JS in separate file to autohide dropdowns on navigation - new dev version

CITATION.cff

@@ -9,7 +9,7 @@ type: software
 license: AGPL-3.0-or-later
 title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers
   with publication ready output'
-version: 25.6.4
+version: 25.7.2
 doi: 10.5281/zenodo.14527429
 identifiers:
 - type: url

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: FreesearchR
 Title: A free and open-source browser based data analysis tool for researchers with publication ready output
-Version: 25.6.4
+Version: 25.7.2
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154")),

NAMESPACE

@@ -17,6 +17,7 @@ export(clean_common_axis)
 export(clean_date)
 export(clean_sep)
 export(columnSelectInput)
+export(compare_missings)
 export(contrast_text)
 export(create_baseline)
 export(create_column_server)

NEWS.md

@@ -1,3 +1,11 @@
+# FreesearchR 25.7.2 - DEV
+
+- *FIX* refining hiding drop downs. All JavaScript is now in separate file. Coded with GAI help from claude.ai.
+
+# FreesearchR 25.7.1
+
+- *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.
+
 # FreesearchR 25.6.4
 
 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.

R/app_version.R

@@ -1 +1 @@
-app_version <- function()'25.6.4'
+app_version <- function()'25.7.2'

R/data_plots.R

@@ -11,97 +11,96 @@
 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(
-    sidebar = bslib::sidebar(
+        bslib::accordion(
-      bslib::accordion(
+          multiple = FALSE,
-        multiple = FALSE,
+          bslib::accordion_panel(
-        bslib::accordion_panel(
+            title = "Creating plot",
-          title = "Creating plot",
+            icon = bsicons::bs_icon("graph-up"),
-          icon = bsicons::bs_icon("graph-up"),
+            shiny::uiOutput(outputId = ns("primary")),
-          shiny::uiOutput(outputId = ns("primary")),
+            shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'),
-          shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'),
+            shiny::tags$br(),
-          shiny::tags$br(),
+            shiny::uiOutput(outputId = ns("type")),
-          shiny::uiOutput(outputId = ns("type")),
+            shiny::uiOutput(outputId = ns("secondary")),
-          shiny::uiOutput(outputId = ns("secondary")),
+            shiny::uiOutput(outputId = ns("tertiary")),
-          shiny::uiOutput(outputId = ns("tertiary")),
+            shiny::br(),
-          shiny::br(),
+            shiny::actionButton(
-          shiny::actionButton(
+              inputId = ns("act_plot"),
-            inputId = ns("act_plot"),
+              label = "Plot",
-            label = "Plot",
+              width = "100%",
-            width = "100%",
+              icon = shiny::icon("palette"),
-            icon = shiny::icon("palette"),
+              disabled = FALSE
-            disabled = FALSE
+            ),
+            shiny::helpText('Adjust settings, then press "Plot".')
           ),
-          shiny::helpText('Adjust settings, then press "Plot".')
+          bslib::accordion_panel(
-        ),
+            title = "Download",
-        # bslib::accordion_panel(
+            icon = bsicons::bs_icon("download"),
-        #   title = "Advanced",
+            shinyWidgets::noUiSliderInput(
-        #   icon = bsicons::bs_icon("gear")
+              inputId = ns("height_slide"),
-        # ),
+              label = "Plot height (mm)",
