mirror of
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big steps
This commit is contained in:
parent
52d1791708
commit
ce2558fe90
19 changed files with 3877 additions and 581 deletions
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@ -1,6 +1,6 @@
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Package: freesearcheR
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Title: Browser Based Data Analysis
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Version: 24.12.1
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Version: 25.1.1
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Authors@R:
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person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0002-7559-1154"))
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@ -49,7 +49,10 @@ Imports:
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shinyWidgets,
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classInt,
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htmltools,
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rlang
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rlang,
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data.table,
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apexcharter,
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teal.modules.general
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Suggests:
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styler,
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devtools,
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9
NEWS.md
9
NEWS.md
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@ -1,3 +1,12 @@
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# freesearcheR 25.1.1
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* UI tweaks.
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* NEW: Option to set class as `hms` using the `{hms}` package.
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* NEW: summary grid with sparklines.
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# freesearcheR 24.12.1
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* Initial release for Zenodo.
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237
R/data-summary.R
Normal file
237
R/data-summary.R
Normal file
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@ -0,0 +1,237 @@
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data_summary_ui <- function(id) {
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ns <- NS(id)
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toastui::datagridOutput(outputId = "tbl_summary")
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}
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data_summary_server <- function(id,
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data) {
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shiny::moduleServer(
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id = id,
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module = function(input, output, session) {
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ns <- session$ns
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data_r <- shiny::reactive({
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if (shiny::is.reactive(data)) {
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data()
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} else {
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data
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}
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})
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output$tbl_summary <- shiny::reactive({
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toastui::renderDatagrid(
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data_r() |>
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overview_vars() |>
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create_overview_datagrid() |>
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add_sparkline(
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column = "vals"
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)
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)
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})
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}
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)
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}
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#' Add sparkline to datagrid
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#'
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#' @param grid grid
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#' @param column clumn to transform
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#'
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#' @returns datagrid
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#' @export
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#'
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#' @examples
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#' grid <- mtcars |>
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#' default_parsing() |>
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#' overview_vars() |>
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#' toastui::datagrid() |>
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#' add_sparkline()
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#' grid
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add_sparkline <- function(grid, column = "vals", color.main = "#2a8484", color.sec = "#84EF84") {
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out <- toastui::grid_sparkline(
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grid = grid,
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column = column,
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renderer = function(data) {
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data_cl <- class(data)
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if (identical(data_cl, "factor")) {
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type <- "column"
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s <- summary(data)
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ds <- data.frame(x = names(s), y = s)
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horizontal <- FALSE
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} else if (any(c("numeric", "integer") %in% data_cl)) {
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if (length(unique(data)) == length(data)) {
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type <- "line"
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ds <- data.frame(x = NA, y = NA)
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horizontal <- FALSE
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} else {
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type <- "box"
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ds <- data.frame(x = 1, y = data)
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horizontal <- TRUE
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}
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} else if (any(c("Date", "POSIXct", "POSIXt", "hms", "difftime") %in% data_cl)) {
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type <- "line"
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ds <- data.frame(x = seq_along(data), y = data)
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horizontal <- FALSE
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} else {
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type <- "line"
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ds <- data.frame(x = NA, y = NA)
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horizontal <- FALSE
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}
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apexcharter::apex(
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ds,
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apexcharter::aes(x, y),
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type = type,
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auto_update = TRUE
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) |>
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apexcharter::ax_chart(sparkline = list(enabled = TRUE)) |>
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apexcharter::ax_plotOptions(
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boxPlot = apexcharter::boxplot_opts(color.upper = color.sec, color.lower = color.main),
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bar = apexcharter::bar_opts(horizontal = horizontal)
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) |>
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apexcharter::ax_colors(
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c(color.main, color.sec)
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)
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}
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)
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toastui::grid_columns(
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grid = out,
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columns = column,
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minWidth = 200
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)
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}
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#' Create a data overview data.frame ready for sparklines
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#'
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#' @param data data
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#'
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#' @returns data.frame
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#' @export
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#'
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#' @examples
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#' mtcars |> overview_vars()
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overview_vars <- function(data) {
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data <- as.data.frame(data)
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dplyr::tibble(
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class = get_classes(data),
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name = names(data),
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n_missing = unname(colSums(is.na(data))),
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p_complete = 1 - n_missing / nrow(data),
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n_unique = get_n_unique(data),
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vals = as.list(data)
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)
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}
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#' Create a data overview datagrid
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#'
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#' @param data data
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#'
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#' @returns datagrid
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#' @export
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#'
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#' @examples
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#' mtcars |>
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#' overview_vars() |>
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#' create_overview_datagrid()
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create_overview_datagrid <- function(data) {
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# browser()
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gridTheme <- getOption("datagrid.theme")
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if (length(gridTheme) < 1) {
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datamods:::apply_grid_theme()
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}
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on.exit(toastui::reset_grid_theme())
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col.names <- names(data)
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std_names <- c(
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"Name" = "name",
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"Class" = "class",
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"Missing" = "n_missing",
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"Complete" = "p_complete",
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"Unique" = "n_unique",
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"Plot" = "vals"
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)
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headers <- lapply(col.names, \(.x){
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if (.x %in% std_names) {
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names(std_names)[match(.x, std_names)]
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} else {
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.x
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}
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}) |> unlist()
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grid <- toastui::datagrid(
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data = data,
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theme = "default",
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colwidths = "auto"
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)
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grid <- toastui::grid_columns(
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grid = grid,
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columns = col.names,
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header = headers,
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resizable = TRUE,
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width = 80
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)
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grid <- add_class_icon(
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grid = grid,
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column = "class"
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)
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# grid <- toastui::grid_format(
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# grid = grid,
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# "p_complete",
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# formatter = toastui::JS("function(obj) {return (obj.value*100).toFixed(0) + '%';}")
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# )
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return(grid)
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}
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#' Convert class grid column to icon
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#'
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#' @param grid grid
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#' @param column column
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#'
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#' @returns datagrid
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#' @export
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#'
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#' @examples
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add_class_icon <- function(grid, column = "class") {
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out <- toastui::grid_format(
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grid = grid,
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column = column,
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formatter = function(value) {
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lapply(
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X = value,
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FUN = function(x) {
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if (identical(x, "numeric")) {
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shiny::icon("chart-line")
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} else if (identical(x, "factor")) {
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shiny::icon("chart-column")
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} else if (identical(x, "integer")) {
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shiny::icon("arrow-down-1-9")
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} else if (identical(x, "character")) {
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shiny::icon("arrow-down-a-z")
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} else if (any(c("Date", "POSIXct", "POSIXt") %in% x)) {
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shiny::icon("calendar-days")
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} else if ("hms" %in% x) {
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shiny::icon("clock")
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} else {
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shiny::icon("table")
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}
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}
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)
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}
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)
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toastui::grid_columns(
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grid = out,
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header = NULL,
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columns = column,
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width = 60
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)
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}
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@ -1,125 +1,125 @@
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#' #' Shiny UI module to load a data file
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#' #'
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#' #' @param id id
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#' #'
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#' #' @return shiny UI
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#' #' @export
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#' #'
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#' m_datafileUI <- function(id) {
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#' ns <- shiny::NS(id)
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#' shiny::tagList(
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#' shiny::fileInput(
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#' inputId = ns("file"),
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#' label = "Upload a file",
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#' multiple = FALSE,
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#' accept = c(
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#' ".csv",
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#' ".xlsx",
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#' ".xls",
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#' ".dta",
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#' ".ods",
