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5c8d84fccd
...
c7b879f458
25 changed files with 1350 additions and 1647 deletions
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@ -9,7 +9,7 @@ type: software
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license: AGPL-3.0-or-later
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title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers
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with publication ready output'
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version: 25.7.2
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version: 25.6.4
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doi: 10.5281/zenodo.14527429
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identifiers:
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- type: url
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@ -1,6 +1,6 @@
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Package: FreesearchR
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Title: A free and open-source browser based data analysis tool for researchers with publication ready output
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Version: 25.7.2
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Version: 25.6.4
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Authors@R: c(
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person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0002-7559-1154")),
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@ -17,7 +17,6 @@ export(clean_common_axis)
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export(clean_date)
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export(clean_sep)
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export(columnSelectInput)
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export(compare_missings)
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export(contrast_text)
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export(create_baseline)
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export(create_column_server)
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8
NEWS.md
8
NEWS.md
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@ -1,11 +1,3 @@
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# FreesearchR 25.7.2 - DEV
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- *FIX* refining hiding drop downs. All JavaScript is now in separate file. Coded with GAI help from claude.ai.
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# FreesearchR 25.7.1
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- *NEW* UI overhaul and navigation update. The interface is simplified to clearly show the relationship between panels and sub-items by abandoning multiple levels on panel to instead show a drop-down menu. This also results in simplified sidebar menus with room to add more controls in the future.
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# FreesearchR 25.6.4
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The app is now also published as a docker container. See the README for instructions. It is mainly to use for hosting the app. Work is ongoing to publish a true standalone app, preferably for both Windows and MacOS.
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@ -1 +1 @@
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app_version <- function()'25.7.2'
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app_version <- function()'25.6.4'
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@ -11,8 +11,10 @@
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data_visuals_ui <- function(id, tab_title = "Plots", ...) {
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ns <- shiny::NS(id)
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# bslib::navset_bar(
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list(
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bslib::layout_sidebar(
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# Sidebar with a slider input
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sidebar = bslib::sidebar(
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bslib::accordion(
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multiple = FALSE,
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@ -35,6 +37,10 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
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),
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shiny::helpText('Adjust settings, then press "Plot".')
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),
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# bslib::accordion_panel(
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# title = "Advanced",
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# icon = bsicons::bs_icon("gear")
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# ),
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bslib::accordion_panel(
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title = "Download",
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icon = bsicons::bs_icon("download"),
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@ -86,21 +92,16 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
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icon = shiny::icon("download")
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)
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)
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)
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),
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shiny::p("We have collected a few notes on visualising data and details on the options included in FreesearchR:", shiny::tags$a(
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href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
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"View notes in new tab",
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target = "_blank",
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rel = "noopener noreferrer"
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))
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),
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bslib::nav_panel(
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title = tab_title,
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shiny::plotOutput(ns("plot"), height = "70vh"),
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shiny::tags$br(),
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shiny::tags$br(),
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shiny::htmlOutput(outputId = ns("code_plot"))
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)
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)
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# )
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}
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@ -724,7 +725,6 @@ get_label <- function(data, var = NULL) {
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#' paste(sample(letters[1:10], 100, TRUE), collapse = "") |> line_break(force = TRUE)
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line_break <- function(data, lineLength = 20, force = FALSE) {
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if (isTRUE(force)) {
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## This eats some letters when splitting a sentence... ??
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gsub(paste0("(.{1,", lineLength, "})(\\s|[[:alnum:]])"), "\\1\n", data)
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} else {
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paste(strwrap(data, lineLength), collapse = "\n")
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@ -746,7 +746,7 @@ line_break <- function(data, lineLength = 20, force = FALSE) {
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wrap_plot_list <- function(data,
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tag_levels = NULL,
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title = NULL,
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axis.font.family = NULL,
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axis.font.family=NULL,
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...) {
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if (ggplot2::is_ggplot(data[[1]])) {
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if (length(data) > 1) {
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@ -1 +1 @@
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hosted_version <- function()'v25.7.2-250703'
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hosted_version <- function()'v25.6.4-250627'
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@ -44,7 +44,14 @@ data_missings_server <- function(id,
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tryCatch(
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{
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out <- compare_missings(df_tbl,by_var)
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if (!is.null(by_var) && by_var != "" && by_var %in% names(df_tbl)) {
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df_tbl[[by_var]] <- ifelse(is.na(df_tbl[[by_var]]), "Missing", "Non-missing")
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out <- gtsummary::tbl_summary(df_tbl, by = by_var) |>
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gtsummary::add_p()
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} else {
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out <- gtsummary::tbl_summary(df_tbl)
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}
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},
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error = function(err) {
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showNotification(paste0("Error: ", err), type = "err")
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@ -122,22 +129,10 @@ missing_demo_app <- function() {
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missing_demo_app()
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#' Pairwise comparison of missings across covariables
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#'
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#' @param data data frame
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#' @param by_var variable to stratify by missingness
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#'
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#' @returns gtsummary list object
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#' @export
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#'
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compare_missings <- function(data,by_var){
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if (!is.null(by_var) && by_var != "" && by_var %in% names(data)) {