-        bslib::accordion_panel(
+              min = 50,
-          title = "Download",
+              max = 300,
-          icon = bsicons::bs_icon("download"),
+              value = 100,
-          shinyWidgets::noUiSliderInput(
+              step = 1,
-            inputId = ns("height_slide"),
+              format = shinyWidgets::wNumbFormat(decimals = 0),
-            label = "Plot height (mm)",
+              color = datamods:::get_primary_color(),
-            min = 50,
+              inline = TRUE
-            max = 300,
+            ),
-            value = 100,
+            # shiny::numericInput(
-            step = 1,
+            #   inputId = ns("height_numeric"),
-            format = shinyWidgets::wNumbFormat(decimals = 0),
+            #   label = "Plot height (mm)",
-            color = datamods:::get_primary_color(),
+            #   min = 50,
-            inline = TRUE
+            #   max = 300,
-          ),
+            #   value = 100
-          # shiny::numericInput(
+            # ),
-          #   inputId = ns("height_numeric"),
+            shinyWidgets::noUiSliderInput(
-          #   label = "Plot height (mm)",
+              inputId = ns("width"),
-          #   min = 50,
+              label = "Plot width (mm)",
-          #   max = 300,
+              min = 50,
-          #   value = 100
+              max = 300,
-          # ),
+              value = 100,
-          shinyWidgets::noUiSliderInput(
+              step = 1,
-            inputId = ns("width"),
+              format = shinyWidgets::wNumbFormat(decimals = 0),
-            label = "Plot width (mm)",
+              color = datamods:::get_primary_color()
-            min = 50,
+            ),
-            max = 300,
+            shiny::selectInput(
-            value = 100,
+              inputId = ns("plot_type"),
-            step = 1,
+              label = "File format",
-            format = shinyWidgets::wNumbFormat(decimals = 0),
+              choices = list(
-            color = datamods:::get_primary_color()
+                "png",
-          ),
+                "tiff",
-          shiny::selectInput(
+                "eps",
-            inputId = ns("plot_type"),
+                "pdf",
-            label = "File format",
+                "jpeg",
-            choices = list(
+                "svg"
-              "png",
+              )
-              "tiff",
+            ),
-              "eps",
+            shiny::br(),
-              "pdf",
+            # Button
-              "jpeg",
+            shiny::downloadButton(
-              "svg"
+              outputId = ns("download_plot"),
+              label = "Download plot",
+              icon = shiny::icon("download")
             )
-          ),
-          shiny::br(),
-          # Button
-          shiny::downloadButton(
-            outputId = ns("download_plot"),
-            label = "Download plot",
-            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$a(
-    ),
+          href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
-    bslib::nav_panel(
+          "View notes in new tab",
-      title = tab_title,
+          target = "_blank",
+          rel = "noopener noreferrer"
+        ))
+      ),
       shiny::plotOutput(ns("plot"), height = "70vh"),
       shiny::tags$br(),
       shiny::tags$br(),
       shiny::htmlOutput(outputId = ns("code_plot"))
     )
   )
+  # )
 }
 