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#' ".rds"
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#' )
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#' ),
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#' shiny::h4("Parameter specifications"),
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#' shiny::helpText(shiny::em("Select the desired variables and press 'Submit'")),
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#' shiny::uiOutput(ns("include_vars")),
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#' DT::DTOutput(ns("data_input")),
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#' shiny::actionButton(ns("submit"), "Submit")
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#' )
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#' }
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#' Shiny UI module to load a data file
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#'
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#' m_datafileServer <- function(id, output.format = "df") {
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#' shiny::moduleServer(id, function(input, output, session, ...) {
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#' ns <- shiny::NS(id)
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#' ds <- shiny::reactive({
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#' REDCapCAST::read_input(input$file$datapath) |> REDCapCAST::parse_data()
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#' })
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#' @param id id
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#'
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#' output$include_vars <- shiny::renderUI({
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#' shiny::req(input$file)
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#' shiny::selectizeInput(
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#' inputId = ns("include_vars"),
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#' selected = NULL,
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#' label = "Covariables to include",
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#' choices = colnames(ds()),
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#' multiple = TRUE
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#' )
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#' })
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#' @return shiny UI
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#' @export
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#'
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#' base_vars <- shiny::reactive({
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#' if (is.null(input$include_vars)) {
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#' out <- colnames(ds())
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#' } else {
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#' out <- input$include_vars
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#' }
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#' out
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#' })
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#'
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#' output$data_input <-
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#' DT::renderDT({
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#' shiny::req(input$file)
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#' ds()[base_vars()]
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#' })
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#'
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#' shiny::eventReactive(input$submit, {
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#' # shiny::req(input$file)
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#'
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#' data <- shiny::isolate({
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#' ds()[base_vars()]
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#' })
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#'
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#' file_export(data,
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#' output.format = output.format,
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#' tools::file_path_sans_ext(input$file$name)
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#' )
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#' })
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#' })
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#' }
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#'
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#'
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#'
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#'
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#'
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#' file_app <- function() {
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#' ui <- shiny::fluidPage(
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#' m_datafileUI("data"),
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#' # DT::DTOutput(outputId = "redcap_prev")
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#' toastui::datagridOutput2(outputId = "redcap_prev")
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#' )
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#' server <- function(input, output, session) {
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#' m_datafileServer("data", output.format = "list")
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#' }
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#' shiny::shinyApp(ui, server)
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#' }
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#'
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#' file_app()
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#'
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#' tdm_data_upload <- teal::teal_data_module(
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#' ui <- function(id) {
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#' shiny::fluidPage(
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#' m_datafileUI(id)
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#' )
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#' },
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#' server = function(id) {
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#' m_datafileServer(id, output.format = "teal")
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#' }
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#' )
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#'
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#' tdm_data_read <- teal::teal_data_module(
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#' ui <- function(id) {
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#' shiny::fluidPage(
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#' m_redcap_readUI(id = "redcap")
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#' )
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#' },
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#' server = function(id) {
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#' moduleServer(
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#' id,
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#' function(input, output, session) {
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#' ns <- session$ns
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#'
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#' m_redcap_readServer(id = "redcap", output.format = "teal")
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#' }
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#' )
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#' }
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#' )
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m_datafileUI <- function(id) {
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ns <- shiny::NS(id)
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shiny::tagList(
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shiny::fileInput(
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inputId = ns("file"),
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label = "Upload a file",
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multiple = FALSE,
|
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accept = c(
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".csv",
|
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".xlsx",
|
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".xls",
|
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".dta",
|
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".ods",
|
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".rds"
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)
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),
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shiny::h4("Parameter specifications"),
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shiny::helpText(shiny::em("Select the desired variables and press 'Submit'")),
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shiny::uiOutput(ns("include_vars")),
|
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DT::DTOutput(ns("data_input")),
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shiny::actionButton(ns("submit"), "Submit")
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)
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}
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m_datafileServer <- function(id, output.format = "df") {
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shiny::moduleServer(id, function(input, output, session, ...) {
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ns <- shiny::NS(id)
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ds <- shiny::reactive({
|
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REDCapCAST::read_input(input$file$datapath) |> REDCapCAST::parse_data()
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})
|
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|
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output$include_vars <- shiny::renderUI({
|
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shiny::req(input$file)
|
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shiny::selectizeInput(
|
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inputId = ns("include_vars"),
|
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selected = NULL,
|
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label = "Covariables to include",
|
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choices = colnames(ds()),
|
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multiple = TRUE
|
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)
|
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})
|
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|
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base_vars <- shiny::reactive({
|
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if (is.null(input$include_vars)) {
|
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out <- colnames(ds())
|
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} else {
|
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out <- input$include_vars
|
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}
|
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out
|
||||
})
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|
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output$data_input <-
|
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DT::renderDT({
|
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shiny::req(input$file)
|
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ds()[base_vars()]
|
||||
})
|
||||
|
||||
shiny::eventReactive(input$submit, {
|
||||
# shiny::req(input$file)
|
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|
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data <- shiny::isolate({
|
||||
ds()[base_vars()]
|
||||
})
|
||||
|
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file_export(data,
|
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output.format = output.format,
|
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tools::file_path_sans_ext(input$file$name)
|
||||
)
|
||||
})
|
||||
})
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
file_app <- function() {
|
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ui <- shiny::fluidPage(
|
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m_datafileUI("data"),
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# DT::DTOutput(outputId = "redcap_prev")
|
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toastui::datagridOutput2(outputId = "redcap_prev")
|
||||
)
|
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server <- function(input, output, session) {
|
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m_datafileServer("data", output.format = "list")
|
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}
|
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shiny::shinyApp(ui, server)
|
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}
|
||||
|
||||
file_app()
|
||||
|
||||
tdm_data_upload <- teal::teal_data_module(
|
||||
ui <- function(id) {
|
||||
shiny::fluidPage(
|
||||
m_datafileUI(id)
|
||||
)
|
||||
},
|
||||
server = function(id) {
|
||||
m_datafileServer(id, output.format = "teal")
|
||||
}
|
||||
)
|
||||
|
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tdm_data_read <- teal::teal_data_module(
|
||||
ui <- function(id) {
|
||||
shiny::fluidPage(
|
||||
m_redcap_readUI(id = "redcap")
|
||||
)
|
||||
},
|
||||
server = function(id) {
|
||||
moduleServer(
|
||||
id,
|
||||
function(input, output, session) {
|
||||
ns <- session$ns
|
||||
|
||||
m_redcap_readServer(id = "redcap", output.format = "teal")
|
||||
}
|
||||
)
|
||||
}
|
||||
)
|
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|
|
|
|||
38
R/helpers.R
38
R/helpers.R
|
|
@ -148,7 +148,7 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
|
|||
teal_data(),
|
||||
{
|
||||
assign(name, value |>
|
||||
dplyr::bind_cols() |>
|
||||
dplyr::bind_cols(.name_repair = "unique_quiet") |>
|
||||
default_parsing())
|
||||
},
|
||||
value = data,
|
||||
|
|
@ -185,8 +185,42 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
|
|||
#' default_parsing() |>
|
||||
#' str()
|
||||
default_parsing <- function(data) {
|
||||
data |>
|
||||
name_labels <- lapply(data,\(.x) REDCapCAST::get_attr(.x,attr = "label"))
|
||||
|
||||
out <- data |>
|
||||
REDCapCAST::parse_data() |>
|
||||
REDCapCAST::as_factor() |>
|
||||
REDCapCAST::numchar2fct()
|
||||
|
||||
purrr::map2(out,name_labels,\(.x,.l){
|
||||
if (!(is.na(.l) | .l=="")) {
|
||||
REDCapCAST::set_attr(.x, .l, attr = "label")
|
||||
} else {
|
||||
attr(x = .x, which = "label") <- NULL
|
||||
.x
|
||||
}
|
||||
# REDCapCAST::set_attr(data = .x, label = .l,attr = "label", overwrite = FALSE)
|
||||
}) |> dplyr::bind_cols()
|
||||
}
|
||||
|
||||
#' Remove NA labels
|
||||
#'
|
||||
#' @param data data
|
||||
#'
|
||||
#' @returns data.frame
|
||||
#' @export
|
||||
#'
|
||||
#' @examples
|
||||
#' ds <- mtcars |> lapply(\(.x) REDCapCAST::set_attr(.x,label=NA,attr = "label"))
|
||||
#' ds |> remove_na_attr() |> str()
|
||||
remove_na_attr <- function(data,attr="label"){
|
||||
out <- data |> lapply(\(.x){
|
||||
ls <- REDCapCAST::get_attr(data = .x,attr = attr)
|
||||
if (is.na(ls) | ls == ""){
|
||||
attr(x = .x, which = attr) <- NULL
|
||||
}
|
||||
.x
|
||||
})
|
||||
|
||||
dplyr::bind_cols(out)
|
||||
}
|
||||
|
|
|
|||
|
|
@ -10,8 +10,8 @@
|
|||
m_redcap_readUI <- function(id, include_title = TRUE) {
|
||||
ns <- shiny::NS(id)
|
||||
|
||||
server_ui <- shiny::column(
|
||||
width = 6,
|
||||
server_ui <- shiny::tagList(
|
||||
# width = 6,
|
||||
shiny::tags$h4("REDCap server information"),
|
||||
shiny::textInput(
|
||||
inputId = ns("uri"),
|
||||
|
|
@ -27,8 +27,8 @@ m_redcap_readUI <- function(id, include_title = TRUE) {
|
|||
|
||||
|
||||
params_ui <-
|
||||
shiny::column(
|
||||
width = 6,
|
||||
shiny::tagList(
|
||||
# width = 6,
|
||||
shiny::tags$h4("Data import parameters"),
|
||||
shiny::helpText("Options here will show, when API and uri are typed"),
|
||||
shiny::uiOutput(outputId = ns("fields")),
|
||||
|
|
@ -63,9 +63,14 @@ m_redcap_readUI <- function(id, include_title = TRUE) {
|
|||
|
||||
shiny::fluidPage(
|
||||
if (include_title) shiny::tags$h3("Import data from REDCap"),
|
||||
fluidRow(
|
||||
bslib::layout_columns(
|
||||
server_ui,
|
||||
params_ui),
|
||||
params_ui,
|
||||
col_widths = bslib::breakpoints(
|
||||
sm = c(12, 12),
|
||||
md = c(12, 12)
|
||||
)
|
||||
),
|
||||
shiny::column(
|
||||
width = 12,
|
||||
# shiny::actionButton(inputId = ns("import"), label = "Import"),
|
||||
|
|
@ -270,7 +275,6 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
|
|||
#'
|
||||
#' @rdname redcap_read_shiny_module
|
||||
tdm_redcap_read <- teal::teal_data_module(
|
||||
|
||||
ui <- function(id) {
|
||||
shiny::fluidPage(
|
||||
m_redcap_readUI(id)
|
||||
|
|
@ -305,7 +309,7 @@ redcap_app <- function() {
|
|||
)
|
||||
)
|
||||
server <- function(input, output, session) {
|
||||
data_val <- shiny::reactiveValues(data=NULL)
|
||||
data_val <- shiny::reactiveValues(data = NULL)
|
||||
|
||||
ds <- m_redcap_readServer("data", output.format = "df")
|
||||
# output$redcap_prev <- DT::renderDT(
|
||||
|
|
@ -329,7 +333,8 @@ redcap_app <- function() {
|
|||
|
||||
filtered_data <- IDEAFilter::IDEAFilter("data_filter",
|
||||
data = ds,
|
||||
verbose = FALSE)
|
||||
verbose = FALSE
|
||||
)
|
||||
|
||||
# filtered_data <- shiny::reactive({
|
||||
# IDEAFilter::IDEAFilter("data_filter",
|
||||
|
|
|
|||
|
|
@ -71,7 +71,7 @@ regression_model <- function(data,
|
|||
.x
|
||||
}
|
||||
}) |>
|
||||
dplyr::bind_cols()
|
||||
dplyr::bind_cols(.name_repair = "unique_quiet")
|
||||
|
||||
if (is.null(fun)) auto.mode <- TRUE
|
||||
|
||||
|
|
|
|||
34
R/sparkline_h_minimal.R
Normal file
34
R/sparkline_h_minimal.R
Normal file
|
|
@ -0,0 +1,34 @@
|
|||
# dependencies
|
||||
library(apexcharter)
|
||||
library(toastui)
|
||||
|
||||
spark_data <- mtcars |>
|
||||
(\(.x){
|
||||
dplyr::tibble(
|
||||
name = names(.x),
|
||||
vals = as.list(.x)
|
||||
)
|
||||
})()
|
||||
|
||||
ui <- fluidPage(
|
||||
toastui::datagridOutput("tbl")
|
||||
)
|
||||
|
||||
server <- function(input, output) {
|
||||
output$tbl <- toastui::renderDatagrid(
|
||||
spark_data |>
|
||||
toastui::datagrid() |>
|
||||
toastui::grid_sparkline(
|
||||
column = "vals",
|
||||
renderer = function(data) {
|
||||
apex(data.frame(x = 1, y = data), aes(x, y), type = "box") |>
|
||||
ax_chart(sparkline = list(enabled = TRUE)) |>
|
||||
ax_plotOptions(
|
||||
bar = bar_opts(horizontal=TRUE)
|
||||
)
|
||||
}
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
shinyApp(ui = ui, server = server)
|
||||
707
R/update-variables-ext.R
Normal file
707
R/update-variables-ext.R
Normal file
|
|
@ -0,0 +1,707 @@
|
|||
library(data.table)
|
||||
library(rlang)
|
||||
|
||||
|
||||
#' Select, rename and convert variables
|
||||
#'
|
||||
#' @param id Module id. See [shiny::moduleServer()].
|
||||
#' @param title Module's title, if `TRUE` use the default title,
|
||||
#' use \code{NULL} for no title or a `shiny.tag` for a custom one.
|
||||
#'
|
||||
#' @return A [shiny::reactive()] function returning the updated data.