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data[[by_var]] <- ifelse(is.na(data[[by_var]]), "Missing", "Non-missing")
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out <- gtsummary::tbl_summary(data, by = by_var) |>
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gtsummary::add_p()
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} else {
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out <- gtsummary::tbl_summary(data)
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}
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out
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}
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@ -44,10 +44,7 @@ regression_ui <- function(id, ...) {
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ns <- shiny::NS(id)
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shiny::tagList(
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# title = "",
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bslib::nav_panel(
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title = "Regression table",
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bslib::layout_sidebar(
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title = "",
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sidebar = bslib::sidebar(
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shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
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bslib::accordion(
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@ -122,19 +119,7 @@ regression_ui <- function(id, ...) {
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# )
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# ),
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shiny::tags$br()
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)
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)
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),
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gt::gt_output(outputId = ns("table2"))
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)
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),
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bslib::nav_panel(
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title = "Coefficient plot",
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bslib::layout_sidebar(
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sidebar = bslib::sidebar(
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bslib::accordion(
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open = "acc_reg",
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multiple = FALSE,
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do.call(
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bslib::accordion_panel,
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c(
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@ -188,19 +173,7 @@ regression_ui <- function(id, ...) {
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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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shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
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)
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),
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bslib::nav_panel(
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title = "Model checks",
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bslib::layout_sidebar(
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sidebar = bslib::sidebar(
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bslib::accordion(
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open = "acc_reg",
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multiple = FALSE,
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bslib::accordion_panel(
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value = "acc_checks",
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title = "Checks",
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@ -209,10 +182,19 @@ regression_ui <- function(id, ...) {
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)
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)
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),
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bslib::nav_panel(
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title = "Regression table",
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gt::gt_output(outputId = ns("table2"))
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),
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bslib::nav_panel(
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title = "Coefficient plot",
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shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
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),
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bslib::nav_panel(
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title = "Model checks",
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shiny::plotOutput(outputId = ns("check"), height = "90vh")
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)
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)
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)
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}
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
33
SESSION.md
33
SESSION.md
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@ -11,11 +11,11 @@
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|collate |en_US.UTF-8 |
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|ctype |en_US.UTF-8 |
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|tz |Europe/Copenhagen |
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|date |2025-07-03 |
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|date |2025-06-27 |
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|rstudio |2025.05.0+496 Mariposa Orchid (desktop) |
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|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
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|quarto |1.7.30 @ /usr/local/bin/quarto |
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|FreesearchR |25.7.2.250703 |
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|FreesearchR |25.6.4.250627 |
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--------------------------------------------------------------------------------
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@ -26,8 +26,6 @@
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|apexcharter |0.4.4 |2024-09-06 |CRAN (R 4.4.1) |
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|askpass |1.2.1 |2024-10-04 |CRAN (R 4.4.1) |
|
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|assertthat |0.2.1 |2019-03-21 |CRAN (R 4.4.1) |
|
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|attachment |0.4.5 |2025-03-14 |CRAN (R 4.4.1) |
|
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|attempt |0.3.1 |2020-05-03 |CRAN (R 4.4.1) |
|
||||
|backports |1.5.0 |2024-05-23 |CRAN (R 4.4.1) |
|
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|base64enc |0.1-3 |2015-07-28 |CRAN (R 4.4.1) |
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|bayestestR |0.15.3 |2025-04-28 |CRAN (R 4.4.1) |
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@ -45,7 +43,6 @@
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|cardx |0.2.4 |2025-04-12 |CRAN (R 4.4.1) |
|
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|caTools |1.18.3 |2024-09-04 |CRAN (R 4.4.1) |
|
||||
|cellranger |1.1.0 |2016-07-27 |CRAN (R 4.4.0) |
|
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|cffr |1.2.0 |2025-01-25 |CRAN (R 4.4.1) |
|
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|checkmate |2.3.2 |2024-07-29 |CRAN (R 4.4.0) |
|
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|class |7.3-23 |2025-01-01 |CRAN (R 4.4.1) |
|
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|classInt |0.4-11 |2025-01-08 |CRAN (R 4.4.1) |
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@ -55,9 +52,6 @@
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|colorspace |2.1-1 |2024-07-26 |CRAN (R 4.4.1) |
|
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|commonmark |1.9.5 |2025-03-17 |CRAN (R 4.4.1) |
|
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|crayon |1.5.3 |2024-06-20 |CRAN (R 4.4.1) |
|
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|credentials |2.0.2 |2024-10-04 |CRAN (R 4.4.1) |
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|crosstalk |1.2.1 |2023-11-23 |CRAN (R 4.4.0) |
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|curl |6.2.2 |2025-03-24 |CRAN (R 4.4.1) |
|
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|data.table |1.17.0 |2025-02-22 |CRAN (R 4.4.1) |
|
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|datamods |1.5.3 |2024-10-02 |CRAN (R 4.4.1) |
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|datawizard |1.0.2 |2025-03-24 |CRAN (R 4.4.1) |
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@ -66,13 +60,11 @@
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|devtools |2.4.5 |2022-10-11 |CRAN (R 4.4.0) |
|
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|DHARMa |0.4.7 |2024-10-18 |CRAN (R 4.4.1) |
|
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|digest |0.6.37 |2024-08-19 |CRAN (R 4.4.1) |
|
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|dockerfiler |0.2.5 |2025-05-07 |CRAN (R 4.4.1) |
|
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|doParallel |1.0.17 |2022-02-07 |CRAN (R 4.4.0) |
|
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|dplyr |1.1.4 |2023-11-17 |CRAN (R 4.4.0) |
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|DT |0.33 |2024-04-04 |CRAN (R 4.4.0) |
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|e1071 |1.7-16 |2024-09-16 |CRAN (R 4.4.1) |
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|easystats |0.7.4 |2025-02-06 |CRAN (R 4.4.1) |
|
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|effectsize |1.0.0 |2024-12-10 |CRAN (R 4.4.1) |
|
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|ellipsis |0.3.2 |2021-04-29 |CRAN (R 4.4.1) |
|
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|emmeans |1.11.1 |2025-05-04 |CRAN (R 4.4.1) |
|
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|esquisse |2.1.0 |2025-02-21 |CRAN (R 4.4.1) |
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@ -90,19 +82,16 @@
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|foreach |1.5.2 |2022-02-02 |CRAN (R 4.4.0) |
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|foreign |0.8-90 |2025-03-31 |CRAN (R 4.4.1) |
|
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|Formula |1.2-5 |2023-02-24 |CRAN (R 4.4.1) |
|
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|FreesearchR |25.7.2 |NA |NA |
|
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|FreesearchR |25.6.4 |NA |NA |
|
