Config/Needs/verdepcheck": "mllg/checkmate, tidyverse/ggplot2, r-lib/lifecycle, yihui/knitr, rstudio/rmarkdown, r-lib/testthat", + "Config/Needs/website": "insightsengineering/nesttemplate", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Joe Zhu [aut, cre] (), Emily de la Rua [aut], F. 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NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See for more information on the available algorithms. Building from included sources requires 'CMake'. On Linux and 'macOS', if a suitable system build of NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from included sources via 'CMake'. On Windows, NLopt is obtained through 'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for 'R >= 4.2.0'.", + "License": "LGPL (>= 3)", + "SystemRequirements": "cmake (>= 3.2.0) which is used only on Linux or macOS systems when no system build of nlopt (>= 2.7.0) can be found.", + "Biarch": "true", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Suggests": [ + "knitr", + "rmarkdown", + "covr", + "tinytest" + ], + "VignetteBuilder": "knitr", + "URL": "https://github.com/astamm/nloptr, https://astamm.github.io/nloptr/", + "BugReports": "https://github.com/astamm/nloptr/issues", + "NeedsCompilation": "yes", + "Author": "Jelmer Ypma [aut], Steven G. Johnson [aut] (author of the NLopt C library), Aymeric Stamm [ctb, cre] (), Hans W. 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The package focuses on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. 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Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.", + "License": "MIT + file LICENSE", + "URL": "https://jeroen.r-universe.dev/openssl", + "BugReports": "https://github.com/jeroen/openssl/issues", + "SystemRequirements": "OpenSSL >= 1.0.2", + "VignetteBuilder": "knitr", + "Imports": [ "askpass" ], - "Hash": "5bfe2927efa9f87766ca9605301ea48f" + "Suggests": [ + "curl", + "testthat (>= 2.1.0)", + "digest", + "knitr", + "rmarkdown", + "jsonlite", + "jose", + "sodium" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Oliver Keyes [ctb]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" }, "openxlsx2": { "Package": "openxlsx2", "Version": "1.12", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Type": "Package", + "Title": "Read, Write and Edit 'xlsx' Files", + "Language": "en-US", + "Authors@R": "c( person(\"Jordan Mark\", \"Barbone\", email = \"jmbarbone@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-9788-3628\")), person(\"Jan Marvin\", \"Garbuszus\", email = \"jan.garbuszus@ruhr-uni-bochum.de\", role = c(\"aut\", \"cre\")), person(\"Olivier\", \"Roy\", role = \"ctb\"), person(family = \"openxlsx authors\", role = \"cph\", comment = \"openxlsx package\"), person(\"Arseny\", \"Kapoulkine\", role = c(\"ctb\", \"cph\"), comment = \"Author of included pugixml code\") )", + "Description": "Simplifies the creation of 'xlsx' files by providing a high level interface to writing, styling and editing worksheets.", + "License": "MIT + file LICENSE", + "URL": "https://janmarvin.github.io/openxlsx2/, https://github.com/JanMarvin/openxlsx2", + "BugReports": "https://github.com/JanMarvin/openxlsx2/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ "R6", "Rcpp", "grDevices", @@ -2206,354 +6695,1225 @@ "utils", "zip" ], - "Hash": "be241f0f1a58220243d69141407a97ac" + "LinkingTo": [ + "Rcpp" + ], + "Suggests": [ + "ggplot2", + "knitr", + "mschart (>= 0.4)", + "rmarkdown", + "rvg", + "testthat (>= 3.0.0)", + "waldo" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "NeedsCompilation": "yes", + "Author": "Jordan Mark Barbone [aut] (), Jan Marvin Garbuszus [aut, cre], Olivier Roy [ctb], openxlsx authors [cph] (openxlsx package), Arseny Kapoulkine [ctb, cph] (Author of included pugixml code)", + "Maintainer": "Jan Marvin Garbuszus ", + "Repository": "CRAN" + }, + "pander": { + "Package": "pander", + "Version": "0.6.5", + "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. 