|
||||
#' @export
|
||||
#'
|
||||
#' @name update-variables
|
||||
#'
|
||||
#' @example examples/variables.R
|
||||
update_variables_ui <- function(id, title = TRUE) {
|
||||
ns <- NS(id)
|
||||
if (isTRUE(title)) {
|
||||
title <- htmltools::tags$h4(
|
||||
i18n("Update & select variables"),
|
||||
class = "datamods-title"
|
||||
)
|
||||
}
|
||||
htmltools::tags$div(
|
||||
class = "datamods-update",
|
||||
shinyWidgets::html_dependency_pretty(),
|
||||
title,
|
||||
htmltools::tags$div(
|
||||
style = "min-height: 25px;",
|
||||
htmltools::tags$div(
|
||||
shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
|
||||
shiny::tagAppendAttributes(
|
||||
shinyWidgets::dropMenu(
|
||||
placement = "bottom-end",
|
||||
shiny::actionButton(
|
||||
inputId = ns("settings"),
|
||||
label = phosphoricons::ph("gear"),
|
||||
class = "pull-right float-right"
|
||||
),
|
||||
shinyWidgets::textInputIcon(
|
||||
inputId = ns("format"),
|
||||
label = i18n("Date format:"),
|
||||
value = "%Y-%m-%d",
|
||||
icon = list(phosphoricons::ph("clock"))
|
||||
),
|
||||
shinyWidgets::textInputIcon(
|
||||
inputId = ns("origin"),
|
||||
label = i18n("Date to use as origin to convert date/datetime:"),
|
||||
value = "1970-01-01",
|
||||
icon = list(phosphoricons::ph("calendar"))
|
||||
),
|
||||
shinyWidgets::textInputIcon(
|
||||
inputId = ns("dec"),
|
||||
label = i18n("Decimal separator:"),
|
||||
value = ".",
|
||||
icon = list("0.00")
|
||||
)
|
||||
),
|
||||
style = "display: inline;"
|
||||
)
|
||||
),
|
||||
htmltools::tags$br(),
|
||||
toastui::datagridOutput(outputId = ns("table"))
|
||||
),
|
||||
htmltools::tags$br(),
|
||||
htmltools::tags$div(
|
||||
id = ns("update-placeholder"),
|
||||
shinyWidgets::alert(
|
||||
id = ns("update-result"),
|
||||
status = "info",
|
||||
phosphoricons::ph("info"),
|
||||
datamods::i18n(paste(
|
||||
"Select, rename and convert variables in table above,",
|
||||
"then apply changes by clicking button below."
|
||||
))
|
||||
)
|
||||
),
|
||||
shiny::actionButton(
|
||||
inputId = ns("validate"),
|
||||
label = htmltools::tagList(
|
||||
phosphoricons::ph("arrow-circle-right", title = i18n("Apply changes")),
|
||||
datamods::i18n("Apply changes")
|
||||
),
|
||||
width = "100%"
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
#' @export
|
||||
#'
|
||||
#' @param id Module's ID
|
||||
#' @param data a \code{data.frame} or a \code{reactive} function returning a \code{data.frame}.
|
||||
#' @param height Height for the table.
|
||||
#' @param return_data_on_init Return initial data when module is called.
|
||||
#' @param try_silent logical: should the report of error messages be suppressed?
|
||||
#'
|
||||
#' @rdname update-variables
|
||||
#'
|
||||
update_variables_server <- function(id,
|
||||
data,
|
||||
height = NULL,
|
||||
return_data_on_init = FALSE,
|
||||
try_silent = FALSE) {
|
||||
shiny::moduleServer(
|
||||
id = id,
|
||||
module = function(input, output, session) {
|
||||
ns <- session$ns
|
||||
updated_data <- shiny::reactiveValues(x = NULL)
|
||||
|
||||
data_r <- shiny::reactive({
|
||||
if (shiny::is.reactive(data)) {
|
||||
data()
|
||||
} else {
|
||||
data
|
||||
}
|
||||
})
|
||||
|
||||
output$data_info <- shiny::renderUI({
|
||||
shiny::req(data_r())
|
||||
data <- data_r()
|
||||
sprintf(i18n("Data has %s observations and %s variables."), nrow(data), ncol(data))
|
||||
})
|
||||
|
||||
variables_r <- shiny::reactive({
|
||||
shiny::validate(
|
||||
shiny::need(data(), i18n("No data to display."))
|
||||
)
|
||||
data <- data_r()
|
||||
if (isTRUE(return_data_on_init)) {
|
||||
updated_data$x <- data
|
||||
} else {
|
||||
updated_data$x <- NULL
|
||||
}
|
||||
summary_vars(data)
|
||||
})
|
||||
|
||||
output$table <- toastui::renderDatagrid({
|
||||
shiny::req(variables_r())
|
||||
# browser()
|
||||
variables <- variables_r()
|
||||
|
||||
# variables <- variables |>
|
||||
# dplyr::mutate(vals=as.list(dplyr::as_tibble(data_r())))
|
||||
|
||||
# variables <- variables |>
|
||||
# dplyr::mutate(n_id=seq_len(nrow(variables)))
|
||||
|
||||
update_variables_datagrid(
|
||||
variables,
|
||||
height = height,
|
||||
selectionId = ns("row_selected"),
|
||||
buttonId = "validate"
|
||||
)
|
||||
})
|
||||
|
||||
shiny::observeEvent(input$validate,
|
||||
{
|
||||
updated_data$list_rename <- NULL
|
||||
updated_data$list_select <- NULL
|
||||
updated_data$list_mutate <- NULL
|
||||
updated_data$list_relabel <- NULL
|
||||
data <- data_r()
|
||||
new_selections <- input$row_selected
|
||||
if (length(new_selections) < 1) {
|
||||
new_selections <- seq_along(data)
|
||||
}
|
||||
# browser()
|
||||
data_inputs <- data.table::as.data.table(input$table_data)
|
||||
data.table::setorderv(data_inputs, "rowKey")
|
||||
|
||||
old_names <- data_inputs$name
|
||||
new_names <- data_inputs$name_toset
|
||||
new_names[new_names == "New name"] <- NA
|
||||
new_names[is.na(new_names)] <- old_names[is.na(new_names)]
|
||||
new_names[new_names == ""] <- old_names[new_names == ""]
|
||||
|
||||
old_label <- data_inputs$label
|
||||
new_label <- data_inputs$label_toset
|
||||
new_label[new_label == "New label"] <- ""
|
||||
new_label[is.na(new_label)] <- old_label[is.na(new_label)]
|
||||
new_label[new_label == ""] <- old_label[new_label == ""]
|
||||
|
||||
new_classes <- data_inputs$class_toset
|
||||
new_classes[new_classes == "Select"] <- NA
|
||||
|
||||
# browser()
|
||||
data_sv <- variables_r()
|
||||
vars_to_change <- get_vars_to_convert(data_sv, setNames(as.list(new_classes), old_names))
|
||||
|
||||
res_update <- try(
|
||||
{
|
||||
# convert
|
||||
if (nrow(vars_to_change) > 0) {
|
||||
data <- convert_to(
|
||||
data = data,
|
||||
variable = vars_to_change$name,
|
||||
new_class = vars_to_change$class_to_set,
|
||||
origin = input$origin,
|
||||
format = input$format,
|
||||
dec = input$dec
|
||||
)
|
||||
}
|
||||
list_mutate <- attr(data, "code_03_convert")
|
||||
|
||||
# rename
|
||||
list_rename <- setNames(
|
||||
as.list(old_names),
|
||||
unlist(new_names, use.names = FALSE)
|
||||
)
|
||||
list_rename <- list_rename[names(list_rename) != unlist(list_rename, use.names = FALSE)]
|
||||
names(data) <- unlist(new_names, use.names = FALSE)
|
||||
|
||||
# relabel
|
||||
list_relabel <- as.list(new_label)
|
||||
data <- purrr::map2(
|
||||
data, list_relabel,
|
||||
\(.data, .label){
|
||||
if (!(is.na(.label) | .label == "")) {
|
||||
REDCapCAST::set_attr(.data, .label, attr = "label")
|
||||
} else {
|
||||
attr(x = .data, which = "label") <- NULL
|
||||
.data
|
||||
}
|
||||
}
|
||||
) |> dplyr::bind_cols(.name_repair = "unique_quiet")
|
||||
|
||||
# select
|
||||
list_select <- setdiff(names(data), names(data)[new_selections])
|
||||
data <- data[, new_selections, drop = FALSE]
|
||||
},
|
||||
silent = try_silent
|
||||
)
|
||||
|
||||
if (inherits(res_update, "try-error")) {
|
||||
datamods:::insert_error(selector = "update")
|
||||
} else {
|
||||
datamods:::insert_alert(
|
||||
selector = ns("update"),
|
||||
status = "success",
|
||||
tags$b(phosphoricons::ph("check"), datamods::i18n("Data successfully updated!"))
|
||||
)
|
||||
updated_data$x <- data
|
||||
updated_data$list_rename <- list_rename
|
||||
updated_data$list_select <- list_select
|
||||
updated_data$list_mutate <- list_mutate
|
||||
updated_data$list_relabel <- list_relabel
|
||||
}
|
||||
},
|
||||
ignoreNULL = TRUE,
|
||||
ignoreInit = TRUE
|
||||
)
|
||||
|
||||
return(shiny::reactive({
|
||||
data <- updated_data$x
|
||||
code <- list()
|
||||
if (!is.null(data) && shiny::isTruthy(updated_data$list_mutate) && length(updated_data$list_mutate) > 0) {
|
||||
code <- c(code, list(rlang::call2("mutate", !!!updated_data$list_mutate)))
|
||||
}
|
||||
if (!is.null(data) && shiny::isTruthy(updated_data$list_rename) && length(updated_data$list_rename) > 0) {
|
||||
code <- c(code, list(rlang::call2("rename", !!!updated_data$list_rename)))
|
||||
}
|
||||
if (!is.null(data) && shiny::isTruthy(updated_data$list_select) && length(updated_data$list_select) > 0) {
|
||||
code <- c(code, list(rlang::expr(select(-any_of(c(!!!updated_data$list_select))))))
|
||||
}
|
||||
if (!is.null(data) && shiny::isTruthy(updated_data$list_relabel) && length(updated_data$list_relabel) > 0) {
|
||||
code <- c(code, list(rlang::call2("purrr::map2(list_relabel,
|
||||
function(.data,.label){
|
||||
REDCapCAST::set_attr(.data,.label,attr = 'label')
|
||||
}) |> dplyr::bind_cols(.name_repair = 'unique_quiet')")))
|
||||
}
|
||||
if (length(code) > 0) {
|
||||
attr(data, "code") <- Reduce(
|
||||
f = function(x, y) rlang::expr(!!x %>% !!y),
|
||||
x = code
|
||||
)
|
||||
}
|
||||
return(data)
|
||||
}))
|
||||
}
|
||||
)
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# utils -------------------------------------------------------------------
|
||||
|
||||
|
||||
#' Get variables classes from a \code{data.frame}
|
||||
#'
|
||||
#' @param data a \code{data.frame}
|
||||
#'
|
||||
#' @return a \code{character} vector as same length as number of variables
|
||||
#' @noRd
|
||||
#'
|
||||
#' @examples
|
||||
#'
|
||||
#' get_classes(mtcars)
|
||||
get_classes <- function(data) {
|
||||
classes <- lapply(
|
||||
X = data,
|
||||
FUN = function(x) {
|
||||
paste(class(x), collapse = ", ")