 
@@ -725,6 +724,7 @@ 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")
@@ -746,7 +746,7 @@ 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) {

R/hosted_version.R

@@ -1 +1 @@
-hosted_version <- function()'v25.6.4-250627'
+hosted_version <- function()'v25.7.2-250703'

R/missings-module.R

@@ -44,14 +44,7 @@ data_missings_server <- function(id,
 
         tryCatch(
           {
-            if (!is.null(by_var) && by_var != "" && by_var %in% names(df_tbl)) {
+            out <- compare_missings(df_tbl,by_var)
-              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")
@@ -129,10 +122,22 @@ 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
+}

R/regression-module.R

@@ -44,155 +44,173 @@ regression_ui <- function(id, ...) {
   ns <- shiny::NS(id)
 
   shiny::tagList(
-    title = "",
+    # title = "",
-    sidebar = bslib::sidebar(
+    bslib::nav_panel(
-      shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
+      title = "Regression table",
-      bslib::accordion(
+      bslib::layout_sidebar(
-        open = "acc_reg",
+        sidebar = bslib::sidebar(
-        multiple = FALSE,
+          shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
-        bslib::accordion_panel(
+          bslib::accordion(
-          value = "acc_reg",
+            open = "acc_reg",
-          title = "Regression",
+            multiple = FALSE,
-          icon = bsicons::bs_icon("calculator"),
+            bslib::accordion_panel(
-          shiny::uiOutput(outputId = ns("outcome_var")),
+              value = "acc_reg",
-          # shiny::selectInput(
+              title = "Regression",
-          #   inputId = "design",
+              icon = bsicons::bs_icon("calculator"),
-          #   label = "Study design",
+              shiny::uiOutput(outputId = ns("outcome_var")),
-          #   selected = "no",
+              # shiny::selectInput(
-          #   inline = TRUE,
+              #   inputId = "design",
-          #   choices = list(
+              #   label = "Study design",
-          #     "Cross-sectional" = "cross-sectional"
+              #   selected = "no",
-          #   )
+              #   inline = TRUE,
-          # ),
+              #   choices = list(
-          shiny::uiOutput(outputId = ns("regression_type")),
+              #     "Cross-sectional" = "cross-sectional"
-          shiny::radioButtons(
+              #   )
-            inputId = ns("all"),
+              # ),
-            label = "Specify covariables",
+              shiny::uiOutput(outputId = ns("regression_type")),
-            inline = TRUE, selected = 2,
+              shiny::radioButtons(
-            choiceNames = c(
+                inputId = ns("all"),
-              "Yes",
+                label = "Specify covariables",
-              "No"
+                inline = TRUE, selected = 2,
-            ),
+                choiceNames = c(
-            choiceValues = c(1, 2)
+                  "Yes",
-          ),
+                  "No"
-          shiny::conditionalPanel(
+                ),
-            condition = "input.all==1",
+                choiceValues = c(1, 2)
-            shiny::uiOutput(outputId = ns("regression_vars")),
+              ),
-            shiny::helpText("If none are selected, all are included."),
+              shiny::conditionalPanel(
-            shiny::tags$br(),
+                condition = "input.all==1",
-            ns = ns
+                shiny::uiOutput(outputId = ns("regression_vars")),
-          ),
+                shiny::helpText("If none are selected, all are included."),
-          bslib::input_task_button(
+                shiny::tags$br(),
-            id = ns("load"),
+                ns = ns
-            label = "Analyse",
+              ),
-            icon = bsicons::bs_icon("pencil"),
+              bslib::input_task_button(
-            label_busy = "Working...",
+                id = ns("load"),
-            icon_busy = fontawesome::fa_i("arrows-rotate",
+                label = "Analyse",
-              class = "fa-spin",
+                icon = bsicons::bs_icon("pencil"),
-              "aria-hidden" = "true"
+                label_busy = "Working...",
-            ),
+                icon_busy = fontawesome::fa_i("arrows-rotate",
-            type = "secondary",
+                  class = "fa-spin",
-            auto_reset = TRUE
+                  "aria-hidden" = "true"
-          ),
+                ),
-          shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
+                type = "secondary",
-          shiny::tags$br(),
+                auto_reset = TRUE
-          shiny::radioButtons(
+              ),
-            inputId = ns("add_regression_p"),
+              shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
-            label = "Show p-value",
-            inline = TRUE,
-            selected = "yes",
-            choices = list(
-              "Yes" = "yes",
-              "No" = "no"
-            )
-          ),
-          # shiny::tags$br(),
-          # shiny::radioButtons(
-          #   inputId = ns("tbl_theme"),
-          #   label = "Show p-value",
-          #   inline = TRUE,
-          #   selected = "jama",
-          #   choices = list(
-          #     "JAMA" = "jama",
-          #     "Lancet" = "lancet",
-          #     "NEJM" = "nejm"
-          #   )
-          # ),
-          shiny::tags$br()