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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": "0.24.0", + "Version": "0.24.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bayestestR", - "datawizard", + "Type": "Package", + "Title": "Processing of Model Parameters", + "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 = \"aut\", email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = \"aut\", email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Søren\", family = \"Højsgaard\", role = \"aut\", email = \"sorenh@math.aau.dk\"), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"aut\", email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Zen J.\", family = \"Lau\", role = \"ctb\", email = \"zenjuen.lau@ntu.edu.sg\"), person(given = \"Vincent\", family = \"Arel-Bundock\", role = \"ctb\", email = \"vincent.arel-bundock@umontreal.ca\", comment = c(ORCID = \"0000-0003-2042-7063\")), person(given = \"Jeffrey\", family = \"Girard\", role = \"ctb\", email = \"me@jmgirard.com\", comment = c(ORCID = \"0000-0002-7359-3746\")), person(given = \"Christina\", family = \"Maimone\", role = \"rev\", email = \"christina.maimone@northwestern.edu\"), person(given = \"Niels\", family = \"Ohlsen\", role = \"rev\"), person(given = \"Douglas Ezra\", family = \"Morrison\", role = \"ctb\", email = \"dmorrison01@ucla.edu\", comment = c(ORCID = \"0000-0002-7195-830X\")), person(given = \"Joseph\", family = \"Luchman\", role = \"ctb\", email = \"jluchman@gmail.com\", comment = c(ORCID = \"0000-0002-8886-9717\")))", + "Maintainer": "Daniel Lüdecke ", + "Description": "Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).", + "License": "GPL-3", + "URL": "https://easystats.github.io/parameters/", + "BugReports": "https://github.com/easystats/parameters/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "bayestestR (>= 0.15.0)", + "datawizard (>= 1.0.0)", + "insight (>= 1.0.0)", "graphics", - "insight", "methods", "stats", "utils" ], - "Hash": "42e4417823caf935fcc47a88ad4706e7" + "Suggests": [ + "AER", + "afex", + "aod", + "BayesFactor (>= 0.9.12-4.7)", + "BayesFM", + "bbmle", + "betareg", + "BH", + "biglm", + "blme", + "boot", + "brglm2", + "brms", + "broom", + "broom.mixed", + "cAIC4", + "car", + "carData", + "cgam", + "ClassDiscovery", + "clubSandwich", + "cluster", + "cobalt", + "coda", + "coxme", + "cplm", + "dbscan", + "did", + "distributional", + "domir (>= 0.2.0)", + "drc", + "DRR", + "effectsize (>= 0.8.6)", + "EGAnet", + "emmeans (>= 1.7.0)", + "epiR", + "estimatr", + "factoextra", + "FactoMineR", + "faraway", + "fastICA", + "fixest", + "fpc", + "gam", + "gamlss", + "gee", + "geepack", + "ggeffects (>= 1.3.2)", + "ggplot2", + "GLMMadaptive", + "glmmTMB (>= 1.1.10)", + "glmtoolbox", + "GPArotation", + "gt", + "haven", + "httr2", + "Hmisc", + "ivreg", + "knitr", + "lavaan", + "lfe", + "lm.beta", + "lme4", + "lmerTest", + "lmtest", + "logistf", + "logitr", + "logspline", + "lqmm", + "M3C", + "marginaleffects (>= 0.20.4)", + "MASS", + "Matrix", + "mclogit", + "mclust", + "MCMCglmm", + "mediation", + "merDeriv", + "metaBMA", + "metafor", + "mfx", + "mgcv", + "mice (>= 3.17.0)", + "mmrm", + "multcomp", + "MuMIn", + "NbClust", + "nFactors", + "nestedLogit", + "nlme", + "nnet", + "openxlsx", + "ordinal", + "panelr", + "pbkrtest", + "PCDimension", + "performance (>= 0.12.0)", + "plm", + "PMCMRplus", + "poorman", + "posterior", + "PROreg (>= 1.3.0)", + "pscl", + "psych", + "pvclust", + "quantreg", + "randomForest", + "RcppEigen", + "rmarkdown", + "rms", + "rstan", + "rstanarm", + "sandwich", + "see (>= 0.8.1)", + "serp", + "sparsepca", + "survey", + "survival", + "svylme", + "testthat (>= 3.2.1)", + "tidyselect", + "tinytable (>= 0.1.0)", + "TMB", + "truncreg", + "vdiffr", + "VGAM", + "WeightIt (>= 1.2.0)", + "withr", + "WRS2" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/Needs/website": "easystats/easystatstemplate", + "Config/rcmdcheck/ignore-inconsequential-notes": "true", + "NeedsCompilation": "no", + "Author": "Daniel Lüdecke [aut, cre] (), Dominique Makowski [aut] (), Mattan S. Ben-Shachar [aut] (), Indrajeet Patil [aut] (), Søren Højsgaard [aut], Brenton M. Wiernik [aut] (), Zen J. Lau [ctb], Vincent Arel-Bundock [ctb] (), Jeffrey Girard [ctb] (), Christina Maimone [rev], Niels Ohlsen [rev], Douglas Ezra Morrison [ctb] (), Joseph Luchman [ctb] ()", + "Repository": "CRAN" }, "patchwork": { "Package": "patchwork", "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "cli", - "farver", - "ggplot2", - "grDevices", - "graphics", - "grid", + "Type": "Package", + "Title": "The Composer of Plots", + "Authors@R": "person(given = \"Thomas Lin\", family = \"Pedersen\", role = c(\"cre\", \"aut\"), email = \"thomasp85@gmail.com\", comment = c(ORCID = \"0000-0002-5147-4711\"))", + "Maintainer": "Thomas Lin Pedersen ", + "Description": "The 'ggplot2' package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. 'patchwork' is a package that expands the API to allow for arbitrarily complex composition of plots by, among others, providing mathematical operators for combining multiple plots. 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Implements parametric bootstrap test for generalized linear mixed models as implemented in 'lme4' and generalized linear models. The package is documented in the paper by Halekoh and Højsgaard, (2012, ). 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Portfolio selection methods based on expected shortfall risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press, and Koenker, R. et al. 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T. Conceicao [aut] (MM-, tau-, CM-, and MTL- nlrob), Maria Anna di Palma [ctb] (initial version of Comedian)", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" + }, + "rpart": { + "Package": "rpart", + "Version": "4.1.24", + "Source": "Repository", + "Priority": "recommended", + "Date": "2025-01-06", + "Authors@R": "c(person(\"Terry\", \"Therneau\", role = \"aut\", email = \"therneau@mayo.edu\"), person(\"Beth\", \"Atkinson\", role = c(\"aut\", \"cre\"), email = \"atkinson@mayo.edu\"), person(\"Brian\", \"Ripley\", role = \"trl\", email = \"ripley@stats.ox.ac.uk\", comment = \"producer of the initial R port, maintainer 1999-2017\"))", + "Description": "Recursive partitioning for classification, regression and survival trees. 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Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")) )", + "Description": "Reporting tables often have structure that goes beyond simple rectangular data. The 'rtables' package provides a framework for declaring complex multi-level tabulations and then applying them to data. This framework models both tabulation and the resulting tables as hierarchical, tree-like objects which support sibling sub-tables, arbitrary splitting or grouping of data in row and column dimensions, cells containing multiple values, and the concept of contextual summary computations. 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Hoffmann-La Roche AG [cph, fnd]", + "Maintainer": "Joe Zhu ", + "Repository": "CRAN" + }, + "rtables.officer": { + "Package": "rtables.officer", + "Version": "0.0.2", + "Source": "Repository", + "Title": "Exporting Tools for 'rtables'", + "Date": "2025-01-14", + "Authors@R": "c( person(\"Gabriel\", \"Becker\", , \"gabembecker@gmail.com\", role = \"ctb\"), person(\"Davide\", \"Garolini\", , \"davide.garolini@roche.com\", role = \"aut\"), person(\"Emily\", \"de la Rua\", , \"emily.de_la_rua@contractors.roche.com\", role = \"aut\"), person(\"Abinaya\", \"Yogasekaram\", , \"abinaya.yogasekaram@contractors.roche.com\", role = \"aut\"), person(\"Joe\", \"Zhu\", , \"joe.zhu@roche.