|
||||
}
|
||||
)
|
||||
unlist(classes, use.names = FALSE)
|
||||
}
|
||||
|
||||
|
||||
#' Get count of unique values in variables of \code{data.frame}
|
||||
#'
|
||||
#' @param data a \code{data.frame}
|
||||
#'
|
||||
#' @return a \code{numeric} vector as same length as number of variables
|
||||
#' @noRd
|
||||
#'
|
||||
#'
|
||||
#' @examples
|
||||
#' get_n_unique(mtcars)
|
||||
get_n_unique <- function(data) {
|
||||
u <- lapply(data, FUN = function(x) {
|
||||
if (is.atomic(x)) {
|
||||
data.table::uniqueN(x)
|
||||
} else {
|
||||
NA_integer_
|
||||
}
|
||||
})
|
||||
unlist(u, use.names = FALSE)
|
||||
}
|
||||
|
||||
|
||||
|
||||
#' Add padding 0 to a vector
|
||||
#'
|
||||
#' @param x a \code{vector}
|
||||
#'
|
||||
#' @return a \code{character} vector
|
||||
#' @noRd
|
||||
#'
|
||||
#' @examples
|
||||
#'
|
||||
#' pad0(1:10)
|
||||
#' pad0(c(1, 15, 150, NA))
|
||||
pad0 <- function(x) {
|
||||
NAs <- which(is.na(x))
|
||||
x <- formatC(x, width = max(nchar(as.character(x)), na.rm = TRUE), flag = "0")
|
||||
x[NAs] <- NA
|
||||
x
|
||||
}
|
||||
|
||||
#' Variables summary
|
||||
#'
|
||||
#' @param data a \code{data.frame}
|
||||
#'
|
||||
#' @return a \code{data.frame}
|
||||
#' @noRd
|
||||
#'
|
||||
#' @examples
|
||||
#'
|
||||
#' summary_vars(iris)
|
||||
#' summary_vars(mtcars)
|
||||
summary_vars <- function(data) {
|
||||
data <- as.data.frame(data)
|
||||
datsum <- dplyr::tibble(
|
||||
name = names(data),
|
||||
label = lapply(data, \(.x) REDCapCAST::get_attr(.x, "label")) |> unlist(),
|
||||
class = get_classes(data),
|
||||
# n_missing = unname(colSums(is.na(data))),
|
||||
# p_complete = 1 - n_missing / nrow(data),
|
||||
n_unique = get_n_unique(data)
|
||||
)
|
||||
|
||||
datsum
|
||||
}
|
||||
|
||||
add_var_toset <- function(data, var_name, default = "") {
|
||||
datanames <- names(data)
|
||||
datanames <- append(
|
||||
x = datanames,
|
||||
values = paste0(var_name, "_toset"),
|
||||
after = which(datanames == var_name)
|
||||
)
|
||||
data[[paste0(var_name, "_toset")]] <- default
|
||||
data[, datanames]
|
||||
}
|
||||
|
||||
#' @importFrom toastui datagrid grid_columns grid_format grid_style_column
|
||||
#' grid_style_column grid_editor grid_editor_opts grid_selection_row
|
||||
#' @examples
|
||||
#' mtcars |>
|
||||
#' summary_vars() |>
|
||||
#' update_variables_datagrid()
|
||||
#'
|
||||
update_variables_datagrid <- function(data, height = NULL, selectionId = NULL, buttonId = NULL) {
|
||||
# browser()
|
||||
data <- add_var_toset(data, "name", "New name")
|
||||
data <- add_var_toset(data, "class", "Select")
|
||||
data <- add_var_toset(data, "label", "New label")
|
||||
|
||||
gridTheme <- getOption("datagrid.theme")
|
||||
if (length(gridTheme) < 1) {
|
||||
datamods:::apply_grid_theme()
|
||||
}
|
||||
on.exit(toastui::reset_grid_theme())
|
||||
|
||||
col.names <- names(data)
|
||||
|
||||
std_names <- c(
|
||||
"name", "name_toset", "label", "label_toset", "class", "class_toset", "n_missing", "p_complete", "n_unique"
|
||||
) |>
|
||||
setNames(c(
|
||||
"Name", "New name", "Label", "New label", "Class", "New class", "Missing", "Complete", "Unique"
|
||||
))
|
||||
|
||||
headers <- lapply(col.names, \(.x){
|
||||
if (.x %in% std_names) {
|
||||
names(std_names)[match(.x, std_names)]
|
||||
} else {
|
||||
.x
|
||||
}
|
||||
}) |> unlist()
|
||||
|
||||
grid <- toastui::datagrid(
|
||||
data = data,
|
||||
theme = "default",
|
||||
colwidths = NULL
|
||||
)
|
||||
grid <- toastui::grid_columns(
|
||||
grid = grid,
|
||||
columns = col.names,
|
||||
header = headers,
|
||||
minWidth = 100
|
||||
)
|
||||
|
||||
# grid <- toastui::grid_format(
|
||||
# grid = grid,
|
||||
# "p_complete",
|
||||
# formatter = toastui::JS("function(obj) {return (obj.value*100).toFixed(0) + '%';}")
|
||||
# )
|
||||
grid <- toastui::grid_style_column(
|
||||
grid = grid,
|
||||
column = "name_toset",
|
||||
fontStyle = "italic"
|
||||
)
|
||||
grid <- toastui::grid_style_column(
|
||||
grid = grid,
|
||||
column = "label_toset",
|
||||
fontStyle = "italic"
|
||||
)
|
||||
grid <- toastui::grid_style_column(
|
||||
grid = grid,
|
||||
column = "class_toset",
|
||||
fontStyle = "italic"
|
||||
)
|
||||
|
||||
# grid <- toastui::grid_columns(
|
||||
# grid = grid,
|
||||
# columns = "name_toset",
|
||||
# editor = list(type = "text"),
|
||||
# validation = toastui::validateOpts()
|
||||
# )
|
||||
#
|
||||
# grid <- toastui::grid_columns(
|
||||
# grid = grid,
|
||||
# columns = "label_toset",
|
||||
# editor = list(type = "text"),
|
||||
# validation = toastui::validateOpts()
|
||||
# )
|
||||
#
|
||||
# grid <- toastui::grid_columns(
|
||||
# grid = grid,
|
||||
# columns = "class_toset",
|
||||
# editor = list(
|
||||
# type = "radio",
|
||||
# options = list(
|
||||
# instantApply = TRUE,
|
||||
# listItems = lapply(
|
||||
# X = c("Select", "character", "factor", "numeric", "integer", "date", "datetime", "hms"),
|
||||
# FUN = function(x) {
|
||||
# list(text = x, value = x)
|
||||
# }
|
||||
# )
|
||||
# )
|
||||
# ),
|
||||
# validation = toastui::validateOpts()
|
||||
# )
|
||||
|
||||
grid <- toastui::grid_editor(
|
||||
grid = grid,
|
||||
column = "name_toset",
|
||||
type = "text"
|
||||
)
|
||||
grid <- toastui::grid_editor(
|
||||
grid = grid,
|
||||
column = "label_toset",
|
||||
type = "text"
|
||||
)
|
||||
grid <- toastui::grid_editor(
|
||||
grid = grid,
|
||||
column = "class_toset",
|
||||
type = "select",
|
||||
choices = c("Select new class", "character", "factor", "numeric", "integer", "date", "datetime", "hms")
|
||||
)
|
||||
grid <- toastui::grid_editor_opts(
|
||||
grid = grid,
|
||||
editingEvent = "click",
|
||||
actionButtonId = NULL,
|
||||
session = NULL
|
||||
)
|
||||
grid <- toastui::grid_selection_row(
|
||||
grid = grid,
|
||||
inputId = selectionId,
|
||||
type = "checkbox",
|
||||
return = "index"
|
||||
)
|
||||
|
||||
return(grid)
|
||||
}
|
||||
|
||||
|
||||
|
||||
#' Convert a variable to specific new class
|
||||
#'
|
||||
#' @param data A \code{data.frame}
|
||||
#' @param variable Name of the variable to convert
|
||||
#' @param new_class Class to set
|
||||
#' @param ... Other arguments passed on to methods.
|
||||
#'
|
||||
#' @return A \code{data.frame}
|
||||
#' @noRd
|
||||
#'
|
||||
#' @importFrom utils type.convert
|
||||
#' @importFrom rlang sym expr
|
||||
#'
|
||||
#' @examples
|
||||
#' dat <- data.frame(
|
||||
#' v1 = month.name,
|
||||
#' v2 = month.abb,
|
||||
#' v3 = 1:12,
|
||||
#' v4 = as.numeric(Sys.Date() + 0:11),
|
||||
#' v5 = as.character(Sys.Date() + 0:11),
|
||||
#' v6 = as.factor(c("a", "a", "b", "a", "b", "a", "a", "b", "a", "b", "b", "a")),
|
||||
#' v7 = as.character(11:22),
|
||||
#' stringsAsFactors = FALSE
|
||||
#' )
|
||||
#'
|
||||
#' str(dat)
|
||||
#'
|
||||
#' str(convert_to(dat, "v3", "character"))
|
||||
#' str(convert_to(dat, "v6", "character"))
|
||||
#' str(convert_to(dat, "v7", "numeric"))
|
||||
#' str(convert_to(dat, "v4", "date", origin = "1970-01-01"))
|
||||
#' str(convert_to(dat, "v5", "date"))
|
||||
#'
|
||||
#' str(convert_to(dat, c("v1", "v3"), c("factor", "character")))
|
||||
#'
|
||||
#' str(convert_to(dat, c("v1", "v3", "v4"), c("factor", "character", "date"), origin = "1970-01-01"))
|
||||
#'
|
||||
convert_to <- function(data,
|
||||
variable,
|
||||
new_class = c("character", "factor", "numeric", "integer", "date", "datetime", "hms"),
|
||||
...) {
|
||||
new_class <- match.arg(new_class, several.ok = TRUE)
|
||||
stopifnot(length(new_class) == length(variable))
|
||||
args <- list(...)
|
||||
if (length(variable) > 1) {
|
||||
for (i in seq_along(variable)) {
|
||||
data <- convert_to(data, variable[i], new_class[i], ...)
|
||||
}
|
||||
return(data)
|
||||
}
|
||||
if (identical(new_class, "character")) {
|
||||
data[[variable]] <- as.character(x = data[[variable]], ...)
|
||||
attr(data, "code_03_convert") <- c(
|
||||
attr(data, "code_03_convert"),
|
||||
setNames(list(expr(as.character(!!sym(variable)))), variable)
|
||||
)
|
||||
} else if (identical(new_class, "factor")) {
|
||||
data[[variable]] <- as.factor(x = data[[variable]])
|
||||
attr(data, "code_03_convert") <- c(
|
||||
attr(data, "code_03_convert"),
|
||||
setNames(list(expr(as.factor(!!sym(variable)))), variable)
|
||||
)
|
||||
} else if (identical(new_class, "numeric")) {
|
||||
data[[variable]] <- as.numeric(type.convert(data[[variable]], as.is = TRUE, ...))
|
||||
attr(data, "code_03_convert") <- c(
|
||||
attr(data, "code_03_convert"),
|
||||
setNames(list(expr(as.numeric(!!sym(variable)))), variable)
|
||||
)
|
||||
} else if (identical(new_class, "integer")) {
|
||||
data[[variable]] <- as.integer(x = data[[variable]], ...)
|
||||
attr(data, "code_03_convert") <- c(
|
||||
attr(data, "code_03_convert"),
|
||||
setNames(list(expr(as.integer(!!sym(variable)))), variable)
|
||||
)
|
||||
} else if (identical(new_class, "date")) {
|
||||
data[[variable]] <- as.Date(x = data[[variable]], ...)
|
||||
attr(data, "code_03_convert") <- c(
|
||||
attr(data, "code_03_convert"),
|
||||
setNames(list(expr(as.Date(!!sym(variable), origin = !!args$origin))), variable)
|
||||
)
|
||||
} else if (identical(new_class, "datetime")) {
|
||||
data[[variable]] <- as.POSIXct(x = data[[variable]], ...)