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|fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) |
|
||||
|gdtools |0.4.2 |2025-03-27 |CRAN (R 4.4.1) |
|
||||
|generics |0.1.3 |2022-07-05 |CRAN (R 4.4.1) |
|
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|gert |2.1.5 |2025-03-25 |CRAN (R 4.4.1) |
|
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|ggalluvial |0.12.5 |2023-02-22 |CRAN (R 4.4.0) |
|
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|ggcorrplot |0.1.4.1 |2023-09-05 |CRAN (R 4.4.0) |
|
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|ggforce |0.4.2 |2024-02-19 |CRAN (R 4.4.0) |
|
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|ggplot2 |3.5.2 |2025-04-09 |CRAN (R 4.4.1) |
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|ggridges |0.5.6 |2024-01-23 |CRAN (R 4.4.0) |
|
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|ggstats |0.9.0 |2025-03-10 |CRAN (R 4.4.1) |
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|gh |1.4.1 |2024-03-28 |CRAN (R 4.4.0) |
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|gitcreds |0.1.2 |2022-09-08 |CRAN (R 4.4.1) |
|
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|glue |1.8.0 |2024-09-30 |CRAN (R 4.4.1) |
|
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|gridExtra |2.3 |2017-09-09 |CRAN (R 4.4.1) |
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|gt |1.0.0 |2025-04-05 |CRAN (R 4.4.1) |
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@ -116,30 +105,24 @@
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|htmltools |0.5.8.1 |2024-04-04 |CRAN (R 4.4.1) |
|
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|htmlwidgets |1.6.4 |2023-12-06 |CRAN (R 4.4.0) |
|
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|httpuv |1.6.16 |2025-04-16 |CRAN (R 4.4.1) |
|
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|httr2 |1.1.2 |2025-03-26 |CRAN (R 4.4.1) |
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|IDEAFilter |0.2.0 |2024-04-15 |CRAN (R 4.4.0) |
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|insight |1.2.0 |2025-04-22 |CRAN (R 4.4.1) |
|
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|iterators |1.0.14 |2022-02-05 |CRAN (R 4.4.1) |
|
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|jquerylib |0.1.4 |2021-04-26 |CRAN (R 4.4.0) |
|
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|jsonlite |2.0.0 |2025-03-27 |CRAN (R 4.4.1) |
|
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|jsonvalidate |1.5.0 |2025-02-07 |CRAN (R 4.4.1) |
|
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|KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.4.1) |
|
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|keyring |1.3.2 |2023-12-11 |CRAN (R 4.4.0) |
|
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|knitr |1.50 |2025-03-16 |CRAN (R 4.4.1) |
|
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|labeling |0.4.3 |2023-08-29 |CRAN (R 4.4.1) |
|
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|labelled |2.14.0 |2025-01-08 |CRAN (R 4.4.1) |
|
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|later |1.4.2 |2025-04-08 |CRAN (R 4.4.1) |
|
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|lattice |0.22-7 |2025-04-02 |CRAN (R 4.4.1) |
|
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|lifecycle |1.0.4 |2023-11-07 |CRAN (R 4.4.1) |
|
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|litedown |0.7 |2025-04-08 |CRAN (R 4.4.1) |
|
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|lme4 |1.1-37 |2025-03-26 |CRAN (R 4.4.1) |
|
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|lubridate |1.9.4 |2024-12-08 |CRAN (R 4.4.1) |
|
||||
|magrittr |2.0.3 |2022-03-30 |CRAN (R 4.4.1) |
|
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|markdown |2.0 |2025-03-23 |CRAN (R 4.4.1) |
|
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|MASS |7.3-65 |2025-02-28 |CRAN (R 4.4.1) |
|
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|Matrix |1.7-3 |2025-03-11 |CRAN (R 4.4.1) |
|
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|memoise |2.0.1 |2021-11-26 |CRAN (R 4.4.0) |
|
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|mgcv |1.9-3 |2025-04-04 |CRAN (R 4.4.1) |
|
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|mime |0.13 |2025-03-17 |CRAN (R 4.4.1) |
|
||||
|miniUI |0.1.2 |2025-04-17 |CRAN (R 4.4.1) |
|
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|minqa |1.2.8 |2024-08-17 |CRAN (R 4.4.1) |
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@ -151,7 +134,6 @@
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|opdisDownsampling |1.0.1 |2024-04-15 |CRAN (R 4.4.0) |
|
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|openssl |2.3.2 |2025-02-03 |CRAN (R 4.4.1) |
|
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|openxlsx2 |1.15 |2025-04-25 |CRAN (R 4.4.1) |
|
||||
|pak |0.8.0.2 |2025-04-08 |CRAN (R 4.4.1) |
|
||||
|parameters |0.24.2 |2025-03-04 |CRAN (R 4.4.1) |
|
||||
|patchwork |1.3.0 |2024-09-16 |CRAN (R 4.4.1) |
|
||||
|pbmcapply |1.5.1 |2022-04-28 |CRAN (R 4.4.1) |
|
||||
|
|
@ -180,7 +162,6 @@
|
|||
|R6 |2.6.1 |2025-02-15 |CRAN (R 4.4.1) |
|
||||
|ragg |1.4.0 |2025-04-10 |CRAN (R 4.4.1) |
|
||||
|rankinPlot |1.1.0 |2023-01-30 |CRAN (R 4.4.0) |
|
||||
|rappdirs |0.3.3 |2021-01-31 |CRAN (R 4.4.1) |
|
||||
|rbibutils |2.3 |2024-10-04 |CRAN (R 4.4.1) |
|
||||
|RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.4.1) |
|
||||
|Rcpp |1.0.14 |2025-01-12 |CRAN (R 4.4.1) |
|
||||
|
|
@ -211,16 +192,13 @@
|
|||
|see |0.11.0 |2025-03-11 |CRAN (R 4.4.1) |
|
||||
|sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.4.1) |
|
||||
|shiny |1.10.0 |2024-12-14 |CRAN (R 4.4.1) |
|
||||
|shiny2docker |0.0.2 |2025-02-09 |CRAN (R 4.4.1) |
|
||||
|shinybusy |0.3.3 |2024-03-09 |CRAN (R 4.4.0) |
|
||||
|shinyjs |2.1.0 |2021-12-23 |CRAN (R 4.4.0) |
|
||||
|shinyTime |1.0.3 |2022-08-19 |CRAN (R 4.4.0) |
|
||||
|shinyWidgets |0.9.0 |2025-02-21 |CRAN (R 4.4.1) |
|
||||
|sourcetools |0.1.7-1 |2023-02-01 |CRAN (R 4.4.1) |
|
||||
|stringi |1.8.7 |2025-03-27 |CRAN (R 4.4.1) |
|
||||
|stringr |1.5.1 |2023-11-14 |CRAN (R 4.4.0) |
|
||||
|styler |1.10.3 |2024-04-07 |CRAN (R 4.4.0) |
|
||||
|sys |3.4.3 |2024-10-04 |CRAN (R 4.4.1) |
|
||||
|systemfonts |1.2.2 |2025-04-04 |CRAN (R 4.4.1) |
|
||||
|testthat |3.2.3 |2025-01-13 |CRAN (R 4.4.1) |
|
||||
|textshaping |1.0.0 |2025-01-20 |CRAN (R 4.4.1) |
|
||||
|
|
@ -235,9 +213,11 @@
|
|||
|tzdb |0.5.0 |2025-03-15 |CRAN (R 4.4.1) |
|
||||
|urlchecker |1.0.1 |2021-11-30 |CRAN (R 4.4.1) |
|
||||
|usethis |3.1.0 |2024-11-26 |CRAN (R 4.4.1) |
|
||||
|utf8 |1.2.4 |2023-10-22 |CRAN (R 4.4.1) |
|
||||
|uuid |1.2-1 |2024-07-29 |CRAN (R 4.4.1) |
|
||||
|V8 |6.0.3 |2025-03-26 |CRAN (R 4.4.1) |
|
||||
|vctrs |0.6.5 |2023-12-01 |CRAN (R 4.4.0) |
|
||||
|viridis |0.6.5 |2024-01-29 |CRAN (R 4.4.0) |
|
||||
|viridisLite |0.4.2 |2023-05-02 |CRAN (R 4.4.1) |
|
||||
|vroom |1.6.5 |2023-12-05 |CRAN (R 4.4.0) |
|
||||
|withr |3.0.2 |2024-10-28 |CRAN (R 4.4.1) |
|
||||
|writexl |1.5.4 |2025-04-15 |CRAN (R 4.4.1) |
|
||||
|
|
@ -245,5 +225,4 @@
|
|||
|xml2 |1.3.8 |2025-03-14 |CRAN (R 4.4.1) |
|
||||
|xtable |1.8-4 |2019-04-21 |CRAN (R 4.4.1) |
|
||||
|yaml |2.3.10 |2024-07-26 |CRAN (R 4.4.1) |
|
||||
|yesno |0.1.3 |2024-07-26 |CRAN (R 4.4.1) |
|
||||
|zip |2.3.2 |2025-02-01 |CRAN (R 4.4.1) |
|
||||
|
|
|
|||
343
app_docker/app.R
343
app_docker/app.R
|
|
@ -5,7 +5,7 @@
|
|||
########
|
||||
|
||||
library(shiny)
|
||||
library(shinyjs)
|
||||
# library(shinyjs)
|
||||
# library(methods)
|
||||
# library(readr)
|
||||
# library(MASS)
|
||||
|
|
@ -49,7 +49,7 @@ library(rlang)
|
|||
#### Current file: /Users/au301842/FreesearchR/R//app_version.R
|
||||
########
|
||||
|
||||
app_version <- function()'25.7.1'
|
||||
app_version <- function()'25.6.3'
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -1611,8 +1611,10 @@ plot_histogram <- function(data, column=NULL, bins = 30, breaks = NULL, color =
|
|||
data_visuals_ui <- function(id, tab_title = "Plots", ...) {
|
||||
ns <- shiny::NS(id)
|
||||
|
||||
# bslib::navset_bar(
|
||||
list(
|
||||
bslib::layout_sidebar(
|
||||
|
||||
# Sidebar with a slider input
|
||||
sidebar = bslib::sidebar(
|
||||
bslib::accordion(
|
||||
multiple = FALSE,
|
||||
|
|
@ -1635,6 +1637,10 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
|
|||
),
|
||||
shiny::helpText('Adjust settings, then press "Plot".')
|
||||
),
|
||||
# bslib::accordion_panel(
|
||||
# title = "Advanced",
|
||||
# icon = bsicons::bs_icon("gear")
|
||||
# ),
|
||||
bslib::accordion_panel(
|
||||
title = "Download",
|
||||
icon = bsicons::bs_icon("download"),
|
||||
|
|
@ -1686,21 +1692,16 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
|
|||
icon = shiny::icon("download")
|
||||
)
|
||||
)
|
||||
)
|
||||
),
|
||||
shiny::p("We have collected a few notes on visualising data and details on the options included in FreesearchR:", shiny::tags$a(
|
||||
href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
|
||||
"View notes in new tab",
|
||||
target = "_blank",
|
||||
rel = "noopener noreferrer"
|
||||
))
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = tab_title,
|
||||
shiny::plotOutput(ns("plot"), height = "70vh"),
|
||||
shiny::tags$br(),
|
||||
shiny::tags$br(),
|
||||
shiny::htmlOutput(outputId = ns("code_plot"))
|
||||
)
|
||||
)
|
||||
# )
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -1936,14 +1937,7 @@ data_visuals_server <- function(id,
|
|||
)
|
||||
|
||||
shiny::withProgress(message = "Drawing the plot. Hold tight for a moment..", {
|
||||
rv$plot <- rlang::exec(
|
||||
create_plot,
|
||||
!!!append_list(
|
||||
data(),
|
||||
parameters,
|
||||
"data"
|
||||
)
|
||||
)
|
||||
rv$plot <- rlang::exec(create_plot, !!!append_list(data(), parameters, "data"))
|
||||
})
|
||||
|
||||
rv$code <- glue::glue("FreesearchR::create_plot(df,{list2str(parameters)})")
|
||||
|
|
@ -1999,12 +1993,13 @@ data_visuals_server <- function(id,
|
|||
paste0("plot.", input$plot_type)
|
||||
}),
|
||||
content = function(file) {
|
||||
if (inherits(rv$plot, "patchwork")) {
|
||||
if (inherits(rv$plot,"patchwork")){
|
||||
plot <- rv$plot
|
||||
} else if (inherits(rv$plot, "ggplot")) {
|
||||
} else if (inherits(rv$plot,"ggplot")){
|
||||
plot <- rv$plot
|
||||
} else {
|
||||
}else {
|
||||
plot <- rv$plot[[1]]
|
||||
|
||||
}
|
||||
# browser()
|
||||
shiny::withProgress(message = "Drawing the plot. Hold on for a moment..", {
|
||||
|
|
@ -2264,12 +2259,12 @@ create_plot <- function(data, type, pri, sec, ter = NULL, ...) {
|
|||
|
||||
out <- do.call(
|
||||
type,
|
||||
modifyList(parameters, list(data = data))
|
||||
modifyList(parameters,list(data=data))
|
||||
)
|
||||
|
||||
code <- rlang::call2(type, !!!parameters, .ns = "FreesearchR")
|
||||
code <- rlang::call2(type,!!!parameters,.ns = "FreesearchR")
|
||||
|
||||
attr(out, "code") <- code
|
||||
attr(out,"code") <- code
|
||||
out
|
||||
}
|
||||
|
||||
|
|
@ -2324,7 +2319,6 @@ get_label <- function(data, var = NULL) {
|
|||
#' paste(sample(letters[1:10], 100, TRUE), collapse = "") |> line_break(force = TRUE)