-        ),
-        do.call(
-          bslib::accordion_panel,
-          c(
-            list(
-              value = "acc_plot",
-              title = "Coefficient plot",
-              icon = bsicons::bs_icon("bar-chart-steps"),
               shiny::tags$br(),
-              shiny::uiOutput(outputId = ns("plot_model"))
+              shiny::radioButtons(
-            ),
+                inputId = ns("add_regression_p"),
-            # plot_download_ui(ns("reg_plot_download"))
+                label = "Show p-value",
-            shiny::tagList(
+                inline = TRUE,
-              shinyWidgets::noUiSliderInput(
+                selected = "yes",
-                inputId = ns("plot_height"),
-                label = "Plot height (mm)",
-                min = 50,
-                max = 300,
-                value = 100,
-                step = 1,
-                format = shinyWidgets::wNumbFormat(decimals = 0),
-                color = datamods:::get_primary_color()
-              ),
-              shinyWidgets::noUiSliderInput(
-                inputId = ns("plot_width"),
-                label = "Plot width (mm)",
-                min = 50,
-                max = 300,
-                value = 100,
-                step = 1,
-                format = shinyWidgets::wNumbFormat(decimals = 0),
-                color = datamods:::get_primary_color()
-              ),
-              shiny::selectInput(
-                inputId = ns("plot_type"),
-                label = "File format",
                 choices = list(
-                  "png",
+                  "Yes" = "yes",
-                  "tiff",
+                  "No" = "no"
-                  "eps",
-                  "pdf",
-                  "jpeg",
-                  "svg"
                 )
               ),
-              shiny::br(),
+              # shiny::tags$br(),
-              # Button
+              # shiny::radioButtons(
-              shiny::downloadButton(
+              #   inputId = ns("tbl_theme"),
-                outputId = ns("download_plot"),
+              #   label = "Show p-value",
-                label = "Download plot",
+              #   inline = TRUE,
-                icon = shiny::icon("download")
+              #   selected = "jama",
+              #   choices = list(
+              #     "JAMA" = "jama",
+              #     "Lancet" = "lancet",
+              #     "NEJM" = "nejm"
+              #   )
+              # ),
+              shiny::tags$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(
+                list(
+                  value = "acc_plot",
+                  title = "Coefficient plot",
+                  icon = bsicons::bs_icon("bar-chart-steps"),
+                  shiny::tags$br(),
+                  shiny::uiOutput(outputId = ns("plot_model"))
+                ),
+                # plot_download_ui(ns("reg_plot_download"))
+                shiny::tagList(
+                  shinyWidgets::noUiSliderInput(
+                    inputId = ns("plot_height"),
+                    label = "Plot height (mm)",
+                    min = 50,
+                    max = 300,
+                    value = 100,
+                    step = 1,
+                    format = shinyWidgets::wNumbFormat(decimals = 0),
+                    color = datamods:::get_primary_color()
+                  ),
+                  shinyWidgets::noUiSliderInput(
+                    inputId = ns("plot_width"),
+                    label = "Plot width (mm)",
+                    min = 50,
+                    max = 300,
+                    value = 100,
+                    step = 1,
+                    format = shinyWidgets::wNumbFormat(decimals = 0),
+                    color = datamods:::get_primary_color()
+                  ),
+                  shiny::selectInput(
+                    inputId = ns("plot_type"),
+                    label = "File format",
+                    choices = list(
+                      "png",
+                      "tiff",
+                      "eps",
+                      "pdf",
+                      "jpeg",
+                      "svg"
+                    )
+                  ),
+                  shiny::br(),
+                  # Button
+                  shiny::downloadButton(
+                    outputId = ns("download_plot"),
+                    label = "Download plot",
+                    icon = shiny::icon("download")
+                  )
+                )
               )
             )
           )
         ),
-        bslib::accordion_panel(
+        shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
-          value = "acc_checks",
-          title = "Checks",
-          icon = bsicons::bs_icon("clipboard-check"),
-          shiny::uiOutput(outputId = ns("plot_checks"))
-        )
       )
     ),
-    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")
+      bslib::layout_sidebar(
+        sidebar = bslib::sidebar(
+          bslib::accordion(
+            open = "acc_reg",
+            multiple = FALSE,
+            bslib::accordion_panel(
+              value = "acc_checks",
+              title = "Checks",
+              icon = bsicons::bs_icon("clipboard-check"),
+              shiny::uiOutput(outputId = ns("plot_checks"))
+            )
+          )
+        ),
+        shiny::plotOutput(outputId = ns("check"), height = "90vh")
+      )
     )
   )
 }