|
||||
attr(data, "code_03_convert") <- c(
|
||||
attr(data, "code_03_convert"),
|
||||
setNames(list(expr(as.POSIXct(!!sym(variable)))), variable)
|
||||
)
|
||||
} else if (identical(new_class, "hms")) {
|
||||
data[[variable]] <- hms::as_hms(x = data[[variable]])
|
||||
attr(data, "code_03_convert") <- c(
|
||||
attr(data, "code_03_convert"),
|
||||
setNames(list(expr(hms::as_hms(!!sym(variable)))), variable)
|
||||
)
|
||||
}
|
||||
return(data)
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
#' Get variable(s) to convert
|
||||
#'
|
||||
#' @param vars Output of [summary_vars()]
|
||||
#' @param classes_input List of inputs containing new classes
|
||||
#'
|
||||
#' @return a `data.table`.
|
||||
#' @noRd
|
||||
#'
|
||||
#' @importFrom data.table data.table as.data.table
|
||||
#'
|
||||
#' @examples
|
||||
#' # 2 variables to convert
|
||||
#' new_classes <- list(
|
||||
#' "Sepal.Length" = "numeric",
|
||||
#' "Sepal.Width" = "numeric",
|
||||
#' "Petal.Length" = "character",
|
||||
#' "Petal.Width" = "numeric",
|
||||
#' "Species" = "character"
|
||||
#' )
|
||||
#' get_vars_to_convert(summary_vars(iris), new_classes)
|
||||
#'
|
||||
#'
|
||||
#' # No changes
|
||||
#' new_classes <- list(
|
||||
#' "Sepal.Length" = "numeric",
|
||||
#' "Sepal.Width" = "numeric",
|
||||
#' "Petal.Length" = "numeric",
|
||||
#' "Petal.Width" = "numeric",
|
||||
#' "Species" = "factor"
|
||||
#' )
|
||||
#' get_vars_to_convert(summary_vars(iris), new_classes)
|
||||
#'
|
||||
#' # Not set = NA or ""
|
||||
#' new_classes <- list(
|
||||
#' "Sepal.Length" = NA,
|
||||
#' "Sepal.Width" = NA,
|
||||
#' "Petal.Length" = NA,
|
||||
#' "Petal.Width" = NA,
|
||||
#' "Species" = NA
|
||||
#' )
|
||||
#' get_vars_to_convert(summary_vars(iris), new_classes)
|
||||
#'
|
||||
#' # Set for one var
|
||||
#' new_classes <- list(
|
||||
#' "Sepal.Length" = "",
|
||||
#' "Sepal.Width" = "",
|
||||
#' "Petal.Length" = "",
|
||||
#' "Petal.Width" = "",
|
||||
#' "Species" = "character"
|
||||
#' )
|
||||
#' get_vars_to_convert(summary_vars(iris), new_classes)
|
||||
#'
|
||||
#' new_classes <- list(
|
||||
#' "mpg" = "character",
|
||||
#' "cyl" = "numeric",
|
||||
#' "disp" = "character",
|
||||
#' "hp" = "numeric",
|
||||
#' "drat" = "character",
|
||||
#' "wt" = "character",
|
||||
#' "qsec" = "numeric",
|
||||
#' "vs" = "character",
|
||||
#' "am" = "numeric",
|
||||
#' "gear" = "character",
|
||||
#' "carb" = "integer"
|
||||
#' )
|
||||
#' get_vars_to_convert(summary_vars(mtcars), new_classes)
|
||||
get_vars_to_convert <- function(vars, classes_input) {
|
||||
vars <- data.table::as.data.table(vars)
|
||||
classes_input <- data.table::data.table(
|
||||
name = names(classes_input),
|
||||
class_to_set = unlist(classes_input, use.names = FALSE),
|
||||
stringsAsFactors = FALSE
|
||||
)
|
||||
classes_input <- classes_input[!is.na(class_to_set) & class_to_set != ""]
|
||||
classes_df <- merge(x = vars, y = classes_input, by = "name")
|
||||
classes_df <- classes_df[!is.na(class_to_set)]
|
||||
classes_df[class != class_to_set]
|
||||
}
|
||||
|
||||
|
||||
File diff suppressed because it is too large
Load diff
|
|
@ -5,6 +5,6 @@ account: agdamsbo
|
|||
server: shinyapps.io
|
||||
hostUrl: https://api.shinyapps.io/v1
|
||||
appId: 13611288
|
||||
bundleId: 9546880
|
||||
bundleId: 9641114
|
||||
url: https://agdamsbo.shinyapps.io/freesearcheR/
|
||||
version: 1
|
||||
|
|
|
|||
|
|
@ -18,8 +18,10 @@ library(broom.helpers)
|
|||
library(easystats)
|
||||
library(patchwork)
|
||||
library(DHARMa)
|
||||
library(datamods)
|
||||
library(apexcharter)
|
||||
library(toastui)
|
||||
library(datamods)
|
||||
library(data.table)
|
||||
library(IDEAFilter)
|
||||
library(shinyWidgets)
|
||||
library(DT)
|
||||
|
|
@ -39,9 +41,9 @@ server <- function(input, output, session) {
|
|||
## everything else.
|
||||
files.to.keep <- list.files("www/")
|
||||
|
||||
output$docs_file <- renderUI({
|
||||
output$docs_file <- shiny::renderUI({
|
||||
# shiny::includeHTML("www/docs.html")
|
||||
HTML(readLines("www/docs.html"))
|
||||
shiny::HTML(readLines("www/docs.html"))
|
||||
})
|
||||
|
||||
##############################################################################
|
||||
|
|
@ -136,17 +138,35 @@ server <- function(input, output, session) {
|
|||
rv$data_original <- from_env$data()
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data modification section
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
######### Modifications
|
||||
|
||||
shiny::observeEvent(rv$data_original, rv$data <- rv$data_original |> default_parsing())
|
||||
shiny::observeEvent(input$data_reset, rv$data <- rv$data_original |> default_parsing())
|
||||
|
||||
######### Overview
|
||||
|
||||
output$tbl_overview <- toastui::renderDatagrid(
|
||||
data_filter() |>
|
||||
overview_vars() |>
|
||||
create_overview_datagrid()|>
|
||||
add_sparkline(
|
||||
column = "vals",
|
||||
color.main = "#2A004E",
|
||||
color.sec = "#C62300"
|
||||
)
|
||||
)
|
||||
|
||||
# data_summary_server(id = "data_summary",
|
||||
# data = data_filter())
|
||||
|
||||
######### Modifications
|
||||
|
||||
|
||||
## Using modified version of the datamods::cut_variable_server function
|
||||
## Further modifications are needed to have cut/bin options based on class of variable
|
||||
## Could be defined server-side
|
||||
|
|
@ -187,7 +207,8 @@ server <- function(input, output, session) {
|
|||
attr(rv$data, "code")
|
||||
})
|
||||
|
||||
updated_data <- datamods::update_variables_server(
|
||||
# updated_data <- datamods::update_variables_server(
|
||||
updated_data <- update_variables_server(
|
||||
id = "vars_update",
|
||||
data = reactive(rv$data),
|
||||
return_data_on_init = FALSE
|
||||
|
|
@ -201,7 +222,7 @@ server <- function(input, output, session) {
|
|||
str(rv$data)
|
||||
})
|
||||
|
||||
observeEvent(updated_data(), {
|
||||
shiny::observeEvent(updated_data(), {
|
||||
rv$data <- updated_data()
|
||||
})
|
||||
|
||||
|
|
@ -308,10 +329,6 @@ server <- function(input, output, session) {
|
|||
# gt::gt()
|
||||
# })
|
||||
|
||||
shiny::observeEvent(input$act_start, {
|
||||
bslib::nav_select(id = "main_panel", selected = "Modifications")
|
||||
})
|
||||
|
||||
shiny::observeEvent(
|
||||
{
|
||||
input$load
|
||||
|
|
@ -326,7 +343,8 @@ server <- function(input, output, session) {
|
|||
data <- data_filter() |>
|
||||
dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |>
|
||||
REDCapCAST::fct_drop.data.frame() |>
|
||||
factorize(vars = input$factor_vars)
|
||||
factorize(vars = input$factor_vars) |>
|
||||
remove_na_attr()
|
||||
|
||||
if (input$strat_var == "none") {
|
||||
by.var <- NULL
|
||||
|
|
@ -479,7 +497,22 @@ server <- function(input, output, session) {
|
|||
# )
|
||||
# })
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Page navigation
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
shiny::observeEvent(input$act_start, {
|
||||
bslib::nav_select(id = "main_panel", selected = "Modifications")
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Reactivity
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
output$uploaded <- shiny::reactive({
|
||||
if (is.null(rv$ds)) {
|
||||
|
|
@ -512,6 +545,12 @@ server <- function(input, output, session) {
|
|||
|
||||
# shiny::outputOptions(output, "has_input", suspendWhenHidden = FALSE)
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Downloads
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
# Could be rendered with other tables or should show progress
|
||||
# Investigate quarto render problems
|
||||
# On temp file handling: https://github.com/quarto-dev/quarto-cli/issues/3992
|
||||
|
|
@ -533,6 +572,26 @@ server <- function(input, output, session) {
|
|||
}
|
||||
)
|
||||
|
||||
output$data_modified <- downloadHandler(
|
||||
filename = shiny::reactive({
|
||||
paste0("modified_data.", input$data_type)
|
||||
}),
|
||||
content = function(file, type = input$data_type) {
|
||||
if (type == "rds"){
|
||||
readr::write_rds(rv$list$data,file = file)
|
||||
} else {
|
||||
haven::write_dta(as.data.frame(rv$list$data),path = file)
|
||||
}
|
||||
|
||||
}
|
||||
)
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Clearing the session on end
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
session$onSessionEnded(function() {
|
||||
cat("Session Ended\n")
|
||||
files <- list.files("www/")
|
||||
|
|
|
|||
|
|
@ -1,6 +1,16 @@
|
|||
# ns <- NS(id)
|
||||
|
||||
ui_elements <- list(
|
||||
##############################################################################
|
||||
#########
|
||||
######### Home panel
|
||||
#########
|
||||
##############################################################################
|
||||
"home" = bslib::nav_panel(
|
||||
title = "freesearcheR",
|
||||
shiny::markdown(readLines("www/intro.md")),
|
||||
icon = shiny::icon("home")
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
######### Import panel
|
||||
|
|
@ -8,9 +18,7 @@ ui_elements <- list(
|
|||
##############################################################################
|
||||
"import" = bslib::nav_panel(
|
||||
title = "Import",
|
||||
shiny::fluidRow(
|
||||
column(
|
||||
width = 6,
|
||||
shiny::tagList(
|
||||
shiny::h4("Choose your data source"),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "output.has_input=='yes'",
|
||||
|
|
@ -22,6 +30,7 @@ ui_elements <- list(
|
|||
# Input: Select a file ----
|
||||
shinyWidgets::radioGroupButtons(
|
||||
inputId = "source",
|
||||
selected = "env",
|
||||
# label = "Choice: ",
|
||||
choices = c(
|
||||
"File upload" = "file",
|
||||
|
|
@ -48,15 +57,6 @@ ui_elements <- list(
|
|||
shiny::conditionalPanel(
|
||||
condition = "input.source=='env'",
|
||||
import_globalenv_ui(id = "env", title = NULL)
|
||||
)
|
||||
|
||||
|
||||
# )
|
||||
),
|
||||
column(
|
||||
width = 6,
|
||||
shiny::markdown(readLines("www/intro.md"))
|
||||
)
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.source=='redcap'",
|
||||
|
|
@ -72,6 +72,7 @@ ui_elements <- list(
|
|||
shiny::helpText('After importing, hit "Start" or navigate to the desired tab.'),
|
||||
shiny::br(),
|
||||
shiny::br()
|
||||
)
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
|
|
@ -82,44 +83,21 @@ ui_elements <- list(
|
|||
# bslib::nav_panel_hidden(
|
||||
bslib::nav_panel(
|
||||
# value = "overview",
|
||||
title = "Modifications",
|
||||
title = "Data",
|
||||
bslib::navset_bar(
|
||||
fillable = TRUE,
|
||||
# bslib::nav_panel(
|
||||
# title = "Edit",
|
||||
# datamods::edit_data_ui(id = "edit_data")
|
||||
# ),
|
||||
# bslib::nav_panel(
|
||||
# title = "Overview",
|
||||
# DT::DTOutput(outputId = "table")
|
||||
# ),
|
||||
bslib::nav_panel(
|
||||
title = "Rename and select",
|
||||
tags$h3("Select, rename and convert variables"),
|
||||
title = "Summary & filter",
|
||||
tags$h3("Data summary and filtering"),
|
||||
fluidRow(
|
||||
column(
|
||||
width = 6,
|
||||
# radioButtons(),
|
||||
shiny::actionButton("data_reset", "Restore original data"),
|
||||
shiny::tags$br(),
|
||||
shiny::helpText("Reset to original imported dataset"),
|
||||
shiny::tags$br(),
|
||||
datamods::update_variables_ui("vars_update")
|
||||
),
|
||||
column(
|
||||
width = 6,
|
||||
tags$b("Original data:"),
|
||||
# verbatimTextOutput("original"),
|
||||
verbatimTextOutput("original_str"),
|
||||
tags$b("Modified data:"),
|
||||
# verbatimTextOutput("modified"),
|
||||
verbatimTextOutput("modified_str")
|
||||
)
|
||||
shiny::column(
|
||||
width = 9,
|
||||
shiny::tags$p(
|
||||
"Below is a short summary table of the provided data.