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7566-2787\")), person(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")) )", + "Description": "Designed to create and display complex tables with R, the 'rtables' R package allows cells in an 'rtables' object to contain any high-dimensional data structure, which can then be displayed with cell-specific formatting instructions. 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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. 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This widget allows intuitive time input in the '[hh]:[mm]:[ss]' or '[hh]:[mm]' (24H) format by using a separate numeric input for each time component. The interface with R uses date-time objects. See the project page for more information and examples.", + "License": "GPL-3 | file LICENSE", + "Imports": [ "htmltools", "shiny" ], - "Hash": "836c3464fb0f2ea865ed4c35dcdc1eda" + "URL": "https://burgerga.github.io/shinyTime/, https://github.com/burgerga/shinyTime", + "BugReports": "https://github.com/burgerga/shinyTime/issues", + "RoxygenNote": "7.2.1", + "Encoding": "UTF-8", + "Language": "en-US", + "Suggests": [ + "testthat (>= 2.1.0)", + "spelling", + "hms" + ], + "NeedsCompilation": "no", + "Author": "Gerhard Burger [aut, cre] ()", + "Maintainer": "Gerhard Burger ", + "Repository": "CRAN" }, "shinyTree": { "Package": "shinyTree", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Type": "Package", + "Title": "jsTree Bindings for Shiny", + "Date": "2023-7-21", + "Authors@R": "c( person(family=\"Trestle Technology, LLC\", role=\"aut\", email=\"cran@trestletechnology.net\"), person(\"Jeff\", \"Allen\", role=\"aut\", email=\"cran@trestletechnology.net\"), person(family=\"Institut de Radioprotection et de Sûreté Nucléaire\", role=c(\"cph\"), email = \"yann.richet@irsn.fr\"), person(\"Ivan\", \"Bozhanov\", role=c(\"ctb\", \"cph\"), comment = \"jsTree\"), person(family=\"The Dojo Foundation\", role=c(\"ctb\", \"cph\"), comment=\"require.js\"), person(family=\"jQuery Foundation, Inc.\", role=c(\"ctb\", \"cph\")), person(\"Mike\", \"Schaffer\", role=c(\"ctb\"), email=\"mschaff@gmail.com\"), person(\"Timm\", \"Danker\", role=c(\"ctb\"), email=\"tidafr@carina.uberspace.de\"), person(\"Michael\", \"Bell\", role=c(\"cre\"), email=\"bell_michael_a@lilly.com\"), person(\"Sebastian\", \"Gatscha\", role=c(\"ctb\"), email=\"kona1@gmx.at\"), person(\"Thorn\", \"Thaler\", role = c(\"ctb\"), email = \"thorn.thaler@thothal.at\"))", + "Maintainer": "Michael Bell ", + "Description": "Exposes bindings to jsTree -- a JavaScript library that supports interactive trees -- to enable a rich, editable trees in Shiny.", + "License": "MIT + file LICENSE", + "Depends": [ + "R (>= 2.15.1)", + "methods" + ], + "Imports": [ + "shiny (>= 0.9.0)", "htmlwidgets", "jsonlite", - "methods", - "promises", - "shiny", - "stringr" + "stringr", + "promises" ], - "Hash": "0493a0d70f834cb251fe4523eb17b82c" + "Suggests": [ + "testthat", + "shinytest", + "data.tree" + ], + "BugReports": "https://github.com/shinyTree/shinyTree/issues", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Trestle Technology, LLC [aut], Jeff Allen [aut], Institut de Radioprotection et de Sûreté Nucléaire [cph], Ivan Bozhanov [ctb, cph] (jsTree), The Dojo Foundation [ctb, cph] (require.js), jQuery Foundation, Inc. [ctb, cph], Mike Schaffer [ctb], Timm Danker [ctb], Michael Bell [cre], Sebastian Gatscha [ctb], Thorn Thaler [ctb]", + "Repository": "CRAN" }, "shinyWidgets": { "Package": "shinyWidgets", "Version": "0.8.7", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bslib", - "grDevices", - "htmltools", - "jsonlite", - "rlang", - "sass", - "shiny" + "Title": "Custom Inputs Widgets for Shiny", + "Authors@R": "c( person(\"Victor\", \"Perrier\", email = \"victor.perrier@dreamrs.fr\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Fanny\", \"Meyer\", role = \"aut\"), person(\"David\", \"Granjon\", role = \"aut\"), person(\"Ian\", \"Fellows\", role = \"ctb\", comment = \"Methods for mutating vertical tabs & updateMultiInput\"), person(\"Wil\", \"Davis\", role = \"ctb\", comment = \"numericRangeInput function\"), person(\"Spencer\", \"Matthews\", role = \"ctb\", comment = \"autoNumeric methods\"), person(family = \"JavaScript and CSS libraries authors\", role = c(\"ctb\", \"cph\"), comment = \"All authors are listed in LICENSE.md\") )", + "Description": "Collection of custom input controls and user interface components for 'Shiny' applications. Give your applications a unique and colorful style !", + "URL": "https://github.com/dreamRs/shinyWidgets, https://dreamrs.github.io/shinyWidgets/", + "BugReports": "https://github.com/dreamRs/shinyWidgets/issues", + "License": "GPL-3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.3.2", + "Depends": [ + "R (>= 3.1.0)" ], - "Hash": "fd8239886f70daa85c36596214958451" + "Imports": [ + "bslib", + "sass", + "shiny (>= 1.6.0)", + "htmltools (>= 0.5.1)", + "jsonlite", + "grDevices", + "rlang" + ], + "Suggests": [ + "testthat", + "covr", + "ggplot2", + "DT", + "scales", + "shinydashboard", + "shinydashboardPlus" + ], + "NeedsCompilation": "no", + "Author": "Victor Perrier [aut, cre, cph], Fanny Meyer [aut], David Granjon [aut], Ian Fellows [ctb] (Methods for mutating vertical tabs & updateMultiInput), Wil Davis [ctb] (numericRangeInput function), Spencer Matthews [ctb] (autoNumeric methods), JavaScript and CSS libraries authors [ctb, cph] (All authors are listed in LICENSE.md)", + "Maintainer": "Victor Perrier ", + "Repository": "CRAN" }, "shinybusy": { "Package": "shinybusy", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "Busy Indicators and Notifications for 'Shiny' Applications", + "Authors@R": "c(person(\"Fanny\", \"Meyer\", role = \"aut\"), person(\"Victor\", \"Perrier\", email = \"victor.perrier@dreamrs.fr\", role = c(\"aut\", \"cre\")), person(\"Silex Technologies\", comment = \"https://www.silex-ip.com\", role = \"fnd\"))", + "Description": "Add indicators (spinner, progress bar, gif) in your 'shiny' applications to show the user that the server is busy. 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Using 'shinycssloaders', you can add a loading animation (\"spinner\") to outputs instead. By wrapping a 'Shiny' output in 'withSpinner()', a spinner will automatically appear while the output is recalculating. You can also manually show and hide the spinner, or add a full-page spinner to cover the entire page. See the demo online at .", + "License": "MIT + file LICENSE", + "URL": "https://github.com/daattali/shinycssloaders, https://daattali.com/shiny/shinycssloaders-demo/", + "BugReports": "https://github.com/daattali/shinycssloaders/issues", + "Depends": [ + "R (>= 3.1)" + ], + "Imports": [ "digest", "glue", "grDevices", - "htmltools", + "htmltools (>= 0.3.5)", "shiny" ], - "Hash": "2b45a467a30d6a88a1892a738c0900cf" + "Suggests": [ + "knitr", + "shinydisconnect", + "shinyjs" + ], + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Dean Attali [aut, cre] (Maintainer/developer of shinycssloaders since 2019, ), Andras Sali [aut] (Original creator of shinycssloaders package), Luke Hass [ctb, cph] (Author of included CSS loader code)", + "Maintainer": "Dean Attali ", + "Repository": "CRAN" }, "shinyjs": { "Package": "shinyjs", "Version": "2.1.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "digest", - "jsonlite", - "shiny" + "Title": "Easily Improve the User Experience of Your Shiny Apps in Seconds", + "Authors@R": "person(\"Dean\", \"Attali\", email = \"daattali@gmail.com\", role = c(\"aut\", \"cre\"), comment= c(ORCID=\"0000-0002-5645-3493\"))", + "Description": "Perform common useful JavaScript operations in Shiny apps that will greatly improve your apps without having to know any JavaScript. 