SESSION.md

@@ -11,11 +11,11 @@
 |collate     |en_US.UTF-8                                |
 |ctype       |en_US.UTF-8                                |
 |tz          |Europe/Copenhagen                          |
-|date        |2025-06-27                                 |
+|date        |2025-07-03                                 |
 |rstudio     |2025.05.0+496 Mariposa Orchid (desktop)    |
 |pandoc      |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
 |quarto      |1.7.30 @ /usr/local/bin/quarto             |
-|FreesearchR |25.6.4.250627                              |
+|FreesearchR |25.7.2.250703                              |
                                                                                 
                                                                                 
 --------------------------------------------------------------------------------
@@ -26,6 +26,8 @@
 |apexcharter       |0.4.4         |2024-09-06 |CRAN (R 4.4.1) |
 |askpass           |1.2.1         |2024-10-04 |CRAN (R 4.4.1) |
 |assertthat        |0.2.1         |2019-03-21 |CRAN (R 4.4.1) |
+|attachment        |0.4.5         |2025-03-14 |CRAN (R 4.4.1) |
+|attempt           |0.3.1         |2020-05-03 |CRAN (R 4.4.1) |
 |backports         |1.5.0         |2024-05-23 |CRAN (R 4.4.1) |
 |base64enc         |0.1-3         |2015-07-28 |CRAN (R 4.4.1) |
 |bayestestR        |0.15.3        |2025-04-28 |CRAN (R 4.4.1) |
@@ -43,6 +45,7 @@
 |cardx             |0.2.4         |2025-04-12 |CRAN (R 4.4.1) |
 |caTools           |1.18.3        |2024-09-04 |CRAN (R 4.4.1) |
 |cellranger        |1.1.0         |2016-07-27 |CRAN (R 4.4.0) |
+|cffr              |1.2.0         |2025-01-25 |CRAN (R 4.4.1) |
 |checkmate         |2.3.2         |2024-07-29 |CRAN (R 4.4.0) |
 |class             |7.3-23        |2025-01-01 |CRAN (R 4.4.1) |
 |classInt          |0.4-11        |2025-01-08 |CRAN (R 4.4.1) |
@@ -52,6 +55,9 @@
 |colorspace        |2.1-1         |2024-07-26 |CRAN (R 4.4.1) |
 |commonmark        |1.9.5         |2025-03-17 |CRAN (R 4.4.1) |
 |crayon            |1.5.3         |2024-06-20 |CRAN (R 4.4.1) |
+|credentials       |2.0.2         |2024-10-04 |CRAN (R 4.4.1) |
+|crosstalk         |1.2.1         |2023-11-23 |CRAN (R 4.4.0) |
+|curl              |6.2.2         |2025-03-24 |CRAN (R 4.4.1) |
 |data.table        |1.17.0        |2025-02-22 |CRAN (R 4.4.1) |
 |datamods          |1.5.3         |2024-10-02 |CRAN (R 4.4.1) |
 |datawizard        |1.0.2         |2025-03-24 |CRAN (R 4.4.1) |
@@ -60,11 +66,13 @@
 |devtools          |2.4.5         |2022-10-11 |CRAN (R 4.4.0) |
 |DHARMa            |0.4.7         |2024-10-18 |CRAN (R 4.4.1) |
 |digest            |0.6.37        |2024-08-19 |CRAN (R 4.4.1) |
+|dockerfiler       |0.2.5         |2025-05-07 |CRAN (R 4.4.1) |
 |doParallel        |1.0.17        |2022-02-07 |CRAN (R 4.4.0) |
 |dplyr             |1.1.4         |2023-11-17 |CRAN (R 4.4.0) |
 |DT                |0.33          |2024-04-04 |CRAN (R 4.4.0) |
 |e1071             |1.7-16        |2024-09-16 |CRAN (R 4.4.1) |
 |easystats         |0.7.4         |2025-02-06 |CRAN (R 4.4.1) |
+|effectsize        |1.0.0         |2024-12-10 |CRAN (R 4.4.1) |
 |ellipsis          |0.3.2         |2021-04-29 |CRAN (R 4.4.1) |
 |emmeans           |1.11.1        |2025-05-04 |CRAN (R 4.4.1) |
 |esquisse          |2.1.0         |2025-02-21 |CRAN (R 4.4.1) |
@@ -82,16 +90,19 @@
 |foreach           |1.5.2         |2022-02-02 |CRAN (R 4.4.0) |
 |foreign           |0.8-90        |2025-03-31 |CRAN (R 4.4.1) |
 |Formula           |1.2-5         |2023-02-24 |CRAN (R 4.4.1) |
-|FreesearchR       |25.6.4        |NA         |NA             |
+|FreesearchR       |25.7.2        |NA         |NA             |
 |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) |