|
||||
On the right hand side you have the option to create filters.
|
||||
At the bottom you'll find a raw overview of the original vs the modified data.")
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Filter and modify",
|
||||
shinyWidgets::html_dependency_winbox(),
|
||||
fluidRow(
|
||||
# column(
|
||||
# width = 3,
|
||||
|
|
@ -136,23 +114,117 @@ ui_elements <- list(
|
|||
# verbatimTextOutput(outputId = "filtered_code")
|
||||
# ),
|
||||
shiny::column(
|
||||
width = 8,
|
||||
toastui::datagridOutput(outputId = "table_mod"),
|
||||
width = 9,
|
||||
toastui::datagridOutput(outputId = "tbl_overview"),
|
||||
# data_summary_ui(id = "data_summary"),
|
||||
shiny::tags$b("Reproducible code:"),
|
||||
shiny::verbatimTextOutput(outputId = "filtered_code")
|
||||
),
|
||||
shiny::column(
|
||||
width = 4,
|
||||
shiny::actionButton("modal_cut", "Create factor from a variable"),
|
||||
width = 3,
|
||||
IDEAFilter::IDEAFilter_ui("data_filter") # ,
|
||||
# shiny::actionButton("save_filter", "Apply the filter")
|
||||
)
|
||||
),
|
||||
fluidRow(
|
||||
column(
|
||||
width = 6,
|
||||
tags$b("Original data:"),
|
||||
# verbatimTextOutput("original"),
|
||||
verbatimTextOutput("original_str")
|
||||
),
|
||||
column(
|
||||
width = 6,
|
||||
tags$b("Modified data:"),
|
||||
# verbatimTextOutput("modified"),
|
||||
verbatimTextOutput("modified_str")
|
||||
)
|
||||
)
|
||||
),
|
||||
# bslib::nav_panel(
|
||||
# title = "Overview",
|
||||
# DT::DTOutput(outputId = "table")
|
||||
# ),
|
||||
bslib::nav_panel(
|
||||
title = "Modify",
|
||||
tags$h3("Subset, rename and convert variables"),
|
||||
fluidRow(
|
||||
shiny::column(
|
||||
width = 9,
|
||||
shiny::tags$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.
|
||||
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.")
|
||||
)
|
||||
),
|
||||
fluidRow(
|
||||
shiny::column(
|
||||
width = 9,
|
||||
update_variables_ui("vars_update")
|
||||
),
|
||||
shiny::column(
|
||||
width = 3,
|
||||
shiny::actionButton("modal_cut", "Create factor variable"),
|
||||
shiny::tags$br(),
|
||||
shiny::helpText("Create factor/categorical variable from an other value."),
|
||||
shiny::tags$br(),
|
||||
shiny::tags$br(),
|
||||
shiny::actionButton("modal_update", "Reorder factor levels"),
|
||||
shiny::tags$br(),
|
||||
shiny::helpText("Reorder the levels of factor/categorical variables."),
|
||||
shiny::tags$br(),
|
||||
IDEAFilter::IDEAFilter_ui("data_filter") # ,
|
||||
shiny::tags$br(),
|
||||
shiny::actionButton("data_reset", "Restore original data"),
|
||||
shiny::tags$br(),
|
||||
shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
|
||||
shiny::tags$br() # ,
|
||||
# shiny::tags$br(),
|
||||
# shiny::tags$br(),
|
||||
# IDEAFilter::IDEAFilter_ui("data_filter") # ,
|
||||
# shiny::actionButton("save_filter", "Apply the filter")
|
||||
)
|
||||
# datamods::update_variables_ui("vars_update")
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Browser",
|
||||
tags$h3("Browse the provided data"),
|
||||
shiny::tags$p(
|
||||
"Below is a data table with all the modified data provided to browse and understand data."
|
||||
),
|
||||
shinyWidgets::html_dependency_winbox(),
|
||||
# fluidRow(
|
||||
# column(
|
||||
# width = 3,
|
||||
# shiny::uiOutput("filter_vars"),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "(typeof input.filter_vars !== 'undefined' && input.filter_vars.length > 0)",
|
||||
# datamods::filter_data_ui("filtering", max_height = "500px")
|
||||
# )
|
||||
# ),
|
||||
# column(
|
||||
# width = 9,
|
||||
# DT::DTOutput(outputId = "filtered_table"),
|
||||
# tags$b("Code dplyr:"),
|
||||
# verbatimTextOutput(outputId = "filtered_code")
|
||||
# ),
|
||||
# shiny::column(
|
||||
# width = 8,
|
||||
toastui::datagridOutput(outputId = "table_mod") # ,
|
||||
# shiny::tags$b("Reproducible code:"),
|
||||
# shiny::verbatimTextOutput(outputId = "filtered_code")
|
||||
# ),
|
||||
# shiny::column(
|
||||
# width = 4,
|
||||
# shiny::actionButton("modal_cut", "Create factor from a variable"),
|
||||
# shiny::tags$br(),
|
||||
# shiny::tags$br(),
|
||||
# shiny::actionButton("modal_update", "Reorder factor levels")#,
|
||||
# # shiny::tags$br(),
|
||||
# # shiny::tags$br(),
|
||||
# # IDEAFilter::IDEAFilter_ui("data_filter") # ,
|
||||
# # shiny::actionButton("save_filter", "Apply the filter")
|
||||
# )
|
||||
# )
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -181,6 +253,20 @@ ui_elements <- list(
|
|||
sidebar = bslib::sidebar(
|
||||
shiny::helpText(em("Please specify relevant settings for your data, and press 'Analyse'")),
|
||||
shiny::uiOutput("outcome_var"),
|
||||
shiny::radioButtons(
|
||||
inputId = "all",
|
||||
label = "Specify covariables",
|
||||
inline = TRUE, selected = 2,
|
||||
choiceNames = c(
|
||||
"Yes",
|
||||
"No"
|
||||
),
|
||||
choiceValues = c(1, 2)
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.all==1",
|
||||
shiny::uiOutput("include_vars")
|
||||
),
|
||||
shiny::uiOutput("strat_var"),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.strat_var!='none'",
|
||||
|
|
@ -196,20 +282,6 @@ ui_elements <- list(
|
|||
),
|
||||
shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
|
||||
),
|
||||
shiny::radioButtons(
|
||||
inputId = "all",
|
||||
label = "Specify covariables",
|
||||
inline = TRUE, selected = 2,
|
||||
choiceNames = c(
|
||||
"Yes",
|
||||
"No"
|
||||
),
|
||||
choiceValues = c(1, 2)
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.all==1",
|
||||
shiny::uiOutput("include_vars")
|
||||
),
|
||||
shiny::radioButtons(
|
||||
inputId = "specify_factors",
|
||||
label = "Specify categorical variables?",
|
||||
|
|
@ -258,13 +330,29 @@ ui_elements <- list(
|
|||
# Button
|
||||
shiny::downloadButton(
|
||||
outputId = "report",
|
||||
label = "Download",
|
||||
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.")
|
||||
## https://github.com/quarto-dev/quarto-cli/issues/7151
|
||||
# )
|
||||
# )
|
||||
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$hr(),
|
||||
shiny::h4("Download data"),
|
||||
shiny::helpText("Choose your favourite output data format to download the modified data."),
|
||||
shiny::selectInput(
|
||||
inputId = "data_type",
|
||||
label = "Data format",
|
||||
selected = NULL,
|
||||
choices = list(
|
||||
"R" = "rds",
|
||||
"stata" = "dta"
|
||||
)
|
||||
),
|
||||
shiny::br(),
|
||||
# Button
|
||||
shiny::downloadButton(
|
||||
outputId = "data_modified",
|
||||
label = "Download data",
|
||||
icon = shiny::icon("download")
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Baseline characteristics",
|
||||
|
|
@ -303,28 +391,39 @@ dark <- custom_theme(
|
|||
# Fonts to consider:
|
||||
# https://webdesignerdepot.com/17-open-source-fonts-youll-actually-love/
|
||||
|
||||
ui <- bslib::page_fluid(
|
||||
ui <- bslib::page_fixed(
|
||||
shiny::tags$style(
|
||||
type = "text/css",
|
||||
# add the name of the tab you want to use as title in data-value
|
||||
shiny::HTML(
|
||||
".container-fluid > .nav > li >
|
||||
a[data-value='freesearcheR'] {font-size: 28px}"
|
||||
)
|
||||
),
|
||||
title = "freesearcheR",
|
||||
theme = light,
|
||||
shiny::useBusyIndicators(),
|
||||
bslib::page_navbar(title = "freesearcheR",
|
||||
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$analyze,
|
||||
ui_elements$docs,
|
||||
# bslib::nav_spacer(),
|
||||
# bslib::nav_item(shinyWidgets::circleButton(inputId = "mode", icon = icon("moon"),status = "primary")),
|
||||
fillable = TRUE,
|
||||
fillable = FALSE,
|
||||
footer = shiny::tags$footer(
|
||||
style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
|
||||
shiny::p(
|
||||
style = "margin: 1",
|
||||
"Data is only stored for analyses and deleted immediately afterwards."),
|
||||
"Data is only stored for analyses and deleted immediately afterwards."