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Testing the hypothesis that two samples come from the same distribution using randomization to create p-values. Included tests are: Kolmogorov-Smirnov, Kuiper, Cramer-von Mises, Anderson-Darling, Wasserstein, and DTS. The default test (two_sample) is based on the DTS test statistic, as it is the most powerful, and thus most useful to most users. The DTS test statistic builds on the Wasserstein distance by using a weighting scheme like that of Anderson-Darling. See the companion paper at or for details of that test statistic, and non-standard uses of the package (parallel for big N, weighted observations, one sample tests, etc). We also include the permutation scheme to make test building simple for others.", + "License": "GPL (>= 2)", + "Encoding": "UTF-8", + "LinkingTo": [ "cpp11" ], - "Hash": "cc7d944f8cf4a557decafe1dc95531de" + "RoxygenNote": "7.2.3", + "URL": "https://twosampletest.com, https://github.com/cdowd/twosamples", + "BugReports": "https://github.com/cdowd/twosamples/issues", + "Suggests": [ + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Connor Dowd [aut, cre] ()", + "Maintainer": "Connor Dowd ", + "Repository": "CRAN" }, "tzdb": { "Package": "tzdb", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11" + "Title": "Time Zone Database Information", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.", + "License": "MIT + file LICENSE", + "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", + "BugReports": "https://github.com/r-lib/tzdb/issues", + "Depends": [ + "R (>= 3.5.0)" ], - "Hash": "f561504ec2897f4d46f0c7657e488ae1" + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.4.2)" + ], + "Biarch": "yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" }, "utf8": { "Package": "utf8", "Version": "1.2.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "Unicode Text Processing", + "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\"), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://ptrckprry.com/r-utf8/, https://github.com/patperry/r-utf8", + "BugReports": "https://github.com/patperry/r-utf8/issues", + "Depends": [ + "R (>= 2.10)" ], - "Hash": "62b65c52671e6665f803ff02954446e9" + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre], Unicode, Inc. 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A lean version of the package called 'viridisLite' that does not include the 'ggplot2' bindings can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)", + "viridisLite (>= 0.4.0)" + ], + "Imports": [ + "ggplot2 (>= 1.0.1)", + "gridExtra" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "scales", + "MASS", + "knitr", + "dichromat", + "colorspace", + "httr", + "mapproj", + "vdiffr", + "svglite (>= 1.2.0)", + "testthat", + "covr", + "rmarkdown", + "maps", + "terra" + ], + "LazyData": "true", + "VignetteBuilder": "knitr", + "URL": "https://sjmgarnier.github.io/viridis/, https://github.com/sjmgarnier/viridis/", + "BugReports": "https://github.com/sjmgarnier/viridis/issues", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" }, "viridisLite": { "Package": "viridisLite", "Version": "0.4.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps (Lite Version)", + "Date": "2023-05-02", + "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", + "Maintainer": "Simon Garnier ", + "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" ], - "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" + ], + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" }, "vroom": { "Package": "vroom", "Version": "1.6.5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Read and Write Rectangular Text Data Quickly", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. 