|
||||
line_break <- function(data, lineLength = 20, force = FALSE) {
|
||||
if (isTRUE(force)) {
|
||||
## This eats some letters when splitting a sentence... ??
|
||||
gsub(paste0("(.{1,", lineLength, "})(\\s|[[:alnum:]])"), "\\1\n", data)
|
||||
} else {
|
||||
paste(strwrap(data, lineLength), collapse = "\n")
|
||||
|
|
@ -2337,17 +2331,11 @@ line_break <- function(data, lineLength = 20, force = FALSE) {
|
|||
#'
|
||||
#' @param data list of ggplot2 objects
|
||||
#' @param tag_levels passed to patchwork::plot_annotation if given. Default is NULL
|
||||
#' @param title panel title
|
||||
#' @param ... ignored for argument overflow
|
||||
#'
|
||||
#' @returns list of ggplot2 objects
|
||||
#' @export
|
||||
#'
|
||||
wrap_plot_list <- function(data,
|
||||
tag_levels = NULL,
|
||||
title = NULL,
|
||||
axis.font.family = NULL,
|
||||
...) {
|
||||
wrap_plot_list <- function(data, tag_levels = NULL) {
|
||||
if (ggplot2::is_ggplot(data[[1]])) {
|
||||
if (length(data) > 1) {
|
||||
out <- data |>
|
||||
|
|
@ -2361,35 +2349,17 @@ wrap_plot_list <- function(data,
|
|||
}
|
||||
})() |>
|
||||
align_axes() |>
|
||||
patchwork::wrap_plots(
|
||||
guides = "collect",
|
||||
axes = "collect",
|
||||
axis_titles = "collect"
|
||||
)
|
||||
patchwork::wrap_plots(guides = "collect", axes = "collect", axis_titles = "collect")
|
||||
if (!is.null(tag_levels)) {
|
||||
out <- out + patchwork::plot_annotation(tag_levels = tag_levels)
|
||||
}
|
||||
if (!is.null(title)) {
|
||||
out <- out +
|
||||
patchwork::plot_annotation(
|
||||
title = title,
|
||||
theme = ggplot2::theme(plot.title = ggplot2::element_text(size = 25))
|
||||
)
|
||||
}
|
||||
} else {
|
||||
out <- data[[1]]
|
||||
out <- data
|
||||
}
|
||||
} else {
|
||||
cli::cli_abort("Can only wrap lists of {.cls ggplot} objects")
|
||||
}
|
||||
|
||||
if (inherits(x = out, what = "patchwork")) {
|
||||
out &
|
||||
ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family))
|
||||
} else {
|
||||
out +
|
||||
ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family))
|
||||
}
|
||||
out
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -4026,7 +3996,7 @@ simple_snake <- function(data){
|
|||
#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R
|
||||
########
|
||||
|
||||
hosted_version <- function()'v25.7.1-250703'
|
||||
hosted_version <- function()'v25.6.3-250626'
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -4735,7 +4705,14 @@ data_missings_server <- function(id,
|
|||
|
||||
tryCatch(
|
||||
{
|
||||
out <- compare_missings(df_tbl,by_var)
|
||||
if (!is.null(by_var) && by_var != "" && by_var %in% names(df_tbl)) {
|
||||
df_tbl[[by_var]] <- ifelse(is.na(df_tbl[[by_var]]), "Missing", "Non-missing")
|
||||
|
||||
out <- gtsummary::tbl_summary(df_tbl, by = by_var) |>
|
||||
gtsummary::add_p()
|
||||
} else {
|
||||
out <- gtsummary::tbl_summary(df_tbl)
|
||||
}
|
||||
},
|
||||
error = function(err) {
|
||||
showNotification(paste0("Error: ", err), type = "err")
|
||||
|
|
@ -4813,25 +4790,13 @@ missing_demo_app <- function() {
|
|||
|
||||
missing_demo_app()
|
||||
|
||||
#' Pairwise comparison of missings across covariables
|
||||
#'
|
||||
#' @param data data frame
|
||||
#' @param by_var variable to stratify by missingness
|
||||
#'
|
||||
#' @returns gtsummary list object
|
||||
#' @export
|
||||
#'
|
||||
compare_missings <- function(data,by_var){
|
||||
if (!is.null(by_var) && by_var != "" && by_var %in% names(data)) {
|
||||
data[[by_var]] <- ifelse(is.na(data[[by_var]]), "Missing", "Non-missing")
|
||||
|
||||
out <- gtsummary::tbl_summary(data, by = by_var) |>
|
||||
gtsummary::add_p()
|
||||
} else {
|
||||
out <- gtsummary::tbl_summary(data)
|
||||
}
|
||||
out
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -4840,27 +4805,17 @@ compare_missings <- function(data,by_var){
|
|||
|
||||
#' Beautiful box plot(s)
|
||||
#'
|
||||
#' @param data data frame
|
||||
#' @param pri primary variable
|
||||
#' @param sec secondary variable
|
||||
#' @param ter tertiary variable
|
||||
#' @param ... passed on to wrap_plot_list
|
||||
#'
|
||||
#' @returns ggplot2 object
|
||||
#' @export
|
||||
#'
|
||||
#' @name data-plots
|
||||
#'
|
||||
#' @examples
|
||||
#' mtcars |> plot_box(pri = "mpg", sec = "gear")
|
||||
#' mtcars |> plot_box(pri = "mpg", sec="cyl")
|
||||
#' mtcars |> plot_box(pri = "mpg", sec = "cyl", ter = "gear")
|
||||
#' mtcars |>
|
||||
#' default_parsing() |>
|
||||
#' plot_box(pri = "mpg", sec = "cyl", ter = "gear")
|
||||
#' mtcars |>
|
||||
#' default_parsing() |>
|
||||
#' plot_box(pri = "mpg", sec = "cyl", ter = "gear",axis.font.family="mono")
|
||||
plot_box <- function(data, pri, sec, ter = NULL,...) {
|
||||
plot_box <- function(data, pri, sec, ter = NULL) {
|
||||
if (!is.null(ter)) {
|
||||
ds <- split(data, data[ter])
|
||||
} else {
|
||||
|
|
@ -4875,7 +4830,7 @@ plot_box <- function(data, pri, sec, ter = NULL,...) {
|
|||
)
|
||||
})
|
||||
|
||||
wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}"),...)
|
||||
wrap_plot_list(out)
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -4891,7 +4846,6 @@ plot_box <- function(data, pri, sec, ter = NULL,...) {
|
|||
#' @examples
|
||||
#' mtcars |> plot_box_single("mpg")
|
||||
#' mtcars |> plot_box_single("mpg","cyl")
|
||||
#' gtsummary::trial |> plot_box_single("age","trt")
|
||||
plot_box_single <- function(data, pri, sec=NULL, seed = 2103) {
|
||||
set.seed(seed)
|
||||
|
||||
|
|
@ -4907,8 +4861,6 @@ plot_box_single <- function(data, pri, sec=NULL, seed = 2103) {
|
|||
ggplot2::geom_boxplot(linewidth = 1.8, outliers = FALSE) +
|
||||
## THis could be optional in future
|
||||
ggplot2::geom_jitter(color = "black", size = 2, alpha = 0.9, width = 0.1, height = .2) +
|
||||
ggplot2::xlab(get_label(data,pri))+
|
||||
ggplot2::ylab(get_label(data,sec)) +
|
||||
ggplot2::coord_flip() +
|
||||
viridis::scale_fill_viridis(discrete = discrete, option = "D") +
|
||||
# ggplot2::theme_void() +
|
||||
|
|
@ -5031,7 +4983,7 @@ plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
|
|||
})
|
||||
|
||||
# names(out)
|
||||
wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}"))
|
||||
wrap_plot_list(out)
|
||||
# patchwork::wrap_plots(out, guides = "collect")
|
||||
}
|
||||
|
||||
|
|
@ -5506,7 +5458,7 @@ plot_violin <- function(data, pri, sec, ter = NULL) {
|
|||
)
|
||||
})
|
||||
|
||||
wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}"))
|
||||
wrap_plot_list(out)
|
||||
# patchwork::wrap_plots(out,guides = "collect")
|
||||
}
|
||||
|
||||
|
|
@ -7420,10 +7372,7 @@ regression_ui <- function(id, ...) {
|
|||
ns <- shiny::NS(id)
|
||||
|
||||
shiny::tagList(
|
||||
# title = "",
|
||||
bslib::nav_panel(
|
||||
title = "Regression table",
|
||||
bslib::layout_sidebar(
|
||||
title = "",
|
||||
sidebar = bslib::sidebar(
|
||||
shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
|
||||
bslib::accordion(
|
||||
|
|
@ -7498,19 +7447,7 @@ regression_ui <- function(id, ...) {
|
|||
# )
|
||||
# ),
|
||||
shiny::tags$br()
|
||||
)
|
||||
)
|
||||
),
|
||||
gt::gt_output(outputId = ns("table2"))
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Coefficient plot",
|
||||
bslib::layout_sidebar(
|
||||
sidebar = bslib::sidebar(
|
||||
bslib::accordion(
|
||||
open = "acc_reg",
|
||||
multiple = FALSE,
|
||||
do.call(
|
||||
bslib::accordion_panel,
|
||||
c(
|
||||
|
|
@ -7564,19 +7501,7 @@ regression_ui <- function(id, ...) {
|
|||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
),
|
||||
shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Model checks",
|
||||
bslib::layout_sidebar(
|
||||
sidebar = bslib::sidebar(
|
||||
bslib::accordion(
|
||||
open = "acc_reg",
|
||||
multiple = FALSE,
|
||||
bslib::accordion_panel(
|
||||
value = "acc_checks",
|
||||
title = "Checks",
|
||||
|
|
@ -7585,10 +7510,19 @@ regression_ui <- function(id, ...) {
|
|||
)
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Regression table",
|
||||
gt::gt_output(outputId = ns("table2"))
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Coefficient plot",
|
||||
shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Model checks",
|
||||
shiny::plotOutput(outputId = ns("check"), height = "90vh")
|
||||
)
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -9897,8 +9831,6 @@ ui_elements <- list(
|
|||
##############################################################################
|
||||
"home" = bslib::nav_panel(
|
||||
title = "FreesearchR",
|
||||
# title = shiny::div(htmltools::img(src="FreesearchR-logo-white-nobg-h80.png")),
|
||||
icon = shiny::icon("house"),
|
||||
shiny::fluidRow(
|
||||
## On building the dev-version for shinyapps.io, the dev_banner() is redefined
|
||||
## Default just output "NULL"
|
||||
|
|
@ -9910,7 +9842,8 @@ ui_elements <- list(
|
|||
shiny::markdown(readLines("www/intro.md")),
|
||||
shiny::column(width = 2)
|
||||
)
|
||||
)
|
||||
),
|
||||
icon = shiny::icon("home")
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
|
|
@ -9918,8 +9851,7 @@ ui_elements <- list(
|
|||
#########
|
||||
##############################################################################
|
||||
"import" = bslib::nav_panel(
|
||||
title = "Get started",
|
||||
icon = shiny::icon("upload"),
|
||||
title = "Import",
|
||||
shiny::fluidRow(
|
||||
shiny::column(width = 2),
|
||||
shiny::column(
|
||||
|
|
@ -10037,13 +9969,15 @@ ui_elements <- list(
|
|||
######### Data overview panel
|
||||
#########
|
||||
##############################################################################
|
||||
"prepare" = bslib::nav_menu(
|
||||
title = "Prepare",
|
||||
icon = shiny::icon("pen-to-square"),
|
||||
"overview" =
|
||||
# bslib::nav_panel_hidden(
|
||||
bslib::nav_panel(
|
||||
# value = "overview",
|
||||
title = "Data",
|
||||
bslib::navset_bar(
|
||||
fillable = TRUE,
|
||||
bslib::nav_panel(
|
||||
title = "Overview",
|
||||
icon = shiny::icon("eye"),
|
||||
value = "nav_prepare_overview",
|
||||
tags$h3("Overview and filtering"),