+|gert              |2.1.5         |2025-03-25 |CRAN (R 4.4.1) |
 |ggalluvial        |0.12.5        |2023-02-22 |CRAN (R 4.4.0) |
 |ggcorrplot        |0.1.4.1       |2023-09-05 |CRAN (R 4.4.0) |
 |ggforce           |0.4.2         |2024-02-19 |CRAN (R 4.4.0) |
 |ggplot2           |3.5.2         |2025-04-09 |CRAN (R 4.4.1) |
 |ggridges          |0.5.6         |2024-01-23 |CRAN (R 4.4.0) |
 |ggstats           |0.9.0         |2025-03-10 |CRAN (R 4.4.1) |
+|gh                |1.4.1         |2024-03-28 |CRAN (R 4.4.0) |
+|gitcreds          |0.1.2         |2022-09-08 |CRAN (R 4.4.1) |
 |glue              |1.8.0         |2024-09-30 |CRAN (R 4.4.1) |
 |gridExtra         |2.3           |2017-09-09 |CRAN (R 4.4.1) |
 |gt                |1.0.0         |2025-04-05 |CRAN (R 4.4.1) |
@@ -105,24 +116,30 @@
 |htmltools         |0.5.8.1       |2024-04-04 |CRAN (R 4.4.1) |
 |htmlwidgets       |1.6.4         |2023-12-06 |CRAN (R 4.4.0) |
 |httpuv            |1.6.16        |2025-04-16 |CRAN (R 4.4.1) |
+|httr2             |1.1.2         |2025-03-26 |CRAN (R 4.4.1) |
 |IDEAFilter        |0.2.0         |2024-04-15 |CRAN (R 4.4.0) |
 |insight           |1.2.0         |2025-04-22 |CRAN (R 4.4.1) |
 |iterators         |1.0.14        |2022-02-05 |CRAN (R 4.4.1) |
 |jquerylib         |0.1.4         |2021-04-26 |CRAN (R 4.4.0) |
 |jsonlite          |2.0.0         |2025-03-27 |CRAN (R 4.4.1) |
+|jsonvalidate      |1.5.0         |2025-02-07 |CRAN (R 4.4.1) |
 |KernSmooth        |2.23-26       |2025-01-01 |CRAN (R 4.4.1) |
 |keyring           |1.3.2         |2023-12-11 |CRAN (R 4.4.0) |
 |knitr             |1.50          |2025-03-16 |CRAN (R 4.4.1) |
 |labeling          |0.4.3         |2023-08-29 |CRAN (R 4.4.1) |
+|labelled          |2.14.0        |2025-01-08 |CRAN (R 4.4.1) |
 |later             |1.4.2         |2025-04-08 |CRAN (R 4.4.1) |
 |lattice           |0.22-7        |2025-04-02 |CRAN (R 4.4.1) |
 |lifecycle         |1.0.4         |2023-11-07 |CRAN (R 4.4.1) |
+|litedown          |0.7           |2025-04-08 |CRAN (R 4.4.1) |
 |lme4              |1.1-37        |2025-03-26 |CRAN (R 4.4.1) |
 |lubridate         |1.9.4         |2024-12-08 |CRAN (R 4.4.1) |
 |magrittr          |2.0.3         |2022-03-30 |CRAN (R 4.4.1) |
+|markdown          |2.0           |2025-03-23 |CRAN (R 4.4.1) |
 |MASS              |7.3-65        |2025-02-28 |CRAN (R 4.4.1) |
 |Matrix            |1.7-3         |2025-03-11 |CRAN (R 4.4.1) |
 |memoise           |2.0.1         |2021-11-26 |CRAN (R 4.4.0) |
+|mgcv              |1.9-3         |2025-04-04 |CRAN (R 4.4.1) |
 |mime              |0.13          |2025-03-17 |CRAN (R 4.4.1) |
 |miniUI            |0.1.2         |2025-04-17 |CRAN (R 4.4.1) |
 |minqa             |1.2.8         |2024-08-17 |CRAN (R 4.4.1) |
@@ -134,6 +151,7 @@
 |opdisDownsampling |1.0.1         |2024-04-15 |CRAN (R 4.4.0) |
 |openssl           |2.3.2         |2025-02-03 |CRAN (R 4.4.1) |
 |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) |
@@ -162,6 +180,7 @@
 |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) |
@@ -192,13 +211,16 @@
 |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) |
@@ -213,11 +235,9 @@
 |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) |
@@ -225,4 +245,5 @@
 |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) |

inst/apps/FreesearchR/www/scripts.js

@@ -0,0 +1,29 @@
+// 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);
+  });
+});

inst/assets/js/FreesearchR.js

@@ -0,0 +1,29 @@
+// 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);
+  });
+});

man/compare_missings.Rd

@@ -0,0 +1,19 @@
+% 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
+}

vignettes/missingness.Rmd

@@ -0,0 +1,26 @@
+---
+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]().