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Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" }, "zip": { "Package": "zip", - "Version": "2.3.1", + "Version": "2.3.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab" + "Title": "Cross-Platform 'zip' Compression", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kuba\", \"Podgórski\", role = \"ctb\"), person(\"Rich\", \"Geldreich\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/zip, https://r-lib.github.io/zip/", + "BugReports": "https://github.com/r-lib/zip/issues", + "Suggests": [ + "covr", + "pillar", + "processx", + "R6", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" }, "zoo": { "Package": "zoo", "Version": "1.8-12", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "lattice", - "stats", - "utils" + "Date": "2023-04-11", + "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", + "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", + "Depends": [ + "R (>= 3.1.0)", + "stats" ], - "Hash": "5c715954112b45499fb1dadc6ee6ee3e" + "Suggests": [ + "AER", + "coda", + "chron", + "ggplot2 (>= 3.0.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", + "graphics", + "grDevices", + "lattice (>= 0.20-27)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://zoo.R-Forge.R-project.org/", + "NeedsCompilation": "yes", + "Author": "Achim Zeileis [aut, cre] (), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" } } } diff --git a/renv/activate.R b/renv/activate.R index 0eb5108..ebbe303 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.0.11" + version <- "1.1.0" attr(version, "sha") <- NULL # the project directory @@ -42,7 +42,7 @@ local({ return(FALSE) # next, check environment variables - # TODO: prefer using the configuration one in the future + # prefer using the configuration one in the future envvars <- c( "RENV_CONFIG_AUTOLOADER_ENABLED", "RENV_AUTOLOADER_ENABLED", @@ -209,10 +209,6 @@ local({ } - startswith <- function(string, prefix) { - substring(string, 1, nchar(prefix)) == prefix - } - bootstrap <- function(version, library) { friendly <- renv_bootstrap_version_friendly(version) @@ -563,6 +559,9 @@ local({ # prepare download options token <- renv_bootstrap_github_token() + if (is.null(token)) + token <- "" + if (nzchar(Sys.which("curl")) && nzchar(token)) { fmt <- "--location --fail --header \"Authorization: token %s\"" extra <- sprintf(fmt, token) @@ -951,8 +950,14 @@ local({ } renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] - is.character(expected) && startswith(expected, version) + if (!is.character(expected)) + return(FALSE) + + pattern <- sprintf("^\\Q%s\\E", version) + grepl(pattern, expected, perl = TRUE) + } renv_bootstrap_validate_version_release <- function(version, description) { @@ -1132,10 +1137,10 @@ local({ renv_bootstrap_exec <- function(project, libpath, version) { if (!renv_bootstrap_load(project, libpath, version)) - renv_bootstrap_run(version, libpath) + renv_bootstrap_run(project, libpath, version) } - renv_bootstrap_run <- function(version, libpath) { + renv_bootstrap_run <- function(project, libpath, version) { # perform bootstrap bootstrap(version, libpath) @@ -1146,7 +1151,7 @@ local({ # try again to load if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { - return(renv::load(project = getwd())) + return(renv::load(project = project)) } # failed to download or load renv; warn the user @@ -1192,98 +1197,101 @@ local({ jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } + renv_json_read_patterns <- function() { + + list( + + # objects + list("{", "\t\n\tobject(\t\n\t"), + list("}", "\t\n\t)\t\n\t"), + + # arrays + list("[", "\t\n\tarray(\t\n\t"), + list("]", "\n\t\n)\n\t\n"), + + # maps + list(":", "\t\n\t=\t\n\t") + + ) + + } + + renv_json_read_envir <- function() { + + envir <- new.env(parent = emptyenv()) + + envir[["+"]] <- `+` + envir[["-"]] <- `-` + + envir[["object"]] <- function(...) { + result <- list(...) + names(result) <- as.character(names(result)) + result + } + + envir[["array"]] <- list + + envir[["true"]] <- TRUE + envir[["false"]] <- FALSE + envir[["null"]] <- NULL + + envir + + } + + renv_json_read_remap <- function(object, patterns) { + + # repair names if necessary + if (!is.null(names(object))) { + + nms <- names(object) + for (pattern in patterns) + nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) + names(object) <- nms + + } + + # repair strings if necessary + if (is.character(object)) { + for (pattern in patterns) + object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) + } + + # recurse for other objects + if (is.recursive(object)) + for (i in seq_along(object)) + object[i] <- list(renv_json_read_remap(object[[i]], patterns)) + + # return remapped object + object + + } + renv_json_read_default <- function(file = NULL, text = NULL) { - # find strings in the JSON + # read json text text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") - pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' - locs <- gregexpr(pattern, text, perl = TRUE)[[1]] - - # if any are found, replace them with placeholders - replaced <- text - strings <- character() - replacements <- character() - - if (!identical(c(locs), -1L)) { - - # get the string values - starts <- locs - ends <- locs + attr(locs, "match.length") - 1L - strings <- substring(text, starts, ends) - - # only keep those requiring escaping - strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) - - # compute replacements - replacements <- sprintf('"\032%i\032"', seq_along(strings)) - - # replace the strings - mapply(function(string, replacement) { - replaced <<- sub(string, replacement, replaced, fixed = TRUE) - }, strings, replacements) - - } - - # transform the JSON into something the R parser understands - transformed <- replaced - transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) - transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) - transformed <- gsub("[]}]", ")", transformed, perl = TRUE) - transformed <- gsub(":", "=", transformed, fixed = TRUE) - text <- paste(transformed, collapse = "\n") - + + # convert into something the R parser will understand + patterns <- renv_json_read_patterns() + transformed <- text + for (pattern in patterns) + transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) + # parse it - json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + rfile <- tempfile("renv-json-", fileext = ".R") + on.exit(unlink(rfile), add = TRUE) + writeLines(transformed, con = rfile) + json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]] - # construct map between source strings, replaced strings - map <- as.character(parse(text = strings)) - names(map) <- as.character(parse(text = replacements)) - - # convert to list - map <- as.list(map) - - # remap strings in object - remapped <- renv_json_read_remap(json, map) - - # evaluate - eval(remapped, envir = baseenv()) + # evaluate in safe environment + result <- eval(json, envir = renv_json_read_envir()) + # fix up strings if necessary + renv_json_read_remap(result, patterns) + } - renv_json_read_remap <- function(json, map) { - - # fix names - if (!is.null(names(json))) { - lhs <- match(names(json), names(map), nomatch = 0L) - rhs <- match(names(map), names(json), nomatch = 0L) - names(json)[rhs] <- map[lhs] - } - - # fix values - if (is.character(json)) - return(map[[json]] %||% json) - - # handle true, false, null - if (is.name(json)) { - text <- as.character(json) - if (text == "true") - return(TRUE) - else if (text == "false") - return(FALSE) - else if (text == "null") - return(NULL) - } - - # recurse - if (is.recursive(json)) { - for (i in seq_along(json)) { - json[i] <- list(renv_json_read_remap(json[[i]], map)) - } - } - - json - - } # load the renv profile, if any renv_bootstrap_profile_load(project)