|
||||
fluidRow(
|
||||
shiny::column(
|
||||
|
|
@ -10085,6 +10019,22 @@ ui_elements <- list(
|
|||
),
|
||||
shiny::column(
|
||||
width = 3,
|
||||
# shiny::actionButton(
|
||||
# inputId = "modal_missings",
|
||||
# label = "Visual overview",
|
||||
# width = "100%",
|
||||
# disabled = TRUE
|
||||
# ),
|
||||
# shiny::br(),
|
||||
# shiny::br(),
|
||||
# shiny::actionButton(
|
||||
# inputId = "modal_browse",
|
||||
# label = "Browse data",
|
||||
# width = "100%",
|
||||
# disabled = TRUE
|
||||
# ),
|
||||
# shiny::br(),
|
||||
# shiny::br(),
|
||||
shiny::tags$h6("Filter data types"),
|
||||
shiny::uiOutput(
|
||||
outputId = "column_filter"
|
||||
|
|
@ -10106,11 +10056,12 @@ ui_elements <- list(
|
|||
),
|
||||
shiny::br(),
|
||||
shiny::br(),
|
||||
# shiny::br(),
|
||||
# shiny::br(),
|
||||
shiny::br()
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Modify",
|
||||
icon = shiny::icon("file-pen"),
|
||||
tags$h3("Subset, rename and convert variables"),
|
||||
fluidRow(
|
||||
shiny::column(
|
||||
|
|
@ -10122,6 +10073,7 @@ ui_elements <- list(
|
|||
)
|
||||
)
|
||||
),
|
||||
# shiny::tags$br(),
|
||||
update_variables_ui("modal_variables"),
|
||||
shiny::tags$br(),
|
||||
shiny::tags$br(),
|
||||
|
|
@ -10177,11 +10129,13 @@ ui_elements <- list(
|
|||
shiny::column(
|
||||
width = 6,
|
||||
shiny::tags$b("Original data:"),
|
||||
# verbatimTextOutput("original"),
|
||||
shiny::verbatimTextOutput("original_str")
|
||||
),
|
||||
shiny::column(
|
||||
width = 6,
|
||||
shiny::tags$b("Modified data:"),
|
||||
# verbatimTextOutput("modified"),
|
||||
shiny::verbatimTextOutput("modified_str")
|
||||
)
|
||||
),
|
||||
|
|
@ -10195,7 +10149,7 @@ ui_elements <- list(
|
|||
shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
|
||||
shiny::tags$br()
|
||||
)
|
||||
# )
|
||||
)
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
|
|
@ -10203,28 +10157,22 @@ ui_elements <- list(
|
|||
#########
|
||||
##############################################################################
|
||||
"describe" =
|
||||
bslib::nav_menu(
|
||||
title = "Evaluate",
|
||||
icon = shiny::icon("magnifying-glass-chart"),
|
||||
# id = "navdescribe",
|
||||
# bslib::navset_bar(
|
||||
# title = "",
|
||||
bslib::nav_panel(
|
||||
title = "Characteristics",
|
||||
icon = bsicons::bs_icon("table"),
|
||||
bslib::layout_sidebar(
|
||||
title = "Evaluate",
|
||||
id = "navdescribe",
|
||||
bslib::navset_bar(
|
||||
title = "",
|
||||
sidebar = bslib::sidebar(
|
||||
shiny::uiOutput(outputId = "data_info_nochar", inline = TRUE),
|
||||
bslib::accordion(
|
||||
open = "acc_chars",
|
||||
multiple = FALSE,
|
||||
bslib::accordion_panel(
|
||||
open = TRUE,
|
||||
value = "acc_chars",
|
||||
title = "Settings",
|
||||
title = "Characteristics",
|
||||
icon = bsicons::bs_icon("table"),
|
||||
shiny::uiOutput("strat_var"),
|
||||
shiny::helpText("Only factor/categorical variables are available for stratification. Go back to the 'Prepare' tab to reclass a variable if it's not on the list."),
|
||||
shiny::helpText("Only factor/categorical variables are available for stratification. Go back to the 'Data' tab to reclass a variable if it's not on the list."),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.strat_var!='none'",
|
||||
shiny::radioButtons(
|
||||
|
|
@ -10248,23 +10196,9 @@ ui_elements <- list(
|
|||
icon = shiny::icon("calculator"),
|
||||
disabled = TRUE
|
||||
)
|
||||
)
|
||||
)
|
||||
),
|
||||
gt::gt_output(outputId = "table1")
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Correlations",
|
||||
icon = bsicons::bs_icon("bounding-box"),
|
||||
bslib::layout_sidebar(
|
||||
sidebar = bslib::sidebar(
|
||||
shiny::uiOutput(outputId = "data_info_nochar", inline = TRUE),
|
||||
bslib::accordion(
|
||||
open = "acc_chars",
|
||||
multiple = FALSE,
|
||||
bslib::accordion_panel(
|
||||
value = "acc_cor",
|
||||
vlaue = "acc_cor",
|
||||
title = "Correlations",
|
||||
icon = bsicons::bs_icon("bounding-box"),
|
||||
shiny::uiOutput("outcome_var_cor"),
|
||||
|
|
@ -10281,29 +10215,26 @@ ui_elements <- list(
|
|||
color = datamods:::get_primary_color()
|
||||
),
|
||||
shiny::helpText("Set the cut-off for considered 'highly correlated'.")
|
||||
)
|
||||
)
|
||||
),
|
||||
data_correlations_ui(id = "correlations", height = 600)
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Missings",
|
||||
icon = bsicons::bs_icon("x-circle"),
|
||||
bslib::layout_sidebar(
|
||||
sidebar = bslib::sidebar(
|
||||
bslib::accordion(
|
||||
open = "acc_chars",
|
||||
multiple = FALSE,
|
||||
bslib::accordion_panel(
|
||||
vlaue = "acc_mis",
|
||||
title = "Missings",
|
||||
icon = bsicons::bs_icon("x-circle"),
|
||||
shiny::uiOutput("missings_var"),
|
||||
shiny::helpText("To consider if data is missing by random, choose the outcome/dependent variable, if it has any missings to evaluate if there is a significant difference across other variables depending on missing data or not.")
|
||||
shiny::helpText("To consider if daata is missing by random, choose the outcome/dependent variable, if it has any missings to evaluate if there is a significant difference across other variables depending on missing data or not.")
|
||||
)
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Characteristics",
|
||||
gt::gt_output(outputId = "table1")
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Correlations",
|
||||
data_correlations_ui(id = "correlations", height = 600)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Missings",
|
||||
data_missings_ui(id = "missingness")
|
||||
)
|
||||
)
|
||||
|
|
@ -10313,23 +10244,27 @@ ui_elements <- list(
|
|||
######### Download panel
|
||||
#########
|
||||
##############################################################################
|
||||
"visuals" = do.call(
|
||||
bslib::nav_panel,
|
||||
c(
|
||||
list(
|
||||
"visuals" = bslib::nav_panel(
|
||||
title = "Visuals",
|
||||
icon = shiny::icon("chart-line"),
|
||||
id = "navvisuals"
|
||||
),
|
||||
data_visuals_ui("visuals")
|
||||
id = "navvisuals",
|
||||
do.call(
|
||||
bslib::navset_bar,
|
||||
c(
|
||||
data_visuals_ui("visuals"),
|
||||
shiny::tagList(
|
||||
bslib::nav_spacer(),
|
||||
bslib::nav_item(
|
||||
# shiny::img(shiny::icon("book")),
|
||||
shiny::tags$a(
|
||||
href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
|
||||
"Notes (external)",
|
||||
target = "_blank",
|
||||
rel = "noopener noreferrer"
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
# do.call(
|
||||
# bslib::navset_bar,
|
||||
# data_visuals_ui("visuals")#,
|
||||
# c(
|
||||
|
||||
# )
|
||||
# )
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
|
|
@ -10339,10 +10274,9 @@ ui_elements <- list(
|
|||
"analyze" =
|
||||
bslib::nav_panel(
|
||||
title = "Regression",
|
||||
icon = shiny::icon("calculator"),
|
||||
id = "navanalyses",
|
||||
do.call(
|
||||
bslib::navset_card_tab,
|
||||
bslib::navset_bar,
|
||||
regression_ui("regression")
|
||||
)
|
||||
),
|
||||
|
|
@ -10354,7 +10288,6 @@ ui_elements <- list(
|
|||
"download" =
|
||||
bslib::nav_panel(
|
||||
title = "Download",
|
||||
icon = shiny::icon("download"),
|
||||
id = "navdownload",
|
||||
shiny::fluidRow(
|
||||
shiny::column(width = 2),
|
||||
|
|
@ -10480,25 +10413,9 @@ dark <- custom_theme(
|
|||
# https://webdesignerdepot.com/17-open-source-fonts-youll-actually-love/
|
||||
|
||||
ui <- bslib::page_fixed(
|
||||
## Code formatting dependencies
|
||||
prismDependencies,
|
||||
prismRDependency,
|
||||
## Version dependent header
|
||||
header_include(),
|
||||
## Automatically close drop-downs on navigation
|
||||
## Thanks to claude.ai
|
||||
tags$script("
|
||||
$(document).on('shown.bs.tab', '#main_panel', function(e) {
|
||||
// Close dropdown in this specific navset only
|
||||
$('#main_panel .dropdown-menu').removeClass('show');
|
||||
$('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false');
|
||||
|
||||
// THE BELOW DOES NOT WORK
|
||||
// Close navbar collapse (burger menu)
|
||||
$('#main_panel .navbar-collapse collapse').removeClass('show');
|
||||
$('#main_panel .navbar-toggle').removeClass('collapsed').attr('aria-expanded', 'false');
|
||||
});
|
||||
"),
|
||||
## This adds the actual favicon
|
||||
## png and ico versions are kept for compatibility
|
||||
shiny::tags$head(tags$link(rel = "shortcut icon", href = "favicon.svg")),
|
||||
|
|
@ -10518,14 +10435,14 @@ ui <- bslib::page_fixed(
|
|||
id = "main_panel",
|
||||
ui_elements$home,
|
||||
ui_elements$import,
|
||||
ui_elements$prepare,
|
||||
ui_elements$overview,
|
||||
ui_elements$describe,
|
||||
ui_elements$visuals,
|
||||
ui_elements$analyze,
|
||||
ui_elements$download,
|
||||
bslib::nav_spacer(),
|
||||
# ui_elements$feedback,
|
||||
# ui_elements$docs,
|
||||
ui_elements$feedback,
|
||||
ui_elements$docs,
|
||||
fillable = FALSE,
|
||||
footer = shiny::tags$footer(
|
||||
style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
|
||||
|
|
@ -10535,7 +10452,7 @@ ui <- bslib::page_fixed(
|
|||
),
|
||||
shiny::p(
|
||||
style = "margin: 1; color: #888;",
|
||||
shiny::tags$a("Documentation", href = "https://agdamsbo.github.io/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", hosted_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer")
|
||||
shiny::tags$a("Docs", href = "https://agdamsbo.github.io/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", hosted_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer")
|
||||
),
|
||||
)
|
||||
)
|
||||
|
|
@ -11247,7 +11164,7 @@ server <- function(input, output, session) {
|
|||
##############################################################################
|
||||
|
||||
shiny::observeEvent(input$act_start, {
|
||||
bslib::nav_select(id = "main_panel", selected = "nav_prepare_overview")
|
||||
bslib::nav_select(id = "main_panel", selected = "Data")
|
||||
})
|
||||
|
||||
##############################################################################
|
||||
|
|
|
|||
Binary file not shown.