|
||||
),
|
||||
shiny::p(
|
||||
style = "margin: 1; color: #888;",
|
||||
"Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target="_blank", rel="noopener noreferrer")
|
||||
"Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target = "_blank", rel = "noopener noreferrer")
|
||||
),
|
||||
)
|
||||
)
|
||||
|
|
|
|||
|
|
@ -56,7 +56,7 @@ margin: 0 0.8em 0.2em -1em; vertical-align: middle;
|
|||
<li><p><label><input type="checkbox">Option to edit variable labels for nicer tables</label></p></li>
|
||||
</ul></li>
|
||||
<li><p><label><input type="checkbox">Plot regression analyses results</label></p></li>
|
||||
<li><p><label><input type="checkbox">Export modified data</label></p></li>
|
||||
<li><p><label><input type="checkbox" checked>Export modified data. 2025-01-09</label></p></li>
|
||||
<li><p><label><input type="checkbox">Include reproducible code for all steps</label></p></li>
|
||||
<li><p><label><input type="checkbox" checked><del>Modify factor levels</del> Factor level modification is possible through converting factors to numeric > cutting numeric with desired fixed values. 2024-12-12</label></p></li>
|
||||
<li><p><label><input type="checkbox" checked>More options for date/datetime/time grouping/factoring. Included weekday and month-only options. 2024-12-12</label></p></li>
|
||||
|
|
|
|||
|
|
@ -36,7 +36,7 @@ Contributions are very welcome. If you find anything odd, or you think of featur
|
|||
|
||||
- [ ] Plot regression analyses results
|
||||
|
||||
- [ ] Export modified data
|
||||
- [x] Export modified data. 2025-01-09
|
||||
|
||||
- [ ] Include reproducible code for all steps
|
||||
|
||||
|
|
|
|||
432
inst/apps/data_analysis_modules/www/intro.html
Normal file
432
inst/apps/data_analysis_modules/www/intro.html
Normal file
File diff suppressed because one or more lines are too long
|
|
@ -1,12 +1,12 @@
|
|||
# Welcome
|
||||
|
||||
This is the ***freesearchR*** web data analysis tool. We intend the ***freesearchR*** to be a powerful and free tool for easy data evaluation and analysis at the hands of the clinician.
|
||||
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.
|
||||
|
||||
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:
|
||||
There are four 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).
|
||||
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)
|
||||
|
||||
|
|
@ -18,4 +18,4 @@ There are four simple steps to go through:
|
|||
|
||||
- Evaluation of model assumptions
|
||||
|
||||
4. Export the the analyses results as for MS Word or [LibreOffice](https://www.libreoffice.org/).
|
||||
4. Export the the analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/) as well as the data with preserved metadata.
|
||||
|
|
|
|||
|
|
@ -97,9 +97,9 @@ footer <- tags$p(
|
|||
# redcap_browser_app <- teal_init(data = tdm_data_upload)
|
||||
|
||||
app <- teal::init(
|
||||
# data=tdm_data_read,
|
||||
data=tdm_data_read,
|
||||
# data = tdm_data_upload,
|
||||
data = tdm_redcap_read,
|
||||
# data = tdm_redcap_read,
|
||||
filter = filters,
|
||||
modules = modules(
|
||||
tm_data_table("Data Table"),
|
||||
|
|
|
|||
484
renv.lock
484
renv.lock
|
|
@ -57,6 +57,27 @@
|
|||
],
|
||||
"Hash": "64ff3427f559ce3f2597a4fe13255cb6"
|
||||
},
|
||||
"Deriv": {
|
||||
"Package": "Deriv",
|
||||
"Version": "4.1.6",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"methods"
|
||||
],
|
||||
"Hash": "cd52c065c9e687c60c56b51f10f7bcd3"
|
||||
},
|
||||
"Formula": {
|
||||
"Package": "Formula",
|
||||
"Version": "1.2-5",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"stats"
|
||||
],
|
||||
"Hash": "7a29697b75e027767a53fde6c903eca7"
|
||||
},
|
||||
"IDEAFilter": {
|
||||
"Package": "IDEAFilter",
|
||||
"Version": "0.2.0",
|
||||
|
|
@ -117,6 +138,19 @@
|
|||
],
|
||||
"Hash": "5122bb14d8736372411f955e1b16bc8a"
|
||||
},
|
||||
"MatrixModels": {
|
||||
"Package": "MatrixModels",
|
||||
"Version": "0.5-3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"Matrix",
|
||||
"R",
|
||||
"methods",
|
||||
"stats"
|
||||
],
|
||||
"Hash": "0776bf7526869e0286b0463cb72fb211"
|
||||
},
|
||||
"R.cache": {
|
||||
"Package": "R.cache",
|
||||
"Version": "0.16.0",
|
||||
|
|
@ -280,6 +314,20 @@
|
|||
],
|
||||
"Hash": "a9e2118c664c2cd694f03de074e8d4b3"
|
||||
},
|
||||
"SparseM": {
|
||||
"Package": "SparseM",
|
||||
"Version": "1.84-2",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"graphics",
|
||||
"methods",
|
||||
"stats",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "e78499cbcbbca98200254bd171379165"
|
||||
},
|
||||
"V8": {
|
||||
"Package": "V8",
|
||||
"Version": "6.0.0",
|
||||
|
|
@ -293,6 +341,18 @@
|
|||
],
|
||||
"Hash": "6603bfcbc7883a5fed41fb13042a3899"
|
||||
},
|
||||
"abind": {
|
||||
"Package": "abind",
|
||||
"Version": "1.4-8",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"methods",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "2288423bb0f20a457800d7fc47f6aa54"
|
||||
},
|
||||
"ape": {
|
||||
"Package": "ape",
|
||||
"Version": "5.8-1",
|
||||
|
|
@ -312,6 +372,23 @@
|
|||
],
|
||||
"Hash": "54e5b03e928da23e75dc5bb633648d27"
|
||||
},
|
||||
"apexcharter": {
|
||||
"Package": "apexcharter",
|
||||
"Version": "0.4.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"ggplot2",
|
||||
"htmltools",
|
||||
"htmlwidgets",
|
||||
"jsonlite",
|
||||
"magrittr",
|
||||
"rlang",
|
||||
"shiny"
|
||||
],
|
||||
"Hash": "4bad120b4c71a078d8637f9cbe1eb1df"
|
||||
},
|
||||
"askpass": {
|
||||
"Package": "askpass",
|
||||
"Version": "1.2.1",
|
||||
|
|
@ -534,6 +611,41 @@
|
|||
],
|
||||
"Hash": "d7e13f49c19103ece9e58ad2d83a7354"
|
||||
},
|
||||
"car": {
|
||||
"Package": "car",
|
||||
"Version": "3.1-3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"Formula",
|
||||
"MASS",
|
||||
"R",
|
||||
"abind",
|
||||
"carData",
|
||||
"grDevices",
|
||||
"graphics",
|
||||
"lme4",
|
||||
"mgcv",
|
||||
"nlme",
|
||||
"nnet",
|
||||
"pbkrtest",
|
||||
"quantreg",
|
||||
"scales",
|
||||
"stats",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "82067bf302d1440b730437693a86406a"
|
||||
},
|
||||
"carData": {
|
||||
"Package": "carData",
|
||||
"Version": "3.0-5",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R"
|
||||
],
|
||||
"Hash": "ac6cdb8552c61bd36b0e54d07cf2aab7"
|
||||
},
|
||||
"cards": {
|
||||
"Package": "cards",
|
||||
"Version": "0.4.0",
|
||||
|
|
@ -688,6 +800,23 @@
|
|||
],
|
||||
"Hash": "8b6512d8f60685736ee3bafdc292190d"
|
||||
},
|
||||
"cowplot": {
|
||||
"Package": "cowplot",
|
||||
"Version": "1.1.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"ggplot2",
|
||||
"grDevices",
|
||||
"grid",
|
||||
"gtable",
|
||||
"methods",
|
||||
"rlang",
|
||||
"scales"
|
||||
],
|
||||
"Hash": "8ef2084dd7d28847b374e55440e4f8cb"
|
||||
},
|
||||
"cpp11": {
|
||||
"Package": "cpp11",
|
||||
"Version": "0.5.1",
|
||||
|
|
@ -794,6 +923,30 @@
|
|||
],
|
||||
"Hash": "33698c4b3127fc9f506654607fb73676"
|
||||
},
|
||||
"doBy": {
|
||||
"Package": "doBy",
|
||||
"Version": "4.6.24",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"Deriv",
|
||||
"MASS",
|
||||
"Matrix",
|
||||
"R",
|
||||
"boot",
|
||||
"broom",
|
||||
"cowplot",
|
||||
"dplyr",
|
||||
"ggplot2",
|
||||
"methods",
|
||||
"microbenchmark",
|
||||
"modelr",
|
||||
"rlang",
|
||||
"tibble",
|
||||
"tidyr"
|
||||
],
|
||||
"Hash": "8ddf795104defe53c5392a588888ec68"
|
||||
},
|
||||
"doParallel": {
|
||||
"Package": "doParallel",
|
||||
"Version": "1.0.17",
|
||||
|
|
@ -886,6 +1039,34 @@
|
|||
],
|
||||
"Hash": "b289af101f62cb7b46c53d1a45ed5198"
|
||||
},
|
||||
"emmeans": {
|
||||
"Package": "emmeans",
|
||||
"Version": "1.10.6",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"estimability",
|
||||
"graphics",
|
||||
"methods",
|
||||
"mvtnorm",
|
||||
"numDeriv",
|
||||
"stats",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "6b0c6fcbdbefe525d2ee713f95880f90"
|
||||
},
|
||||
"estimability": {
|
||||
"Package": "estimability",
|
||||
"Version": "1.5.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"stats"
|
||||
],
|
||||
"Hash": "21ec52af13afbcab1cb317567b639b0a"
|
||||
},
|
||||
"evaluate": {
|
||||
"Package": "evaluate",
|
||||
"Version": "1.0.1",
|
||||
|
|
@ -1141,6 +1322,25 @@
|
|||
],
|
||||
"Hash": "14b3b3b923944afb9542dbef4c68bf4b"
|
||||
},
|
||||
"ggmosaic": {
|
||||
"Package": "ggmosaic",
|
||||
"Version": "0.3.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"dplyr",
|
||||
"ggplot2",
|
||||
"ggrepel",
|
||||
"plotly",
|
||||
"productplots",