|
Before Width: | Height: | Size: 80 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 246 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 6.6 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 85 KiB |
|
|
@ -5,7 +5,7 @@
|
|||
########
|
||||
|
||||
library(shiny)
|
||||
library(shinyjs)
|
||||
# library(shinyjs)
|
||||
# library(methods)
|
||||
# library(readr)
|
||||
# library(MASS)
|
||||
|
|
@ -49,7 +49,7 @@ library(rlang)
|
|||
#### Current file: /Users/au301842/FreesearchR/R//app_version.R
|
||||
########
|
||||
|
||||
app_version <- function()'25.7.2'
|
||||
app_version <- function()'25.6.4'
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -1611,8 +1611,10 @@ plot_histogram <- function(data, column=NULL, bins = 30, breaks = NULL, color =
|
|||
data_visuals_ui <- function(id, tab_title = "Plots", ...) {
|
||||
ns <- shiny::NS(id)
|
||||
|
||||
# bslib::navset_bar(
|
||||
list(
|
||||
bslib::layout_sidebar(
|
||||
|
||||
# Sidebar with a slider input
|
||||
sidebar = bslib::sidebar(
|
||||
bslib::accordion(
|
||||
multiple = FALSE,
|
||||
|
|
@ -1635,6 +1637,10 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
|
|||
),
|
||||
shiny::helpText('Adjust settings, then press "Plot".')
|
||||
),
|
||||
# bslib::accordion_panel(
|
||||
# title = "Advanced",
|
||||
# icon = bsicons::bs_icon("gear")
|
||||
# ),
|
||||
bslib::accordion_panel(
|
||||
title = "Download",
|
||||
icon = bsicons::bs_icon("download"),
|
||||
|
|
@ -1686,21 +1692,16 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
|
|||
icon = shiny::icon("download")
|
||||
)
|
||||
)
|
||||
)
|
||||
),
|
||||
shiny::p("We have collected a few notes on visualising data and details on the options included in FreesearchR:", shiny::tags$a(
|
||||
href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
|
||||
"View notes in new tab",
|
||||
target = "_blank",
|
||||
rel = "noopener noreferrer"
|
||||
))
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = tab_title,
|
||||
shiny::plotOutput(ns("plot"), height = "70vh"),
|
||||
shiny::tags$br(),
|
||||
shiny::tags$br(),
|
||||
shiny::htmlOutput(outputId = ns("code_plot"))
|
||||
)
|
||||
)
|
||||
# )
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -2324,7 +2325,6 @@ get_label <- function(data, var = NULL) {
|
|||
#' paste(sample(letters[1:10], 100, TRUE), collapse = "") |> line_break(force = TRUE)
|
||||
line_break <- function(data, lineLength = 20, force = FALSE) {
|
||||
if (isTRUE(force)) {
|
||||
## This eats some letters when splitting a sentence... ??
|
||||
gsub(paste0("(.{1,", lineLength, "})(\\s|[[:alnum:]])"), "\\1\n", data)
|
||||
} else {
|
||||
paste(strwrap(data, lineLength), collapse = "\n")
|
||||
|
|
@ -2346,7 +2346,7 @@ line_break <- function(data, lineLength = 20, force = FALSE) {
|
|||
wrap_plot_list <- function(data,
|
||||
tag_levels = NULL,
|
||||
title = NULL,
|
||||
axis.font.family = NULL,
|
||||
axis.font.family=NULL,
|
||||
...) {
|
||||
if (ggplot2::is_ggplot(data[[1]])) {
|
||||
if (length(data) > 1) {
|
||||
|
|
@ -4026,7 +4026,7 @@ simple_snake <- function(data){
|
|||
#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R
|
||||
########
|
||||
|
||||
hosted_version <- function()'v25.7.2-250703'
|
||||
hosted_version <- function()'v25.6.4-250627'
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -4735,7 +4735,14 @@ data_missings_server <- function(id,
|
|||
|
||||
tryCatch(
|
||||
{
|
||||
out <- compare_missings(df_tbl,by_var)
|
||||
if (!is.null(by_var) && by_var != "" && by_var %in% names(df_tbl)) {
|
||||
df_tbl[[by_var]] <- ifelse(is.na(df_tbl[[by_var]]), "Missing", "Non-missing")
|
||||
|
||||
out <- gtsummary::tbl_summary(df_tbl, by = by_var) |>
|
||||
gtsummary::add_p()
|
||||
} else {
|
||||
out <- gtsummary::tbl_summary(df_tbl)
|
||||
}
|
||||
},
|
||||
error = function(err) {
|
||||
showNotification(paste0("Error: ", err), type = "err")
|
||||
|
|
@ -4813,25 +4820,13 @@ missing_demo_app <- function() {
|
|||
|
||||
missing_demo_app()
|
||||
|
||||
#' Pairwise comparison of missings across covariables
|
||||
#'
|
||||
#' @param data data frame
|
||||
#' @param by_var variable to stratify by missingness
|
||||
#'
|
||||
#' @returns gtsummary list object
|
||||
#' @export
|
||||
#'
|
||||
compare_missings <- function(data,by_var){
|
||||
if (!is.null(by_var) && by_var != "" && by_var %in% names(data)) {
|
||||
data[[by_var]] <- ifelse(is.na(data[[by_var]]), "Missing", "Non-missing")
|
||||
|
||||
out <- gtsummary::tbl_summary(data, by = by_var) |>
|
||||
gtsummary::add_p()
|
||||
} else {
|
||||
out <- gtsummary::tbl_summary(data)
|
||||
}
|
||||
out
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -7420,10 +7415,7 @@ regression_ui <- function(id, ...) {
|
|||
ns <- shiny::NS(id)
|
||||
|
||||
shiny::tagList(
|
||||
# title = "",
|
||||
bslib::nav_panel(
|
||||
title = "Regression table",
|
||||
bslib::layout_sidebar(
|
||||
title = "",
|
||||
sidebar = bslib::sidebar(
|
||||
shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
|
||||
bslib::accordion(
|
||||
|
|
@ -7498,19 +7490,7 @@ regression_ui <- function(id, ...) {
|
|||
# )
|
||||
# ),
|
||||
shiny::tags$br()
|
||||
)
|
||||
)
|
||||
),
|
||||
gt::gt_output(outputId = ns("table2"))
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Coefficient plot",
|
||||
bslib::layout_sidebar(
|
||||
sidebar = bslib::sidebar(
|
||||
bslib::accordion(
|
||||
open = "acc_reg",
|
||||
multiple = FALSE,
|
||||
do.call(
|
||||
bslib::accordion_panel,
|
||||
c(
|
||||
|
|
@ -7564,19 +7544,7 @@ regression_ui <- function(id, ...) {
|
|||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
),
|
||||
shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Model checks",
|
||||
bslib::layout_sidebar(
|
||||
sidebar = bslib::sidebar(
|
||||
bslib::accordion(
|
||||
open = "acc_reg",
|
||||
multiple = FALSE,
|
||||
bslib::accordion_panel(
|
||||
value = "acc_checks",
|
||||
title = "Checks",
|
||||
|
|
@ -7585,10 +7553,19 @@ regression_ui <- function(id, ...) {
|
|||
)
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Regression table",
|
||||
gt::gt_output(outputId = ns("table2"))
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Coefficient plot",
|
||||
shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Model checks",
|
||||
shiny::plotOutput(outputId = ns("check"), height = "90vh")
|
||||
)
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -9867,8 +9844,7 @@ grepl_fix <- function(data, pattern, type = c("prefix", "infix", "suffix")) {
|
|||
|
||||
header_include <- function(){
|
||||
shiny::tags$head(
|
||||
tags$link(rel = "stylesheet", type = "text/css", href = "style.css"),
|
||||
tags$script(src="scripts.js"))
|
||||
tags$link(rel = "stylesheet", type = "text/css", href = "style.css"))
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -9897,8 +9873,6 @@ ui_elements <- list(
|
|||
##############################################################################
|
||||
"home" = bslib::nav_panel(
|
||||
title = "FreesearchR",
|
||||
# title = shiny::div(htmltools::img(src="FreesearchR-logo-white-nobg-h80.png")),
|
||||
icon = shiny::icon("house"),
|
||||
shiny::fluidRow(
|
||||
## On building the dev-version for shinyapps.io, the dev_banner() is redefined
|
||||
## Default just output "NULL"
|
||||
|
|
@ -9910,7 +9884,8 @@ ui_elements <- list(
|
|||
shiny::markdown(readLines("www/intro.md")),
|
||||
shiny::column(width = 2)
|
||||
)
|
||||
)
|
||||
),
|
||||
icon = shiny::icon("home")
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
|
|
@ -9918,8 +9893,7 @@ ui_elements <- list(
|
|||
#########
|
||||
##############################################################################
|
||||
"import" = bslib::nav_panel(
|
||||
title = "Get started",
|
||||
icon = shiny::icon("play"),
|
||||
title = "Import",
|
||||
shiny::fluidRow(
|
||||
shiny::column(width = 2),
|
||||
shiny::column(
|
||||
|
|
@ -10037,13 +10011,15 @@ ui_elements <- list(
|
|||
######### Data overview panel
|
||||
#########
|
||||
##############################################################################
|
||||
"prepare" = bslib::nav_menu(
|
||||
title = "Prepare",
|
||||
icon = shiny::icon("pen-to-square"),
|
||||
"overview" =
|
||||
# bslib::nav_panel_hidden(
|
||||
bslib::nav_panel(
|
||||
# value = "overview",
|
||||
title = "Data",
|
||||
bslib::navset_bar(
|
||||
fillable = TRUE,
|
||||
bslib::nav_panel(
|
||||
title = "Overview",
|
||||
icon = shiny::icon("eye"),
|
||||
value = "nav_prepare_overview",
|
||||
tags$h3("Overview and filtering"),
|
||||
fluidRow(
|
||||
shiny::column(
|
||||
|
|
@ -10085,6 +10061,22 @@ ui_elements <- list(
|
|||
),
|
||||
shiny::column(
|
||||
width = 3,
|
||||
# shiny::actionButton(
|
||||
# inputId = "modal_missings",
|
||||
# label = "Visual overview",
|
||||
# width = "100%",
|
||||
# disabled = TRUE
|
||||
# ),
|
||||
# shiny::br(),
|
||||
# shiny::br(),
|
||||
# shiny::actionButton(
|
||||
# inputId = "modal_browse",
|
||||
# label = "Browse data",
|
||||
# width = "100%",
|
||||
# disabled = TRUE
|
||||
# ),
|
||||
# shiny::br(),
|
||||
# shiny::br(),
|
||||
shiny::tags$h6("Filter data types"),
|
||||
shiny::uiOutput(
|
||||
outputId = "column_filter"
|
||||
|
|
@ -10106,11 +10098,12 @@ ui_elements <- list(
|
|||
),
|
||||
shiny::br(),
|
||||
shiny::br(),
|
||||
# shiny::br(),
|
||||
# shiny::br(),
|
||||
shiny::br()
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Modify",
|
||||
icon = shiny::icon("file-pen"),
|
||||
tags$h3("Subset, rename and convert variables"),
|
||||
fluidRow(
|
||||
shiny::column(
|
||||
|
|
@ -10122,6 +10115,7 @@ ui_elements <- list(
|
|||
)
|
||||
)
|
||||
),
|
||||
# shiny::tags$br(),
|
||||
update_variables_ui("modal_variables"),
|
||||
shiny::tags$br(),
|
||||
shiny::tags$br(),
|
||||
|
|
@ -10177,11 +10171,13 @@ ui_elements <- list(
|
|||
shiny::column(
|
||||
width = 6,
|
||||
shiny::tags$b("Original data:"),
|
||||
# verbatimTextOutput("original"),
|
||||
shiny::verbatimTextOutput("original_str")
|
||||
),
|
||||
shiny::column(
|
||||
width = 6,
|
||||
shiny::tags$b("Modified data:"),
|
||||
# verbatimTextOutput("modified"),
|
||||
shiny::verbatimTextOutput("modified_str")
|
||||
)
|
||||
),
|
||||
|
|
@ -10195,7 +10191,7 @@ ui_elements <- list(
|
|||
shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
|
||||
shiny::tags$br()
|
||||
)
|
||||
# )
|
||||
)
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
|
|
@ -10203,28 +10199,22 @@ ui_elements <- list(
|
|||
#########
|
||||
##############################################################################
|
||||
"describe" =
|
||||
bslib::nav_menu(
|
||||
title = "Evaluate",
|
||||
icon = shiny::icon("magnifying-glass-chart"),
|
||||
# id = "navdescribe",
|
||||
# bslib::navset_bar(
|
||||
# title = "",
|
||||
bslib::nav_panel(
|
||||
title = "Characteristics",
|
||||
icon = bsicons::bs_icon("table"),
|
||||
bslib::layout_sidebar(
|
||||
title = "Evaluate",
|
||||
id = "navdescribe",
|
||||
bslib::navset_bar(
|
||||
title = "",
|
||||
sidebar = bslib::sidebar(
|
||||
shiny::uiOutput(outputId = "data_info_nochar", inline = TRUE),
|
||||
bslib::accordion(
|
||||
open = "acc_chars",
|
||||
multiple = FALSE,
|
||||
bslib::accordion_panel(
|
||||
open = TRUE,
|
||||
value = "acc_chars",
|
||||
title = "Settings",
|
||||
title = "Characteristics",
|
||||
icon = bsicons::bs_icon("table"),
|
||||
shiny::uiOutput("strat_var"),
|
||||
shiny::helpText("Only factor/categorical variables are available for stratification. Go back to the 'Prepare' tab to reclass a variable if it's not on the list."),
|
||||
shiny::helpText("Only factor/categorical variables are available for stratification. Go back to the 'Data' tab to reclass a variable if it's not on the list."),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.strat_var!='none'",
|
||||
shiny::radioButtons(
|
||||
|
|
@ -10248,23 +10238,9 @@ ui_elements <- list(
|
|||
icon = shiny::icon("calculator"),
|
||||
disabled = TRUE
|
||||
)
|
||||
)
|
||||
)
|
||||
),
|
||||
gt::gt_output(outputId = "table1")
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Correlations",
|
||||
icon = bsicons::bs_icon("bounding-box"),
|
||||
bslib::layout_sidebar(
|
||||
sidebar = bslib::sidebar(
|
||||
shiny::uiOutput(outputId = "data_info_nochar", inline = TRUE),
|
||||
bslib::accordion(
|
||||
open = "acc_chars",
|
||||
multiple = FALSE,
|
||||
bslib::accordion_panel(
|
||||
value = "acc_cor",
|
||||
vlaue = "acc_cor",
|
||||
title = "Correlations",
|
||||
icon = bsicons::bs_icon("bounding-box"),
|
||||
shiny::uiOutput("outcome_var_cor"),
|
||||
|
|
@ -10281,29 +10257,26 @@ ui_elements <- list(
|
|||
color = datamods:::get_primary_color()
|
||||
),
|
||||
shiny::helpText("Set the cut-off for considered 'highly correlated'.")
|
||||
)
|
||||
)
|
||||
),
|
||||
data_correlations_ui(id = "correlations", height = 600)
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Missings",
|
||||
icon = bsicons::bs_icon("x-circle"),
|
||||
bslib::layout_sidebar(
|
||||
sidebar = bslib::sidebar(
|
||||
bslib::accordion(
|
||||
open = "acc_chars",
|
||||
multiple = FALSE,
|
||||
bslib::accordion_panel(
|
||||
vlaue = "acc_mis",
|
||||
title = "Missings",
|
||||
icon = bsicons::bs_icon("x-circle"),
|
||||
shiny::uiOutput("missings_var"),
|
||||
shiny::helpText("To consider if data is missing by random, choose the outcome/dependent variable, if it has any missings to evaluate if there is a significant difference across other variables depending on missing data or not.")
|
||||
shiny::helpText("To consider if daata is missing by random, choose the outcome/dependent variable, if it has any missings to evaluate if there is a significant difference across other variables depending on missing data or not.")
|
||||
)
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Characteristics",
|
||||
gt::gt_output(outputId = "table1")
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Correlations",
|
||||
data_correlations_ui(id = "correlations", height = 600)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Missings",
|
||||
data_missings_ui(id = "missingness")
|
||||
)
|
||||
)
|
||||
|
|
@ -10313,23 +10286,27 @@ ui_elements <- list(
|
|||
######### Download panel
|
||||
#########
|
||||
##############################################################################
|
||||
"visuals" = do.call(
|
||||
bslib::nav_panel,
|
||||
c(
|
||||
list(
|
||||
"visuals" = bslib::nav_panel(
|
||||
title = "Visuals",
|
||||
icon = shiny::icon("chart-line"),
|
||||
id = "navvisuals"
|
||||
),
|
||||
data_visuals_ui("visuals")
|
||||
id = "navvisuals",
|
||||
do.call(
|
||||
bslib::navset_bar,
|
||||
c(
|
||||
data_visuals_ui("visuals"),
|
||||
shiny::tagList(
|
||||
bslib::nav_spacer(),
|
||||
bslib::nav_item(
|
||||
# shiny::img(shiny::icon("book")),
|
||||
shiny::tags$a(
|
||||
href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
|
||||
"Notes (external)",
|
||||
target = "_blank",
|
||||
rel = "noopener noreferrer"
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
# do.call(
|
||||
# bslib::navset_bar,
|
||||
# data_visuals_ui("visuals")#,
|
||||
# c(
|
||||
|
||||
# )
|
||||
# )
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
|
|
@ -10339,10 +10316,9 @@ ui_elements <- list(
|
|||
"analyze" =
|
||||
bslib::nav_panel(
|
||||
title = "Regression",
|
||||
icon = shiny::icon("calculator"),
|
||||
id = "navanalyses",
|
||||
do.call(
|
||||
bslib::navset_card_tab,
|
||||
bslib::navset_bar,
|
||||
regression_ui("regression")
|
||||
)
|
||||
),
|
||||
|
|
@ -10354,7 +10330,6 @@ ui_elements <- list(
|
|||
"download" =
|
||||
bslib::nav_panel(
|
||||
title = "Download",
|
||||
icon = shiny::icon("download"),
|
||||
id = "navdownload",
|
||||
shiny::fluidRow(
|
||||
shiny::column(width = 2),
|
||||
|
|
@ -10480,42 +10455,9 @@ dark <- custom_theme(
|
|||
# https://webdesignerdepot.com/17-open-source-fonts-youll-actually-love/
|
||||
|
||||
ui <- bslib::page_fixed(
|
||||
## Code formatting dependencies
|
||||
prismDependencies,
|
||||
prismRDependency,
|
||||
## Version dependent header
|
||||
header_include(),
|
||||
## Automatically close drop-downs on navigation
|
||||
## Thanks to claude.ai
|
||||
# tags$script("
|
||||
# $(document).on('shown.bs.tab', '#main_panel', function(e) {
|
||||
# // Close dropdown in this specific navset only
|
||||
# $('#main_panel .dropdown-menu').removeClass('show');
|
||||
# $('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false');
|
||||
# });
|
||||
#
|
||||
# $(document).on('shiny:sessioninitialized', function() {
|
||||
# // Function to collapse navbar on mobile
|
||||
# function collapseNavbar() {
|
||||
# var navbar = $('.navbar-collapse');
|
||||
# if (navbar.hasClass('show')) {
|
||||
# navbar.removeClass('show');
|
||||
# $('.navbar-toggler').addClass('collapsed');
|
||||
# $('.navbar-toggler').attr('aria-expanded', 'false');
|
||||
# }
|
||||
# }
|
||||
#
|
||||
# // Add click event to navigation tabs
|
||||
# $(document).on('click', '.nav-link[data-bs-toggle=\"tab\"]', function() {
|
||||
# setTimeout(collapseNavbar, 10);
|
||||
# });
|
||||
#
|
||||
# // Also handle direct clicks on nav items
|
||||
# $(document).on('click', '.navbar-nav .nav-link', function() {
|
||||
# setTimeout(collapseNavbar, 10);
|
||||
# });
|
||||
# });
|
||||
# "),
|
||||
## This adds the actual favicon
|
||||
## png and ico versions are kept for compatibility
|
||||
shiny::tags$head(tags$link(rel = "shortcut icon", href = "favicon.svg")),
|
||||
|
|
@ -10535,14 +10477,14 @@ ui <- bslib::page_fixed(
|
|||
id = "main_panel",
|
||||
ui_elements$home,
|
||||
ui_elements$import,
|
||||
ui_elements$prepare,
|
||||
ui_elements$overview,
|
||||
ui_elements$describe,
|
||||
ui_elements$visuals,
|
||||
ui_elements$analyze,
|
||||
ui_elements$download,
|
||||
bslib::nav_spacer(),
|
||||
# ui_elements$feedback,
|
||||
# ui_elements$docs,
|
||||
ui_elements$feedback,
|
||||
ui_elements$docs,
|
||||
fillable = FALSE,
|
||||
footer = shiny::tags$footer(
|
||||
style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
|
||||
|
|
@ -10552,7 +10494,7 @@ ui <- bslib::page_fixed(
|
|||
),
|
||||
shiny::p(
|
||||
style = "margin: 1; color: #888;",
|
||||
shiny::tags$a("Documentation", href = "https://agdamsbo.github.io/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", hosted_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer")
|
||||
shiny::tags$a("Docs", href = "https://agdamsbo.github.io/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", hosted_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer")
|
||||
),
|
||||
)
|
||||
)
|
||||
|
|
@ -11264,7 +11206,7 @@ server <- function(input, output, session) {
|
|||
##############################################################################
|
||||
|
||||
shiny::observeEvent(input$act_start, {
|
||||
bslib::nav_select(id = "main_panel", selected = "nav_prepare_overview")
|
||||
bslib::nav_select(id = "main_panel", selected = "Data")
|
||||
})
|
||||
|
||||
##############################################################################
|
||||
|
|
|
|||
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|
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|
Before Width: | Height: | Size: 246 KiB |
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|
Before Width: | Height: | Size: 6.6 KiB |
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|
Before Width: | Height: | Size: 85 KiB |
|
|
@ -1,29 +0,0 @@
|
|||
// Automatically close drop-downs on navigation
|
||||
// Thanks to claude.ai
|
||||
$(document).on('shown.bs.tab', '#main_panel', function(e) {
|
||||
// Close dropdown in this specific navset only
|
||||
$('#main_panel .dropdown-menu').removeClass('show');
|
||||
$('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false');
|
||||
});
|
||||
|
||||
$(document).on('shiny:sessioninitialized', function() {
|
||||
// Function to collapse navbar on mobile
|
||||
function collapseNavbar() {
|
||||
var navbar = $('.navbar-collapse');
|
||||
if (navbar.hasClass('show')) {
|
||||
navbar.removeClass('show');
|
||||
$('.navbar-toggler').addClass('collapsed');
|
||||
$('.navbar-toggler').attr('aria-expanded', 'false');
|
||||
}
|
||||
}
|
||||
|
||||
// Add click event to navigation tabs
|
||||
$(document).on('click', '.nav-link[data-bs-toggle=\"tab\"]', function() {
|
||||
setTimeout(collapseNavbar, 10);
|
||||
});
|
||||
|
||||
// Also handle direct clicks on nav items
|
||||
$(document).on('click', '.navbar-nav .nav-link', function() {
|
||||
setTimeout(collapseNavbar, 10);
|
||||
});
|
||||
});
|
||||
|
|
@ -1,29 +0,0 @@
|
|||
// Automatically close drop-downs on navigation
|
||||
// Thanks to claude.ai
|
||||
$(document).on('shown.bs.tab', '#main_panel', function(e) {
|
||||
// Close dropdown in this specific navset only
|
||||
$('#main_panel .dropdown-menu').removeClass('show');
|
||||
$('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false');
|
||||
});
|
||||
|
||||
$(document).on('shiny:sessioninitialized', function() {
|
||||
// Function to collapse navbar on mobile
|
||||
function collapseNavbar() {
|
||||
var navbar = $('.navbar-collapse');
|
||||
if (navbar.hasClass('show')) {
|
||||
navbar.removeClass('show');
|
||||
$('.navbar-toggler').addClass('collapsed');
|
||||
$('.navbar-toggler').attr('aria-expanded', 'false');
|
||||
}
|
||||
}
|
||||
|
||||
// Add click event to navigation tabs
|
||||
$(document).on('click', '.nav-link[data-bs-toggle=\"tab\"]', function() {
|
||||
setTimeout(collapseNavbar, 10);
|
||||
});
|
||||
|
||||
// Also handle direct clicks on nav items
|
||||
$(document).on('click', '.navbar-nav .nav-link', function() {
|
||||
setTimeout(collapseNavbar, 10);
|
||||
});
|
||||
});
|
||||
|
|
@ -1,19 +0,0 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/missings-module.R
|
||||
\name{compare_missings}
|
||||
\alias{compare_missings}
|
||||
\title{Pairwise comparison of missings across covariables}
|
||||
\usage{
|
||||
compare_missings(data, by_var)
|
||||
}
|
||||
\arguments{
|
||||
\item{data}{data frame}
|
||||
|
||||
\item{by_var}{variable to stratify by missingness}
|
||||
}
|
||||
\value{
|
||||
gtsummary list object
|
||||
}
|
||||
\description{
|
||||
Pairwise comparison of missings across covariables
|
||||
}
|
||||
|
|
@ -1,26 +0,0 @@
|
|||
---
|
||||
title: "Missingness in data"
|
||||
output: rmarkdown::html_vignette
|
||||
vignette: >
|
||||
%\VignetteIndexEntry{missingness}
|
||||
%\VignetteEngine{knitr::rmarkdown}
|
||||
%\VignetteEncoding{UTF-8}
|
||||
---
|
||||
|
||||
```{r, include = FALSE}
|
||||
knitr::opts_chunk$set(
|
||||
collapse = TRUE,
|
||||
comment = "#>"
|
||||
)
|
||||
options(rmarkdown.html_vignette.check_title = FALSE)
|
||||
```
|
||||
|
||||
```{r setup}
|
||||
library(FreesearchR)
|
||||
```
|
||||
|
||||
## Considering missing observations
|
||||
|
||||
### Further reading
|
||||
|
||||
The authors behind the [{finalfit}-package]() have shared a very comprehensive article on what to do and think about missing observations in your data. Please [have a look here]().
|
||||
Loading…
Add table
Reference in a new issue