|
||||
"purrr",
|
||||
"rlang",
|
||||
"scales",
|
||||
"tidyr"
|
||||
],
|
||||
"Hash": "9c716443a2b821aa997c5675386bd34b"
|
||||
},
|
||||
"ggplot2": {
|
||||
"Package": "ggplot2",
|
||||
"Version": "3.5.1",
|
||||
|
|
@ -1166,6 +1366,22 @@
|
|||
],
|
||||
"Hash": "44c6a2f8202d5b7e878ea274b1092426"
|
||||
},
|
||||
"ggrepel": {
|
||||
"Package": "ggrepel",
|
||||
"Version": "0.9.6",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"Rcpp",
|
||||
"ggplot2",
|
||||
"grid",
|
||||
"rlang",
|
||||
"scales",
|
||||
"withr"
|
||||
],
|
||||
"Hash": "3d4156850acc1161f2f24bc61c9217c1"
|
||||
},
|
||||
"glue": {
|
||||
"Package": "glue",
|
||||
"Version": "1.8.0",
|
||||
|
|
@ -1177,6 +1393,20 @@
|
|||
],
|
||||
"Hash": "5899f1eaa825580172bb56c08266f37c"
|
||||
},
|
||||
"gridExtra": {
|
||||
"Package": "gridExtra",
|
||||
"Version": "2.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"grDevices",
|
||||
"graphics",
|
||||
"grid",
|
||||
"gtable",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "7d7f283939f563670a697165b2cf5560"
|
||||
},
|
||||
"gt": {
|
||||
"Package": "gt",
|
||||
"Version": "0.11.1",
|
||||
|
|
@ -1652,6 +1882,18 @@
|
|||
],
|
||||
"Hash": "110ee9d83b496279960e162ac97764ce"
|
||||
},
|
||||
"microbenchmark": {
|
||||
"Package": "microbenchmark",
|
||||
"Version": "1.5.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"graphics",
|
||||
"stats"
|
||||
],
|
||||
"Hash": "f9d226d88d4087d817d4e616626ce8e5"
|
||||
},
|
||||
"mime": {
|
||||
"Package": "mime",
|
||||
"Version": "0.12",
|
||||
|
|
@ -1703,6 +1945,24 @@
|
|||
],
|
||||
"Hash": "f519814037d08eee1343c2e7b5992cc4"
|
||||
},
|
||||
"modelr": {
|
||||
"Package": "modelr",
|
||||
"Version": "0.1.11",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"broom",
|
||||
"magrittr",
|
||||
"purrr",
|
||||
"rlang",
|
||||
"tibble",
|
||||
"tidyr",
|
||||
"tidyselect",
|
||||
"vctrs"
|
||||
],
|
||||
"Hash": "4f50122dc256b1b6996a4703fecea821"
|
||||
},
|
||||
"munsell": {
|
||||
"Package": "munsell",
|
||||
"Version": "0.5.1",
|
||||
|
|
@ -1714,6 +1974,17 @@
|
|||
],
|
||||
"Hash": "4fd8900853b746af55b81fda99da7695"
|
||||
},
|
||||
"mvtnorm": {
|
||||
"Package": "mvtnorm",
|
||||
"Version": "1.3-2",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"stats"
|
||||
],
|
||||
"Hash": "9e8405eacb262c0a939e121650247f4b"
|
||||
},
|
||||
"nlme": {
|
||||
"Package": "nlme",
|
||||
"Version": "3.1-166",
|
||||
|
|
@ -1735,6 +2006,28 @@
|
|||
"Repository": "CRAN",
|
||||
"Hash": "27550641889a3abf3aec4d91186311ec"
|
||||
},
|
||||
"nnet": {
|
||||
"Package": "nnet",
|
||||
"Version": "7.3-19",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"stats",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "2c797b46eea7fb58ede195bc0b1f1138"
|
||||
},
|
||||
"numDeriv": {
|
||||
"Package": "numDeriv",
|
||||
"Version": "2016.8-1.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "RSPM",
|
||||
"Requirements": [
|
||||
"R"
|
||||
],
|
||||
"Hash": "df58958f293b166e4ab885ebcad90e02"
|
||||
},
|
||||
"officer": {
|
||||
"Package": "officer",
|
||||
"Version": "0.6.7",
|
||||
|
|
@ -1838,6 +2131,24 @@
|
|||
],
|
||||
"Hash": "e23fb9ecb1258207bcb763d78d513439"
|
||||
},
|
||||
"pbkrtest": {
|
||||
"Package": "pbkrtest",
|
||||
"Version": "0.5.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"MASS",
|
||||
"Matrix",
|
||||
"R",
|
||||
"broom",
|
||||
"doBy",
|
||||
"dplyr",
|
||||
"lme4",
|
||||
"methods",
|
||||
"numDeriv"
|
||||
],
|
||||
"Hash": "938e6bbc4ac57534f8b43224506a8966"
|
||||
},
|
||||
"pbmcapply": {
|
||||
"Package": "pbmcapply",
|
||||
"Version": "1.5.1",
|
||||
|
|
@ -1981,6 +2292,17 @@
|
|||
],
|
||||
"Hash": "0c90a7d71988856bad2a2a45dd871bb9"
|
||||
},
|
||||
"productplots": {
|
||||
"Package": "productplots",
|
||||
"Version": "0.1.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"ggplot2",
|
||||
"plyr"
|
||||
],
|
||||
"Hash": "75630cc31052ba299a52bb1adbf59fae"
|
||||
},
|
||||
"progress": {
|
||||
"Package": "progress",
|
||||
"Version": "1.2.3",
|
||||
|
|
@ -2094,6 +2416,24 @@
|
|||
],
|
||||
"Hash": "a22b3777f51fd005a7cd4c2bccc385ae"
|
||||
},
|
||||
"quantreg": {
|
||||
"Package": "quantreg",
|
||||
"Version": "5.99.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"MASS",
|
||||
"Matrix",
|
||||
"MatrixModels",
|
||||
"R",
|
||||
"SparseM",
|
||||
"graphics",
|
||||
"methods",
|
||||
"stats",
|
||||
"survival"
|
||||
],
|
||||
"Hash": "c48844cd7961de506a1b4d22b2e082c7"
|
||||
},
|
||||
"quarto": {
|
||||
"Package": "quarto",
|
||||
"Version": "1.4.4",
|
||||
|
|
@ -2484,6 +2824,22 @@
|
|||
],
|
||||
"Hash": "836c3464fb0f2ea865ed4c35dcdc1eda"
|
||||
},
|
||||
"shinyTree": {
|
||||
"Package": "shinyTree",
|
||||
"Version": "0.3.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"htmlwidgets",
|
||||
"jsonlite",
|
||||
"methods",
|
||||
"promises",
|
||||
"shiny",
|
||||
"stringr"
|
||||
],
|
||||
"Hash": "0493a0d70f834cb251fe4523eb17b82c"
|
||||
},
|
||||
"shinyWidgets": {
|
||||
"Package": "shinyWidgets",
|
||||
"Version": "0.8.7",
|
||||
|
|
@ -2542,6 +2898,19 @@
|
|||
],
|
||||
"Hash": "802e4786b353a4bb27116957558548d5"
|
||||
},
|
||||
"shinyvalidate": {
|
||||
"Package": "shinyvalidate",
|
||||
"Version": "0.1.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"glue",
|
||||
"htmltools",
|
||||
"rlang",
|
||||
"shiny"
|
||||
],
|
||||
"Hash": "fe6e75a1c1722b2d23cb4d4dbe1006df"
|
||||
},
|
||||
"sodium": {
|
||||
"Package": "sodium",
|
||||
"Version": "1.4.0",
|
||||
|
|
@ -2619,6 +2988,22 @@
|
|||
],
|
||||
"Hash": "93a2b1beac2437bdcc4724f8bf867e2c"
|
||||
},
|
||||
"survival": {
|
||||
"Package": "survival",
|
||||
"Version": "3.8-3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"Matrix",
|
||||
"R",
|
||||
"graphics",
|
||||
"methods",
|
||||
"splines",
|
||||
"stats",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "fe42836742a4f065b3f3f5de81fccab9"
|
||||
},
|
||||
"sys": {
|
||||
"Package": "sys",
|
||||
"Version": "3.4.3",
|
||||
|
|
@ -2714,6 +3099,44 @@
|
|||
],
|
||||
"Hash": "b5d3366368999eb2262c2a646a1f0c87"
|
||||
},
|
||||
"teal.modules.general": {
|
||||
"Package": "teal.modules.general",
|
||||
"Version": "0.3.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"DT",
|
||||
"R",
|
||||
"checkmate",
|
||||
"dplyr",
|
||||
"forcats",
|
||||
"ggmosaic",
|
||||
"ggplot2",
|
||||
"grid",
|
||||
"logger",
|
||||
"scales",
|
||||
"shiny",
|
||||
"shinyTree",
|
||||
"shinyWidgets",
|
||||
"shinyjs",
|
||||
"shinyvalidate",
|
||||
"stats",
|
||||
"stringr",
|
||||
"teal",
|
||||
"teal.code",
|
||||
"teal.data",
|
||||
"teal.logger",
|
||||
"teal.reporter",
|
||||
"teal.transform",
|
||||
"teal.widgets",
|
||||
"tern",
|
||||
"tibble",
|
||||
"tidyr",
|
||||
"tools",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "f54d7bc27cd048cec3a842f980c74e9b"
|
||||
},
|
||||
"teal.reporter": {
|
||||
"Package": "teal.reporter",
|
||||
"Version": "0.3.1",
|
||||
|
|
@ -2766,6 +3189,31 @@
|
|||
],
|
||||
"Hash": "a29de94bc89bad9a12a914c17e8269f1"
|
||||
},
|
||||
"teal.transform": {
|
||||
"Package": "teal.transform",
|
||||
"Version": "0.5.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"checkmate",
|
||||
"dplyr",
|
||||
"lifecycle",
|
||||
"logger",
|
||||
"methods",
|
||||
"rlang",
|
||||
"shiny",
|
||||
"shinyjs",
|
||||
"shinyvalidate",
|
||||
"stats",
|
||||
"teal.data",
|
||||
"teal.logger",
|
||||
"teal.widgets",
|
||||
"tidyr",
|
||||
"tidyselect"
|
||||
],
|
||||
"Hash": "988a30f3f0f20b2633b41103a8eb4e56"
|
||||
},
|
||||
"teal.widgets": {
|
||||
"Package": "teal.widgets",
|
||||
"Version": "0.4.2",
|
||||
|
|
@ -2789,6 +3237,42 @@
|
|||
],
|
||||
"Hash": "46a99bbdcd97f8f25070ad23c3b23ad9"
|
||||
},
|
||||
"tern": {
|
||||
"Package": "tern",
|
||||
"Version": "0.9.6",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"MASS",
|
||||
"R",
|
||||
"Rdpack",
|
||||
"broom",
|
||||
"car",
|
||||
"checkmate",
|
||||
"cowplot",
|
||||
"dplyr",
|
||||
"emmeans",
|
||||
"forcats",
|
||||
"formatters",
|
||||
"ggplot2",
|
||||
"grid",
|
||||
"gridExtra",
|
||||
"gtable",
|
||||
"labeling",
|
||||
"lifecycle",
|
||||
"magrittr",
|
||||
"methods",
|
||||
"rlang",
|
||||
"rtables",
|
||||
"scales",
|
||||
"stats",
|
||||
"survival",
|
||||
"tibble",
|
||||
"tidyr",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "35fe86bc358b15525217e775f5318d33"
|
||||
},
|
||||
"textshaping": {
|
||||
"Package": "textshaping",
|
||||
"Version": "0.4.1",
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue