new 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: 25.7.1
 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: 25.7.1
 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 +1,7 @@
+# FreesearchR 25.7.1 - DEV
+
+- *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()'25.7.1'

R/hosted_version.R

@@ -1 +1 @@
-hosted_version <- function()'v25.6.4-250627'
+hosted_version <- function()'v25.7.1-250703'

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 |25.7.1.250703                              |
                                                                                 
                                                                                 
 --------------------------------------------------------------------------------
@@ -52,6 +52,7 @@
 |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) |
+|crosstalk         |1.2.1         |2023-11-23 |CRAN (R 4.4.0) |
 |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) |
@@ -65,6 +66,7 @@
 |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) |
@@ -82,7 +84,7 @@
 |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       |25.7.1        |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) |
@@ -114,15 +116,19 @@
 |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) |
@@ -213,11 +219,8 @@
 |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) |
 |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) |

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()'25.6.3'
+app_version <- function()'25.7.1'
 
 
 ########
@@ -1611,10 +1611,8 @@ 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,
@@ -1637,10 +1635,6 @@ 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"),
@@ -1692,16 +1686,21 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
               icon = shiny::icon("download")
             )
           )
-      )
         ),
-    bslib::nav_panel(
+        shiny::p("We have collected a few notes on visualising data and details on the options included in FreesearchR:", shiny::tags$a(
-      title = tab_title,
+          href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
+          "View notes in new tab",
+          target = "_blank",
+          rel = "noopener noreferrer"
+        ))
+      ),
       shiny::plotOutput(ns("plot"), height = "70vh"),
       shiny::tags$br(),
       shiny::tags$br(),
       shiny::htmlOutput(outputId = ns("code_plot"))
     )
   )
+  # )
 }
 
 
@@ -1937,7 +1936,14 @@ 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$code <- glue::glue("FreesearchR::create_plot(df,{list2str(parameters)})")
@@ -1993,13 +1999,12 @@ data_visuals_server <- function(id,
           paste0("plot.", input$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..", {
@@ -2259,12 +2264,12 @@ 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
 }
 
@@ -2319,6 +2324,7 @@ 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")
@@ -2331,11 +2337,17 @@ 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) {
+wrap_plot_list <- function(data,
+                           tag_levels = NULL,
+                           title = NULL,
+                           axis.font.family = NULL,
+                           ...) {
   if (ggplot2::is_ggplot(data[[1]])) {
     if (length(data) > 1) {
       out <- data |>
@@ -2349,17 +2361,35 @@ wrap_plot_list <- function(data, tag_levels = NULL) {
           }
         })() |>
         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
+      out <- data[[1]]
     }
   } else {
     cli::cli_abort("Can only wrap lists of {.cls ggplot} objects")
   }
-  out
+
+  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))
+  }
 }
 
 
@@ -3996,7 +4026,7 @@ simple_snake <- function(data){
 #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R 
 ########
 
-hosted_version <- function()'v25.6.3-250626'
+hosted_version <- function()'v25.7.1-250703'
 
 
 ########
@@ -4705,14 +4735,7 @@ 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")
@@ -4790,13 +4813,25 @@ 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
+}
 
 
 ########
@@ -4805,17 +4840,27 @@ missing_demo_app()
 
 #' 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 = "cyl", ter = "gear")
+#' mtcars |> plot_box(pri = "mpg", sec = "gear")
+#' mtcars |> plot_box(pri = "mpg", sec="cyl")
 #' mtcars |>
 #'   default_parsing() |>
 #'   plot_box(pri = "mpg", sec = "cyl", ter = "gear")
-plot_box <- function(data, pri, sec, ter = NULL) {
+#' mtcars |>
+#'   default_parsing() |>
+#'   plot_box(pri = "mpg", sec = "cyl", ter = "gear",axis.font.family="mono")
+plot_box <- function(data, pri, sec, ter = NULL,...) {
   if (!is.null(ter)) {
     ds <- split(data, data[ter])
   } else {
@@ -4830,7 +4875,7 @@ plot_box <- function(data, pri, sec, ter = NULL) {
     )
   })
 
-  wrap_plot_list(out)
+  wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}"),...)
 }
 
 
@@ -4846,6 +4891,7 @@ 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)
 
@@ -4861,6 +4907,8 @@ 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() +
@@ -4983,7 +5031,7 @@ plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
   })
 
   # names(out)
-  wrap_plot_list(out)
+  wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}"))
   # patchwork::wrap_plots(out, guides = "collect")
 }
 
@@ -5458,7 +5506,7 @@ plot_violin <- function(data, pri, sec, ter = NULL) {
     )
   })
 
-  wrap_plot_list(out)
+  wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}"))
   # patchwork::wrap_plots(out,guides = "collect")
 }
 
@@ -7372,7 +7420,10 @@ regression_ui <- function(id, ...) {
   ns <- shiny::NS(id)
 
   shiny::tagList(
-    title = "",
+    # title = "",
+    bslib::nav_panel(
+      title = "Regression table",
+      bslib::layout_sidebar(
         sidebar = bslib::sidebar(
           shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
           bslib::accordion(
@@ -7447,7 +7498,19 @@ 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(
@@ -7501,7 +7564,19 @@ 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",
@@ -7510,19 +7585,10 @@ 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")
       )
     )
+  )
 }
 
 
@@ -9831,6 +9897,8 @@ 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"
@@ -9842,8 +9910,7 @@ ui_elements <- list(
         shiny::markdown(readLines("www/intro.md")),
         shiny::column(width = 2)
       )
-    ),
+    )
-    icon = shiny::icon("home")
   ),
   ##############################################################################
   #########
@@ -9851,7 +9918,8 @@ ui_elements <- list(
   #########
   ##############################################################################
   "import" = bslib::nav_panel(
-    title = "Import",
+    title = "Get started",
+    icon = shiny::icon("upload"),
     shiny::fluidRow(
       shiny::column(width = 2),
       shiny::column(
@@ -9969,15 +10037,13 @@ ui_elements <- list(
   #########  Data overview panel
   #########
   ##############################################################################
-  "overview" =
+  "prepare" = bslib::nav_menu(
-  # bslib::nav_panel_hidden(
+    title = "Prepare",
-    bslib::nav_panel(
+    icon = shiny::icon("pen-to-square"),
-      # value = "overview",
-      title = "Data",
-      bslib::navset_bar(
-        fillable = TRUE,
     bslib::nav_panel(
       title = "Overview",
+      icon = shiny::icon("eye"),
+      value = "nav_prepare_overview",
       tags$h3("Overview and filtering"),
       fluidRow(
         shiny::column(
@@ -10019,22 +10085,6 @@ ui_elements <- list(
         ),
         shiny::column(
           width = 3,
-              # shiny::actionButton(
-              #   inputId = "modal_missings",
-              #   label = "Visual overview",
-              #   width = "100%",
-              #   disabled = TRUE
-              # ),
-              # shiny::br(),
-              # shiny::br(),
-              # shiny::actionButton(
-              #   inputId = "modal_browse",
-              #   label = "Browse data",
-              #   width = "100%",
-              #   disabled = TRUE
-              # ),
-              # shiny::br(),
-              # shiny::br(),
           shiny::tags$h6("Filter data types"),
           shiny::uiOutput(
             outputId = "column_filter"
@@ -10056,12 +10106,11 @@ ui_elements <- list(
       ),
       shiny::br(),
       shiny::br(),
-          # shiny::br(),
-          # shiny::br(),
       shiny::br()
     ),
     bslib::nav_panel(
       title = "Modify",
+      icon = shiny::icon("file-pen"),
       tags$h3("Subset, rename and convert variables"),
       fluidRow(
         shiny::column(
@@ -10073,7 +10122,6 @@ ui_elements <- list(
           )
         )
       ),
-          # shiny::tags$br(),
       update_variables_ui("modal_variables"),
       shiny::tags$br(),
       shiny::tags$br(),
@@ -10129,13 +10177,11 @@ 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")
         )
       ),
@@ -10149,7 +10195,7 @@ ui_elements <- list(
       shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
       shiny::tags$br()
     )
-      )
+    # )
   ),
   ##############################################################################
   #########
@@ -10157,22 +10203,28 @@ ui_elements <- list(
   #########
   ##############################################################################
   "describe" =
-    bslib::nav_panel(
+    bslib::nav_menu(
       title = "Evaluate",
-      id = "navdescribe",
+      icon = shiny::icon("magnifying-glass-chart"),
-      bslib::navset_bar(
+      # id = "navdescribe",
-        title = "",
+      # bslib::navset_bar(
+      #   title = "",
+      bslib::nav_panel(
+        title = "Characteristics",
+        icon = bsicons::bs_icon("table"),
+        bslib::layout_sidebar(
           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 = "Characteristics",
+                title = "Settings",
                 icon = bsicons::bs_icon("table"),
                 shiny::uiOutput("strat_var"),
-              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::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::conditionalPanel(
                   condition = "input.strat_var!='none'",
                   shiny::radioButtons(
@@ -10196,9 +10248,23 @@ 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(
-              vlaue = "acc_cor",
+                value = "acc_cor",
                 title = "Correlations",
                 icon = bsicons::bs_icon("bounding-box"),
                 shiny::uiOutput("outcome_var_cor"),
@@ -10215,26 +10281,29 @@ 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 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.")
+                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.")
               )
             )
           ),
-        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")
         )
       )
@@ -10244,27 +10313,23 @@ ui_elements <- list(
   #########  Download panel
   #########
   ##############################################################################
-  "visuals" = bslib::nav_panel(
+  "visuals" = do.call(
-    title = "Visuals",
+    bslib::nav_panel,
-    id = "navvisuals",
-    do.call(
-      bslib::navset_bar,
     c(
-        data_visuals_ui("visuals"),
+      list(
-        shiny::tagList(
+        title = "Visuals",
-          bslib::nav_spacer(),
+        icon = shiny::icon("chart-line"),
-          bslib::nav_item(
+        id = "navvisuals"
-            # shiny::img(shiny::icon("book")),
+      ),
-            shiny::tags$a(
+      data_visuals_ui("visuals")
-              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(
+
+    # )
+    # )
   ),
   ##############################################################################
   #########
@@ -10274,9 +10339,10 @@ ui_elements <- list(
   "analyze" =
     bslib::nav_panel(
       title = "Regression",
+      icon = shiny::icon("calculator"),
       id = "navanalyses",
       do.call(
-        bslib::navset_bar,
+        bslib::navset_card_tab,
         regression_ui("regression")
       )
     ),
@@ -10288,6 +10354,7 @@ ui_elements <- list(
   "download" =
     bslib::nav_panel(
       title = "Download",
+      icon = shiny::icon("download"),
       id = "navdownload",
       shiny::fluidRow(
         shiny::column(width = 2),
@@ -10413,9 +10480,25 @@ 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$link(rel = "shortcut icon", href = "favicon.svg")),
@@ -10435,14 +10518,14 @@ ui <- bslib::page_fixed(
         id = "main_panel",
         ui_elements$home,
         ui_elements$import,
-        ui_elements$overview,
+        ui_elements$prepare,
         ui_elements$describe,
         ui_elements$visuals,
         ui_elements$analyze,
         ui_elements$download,
         bslib::nav_spacer(),
-        ui_elements$feedback,
+        # ui_elements$feedback,
-        ui_elements$docs,
+        # ui_elements$docs,
         fillable = FALSE,
         footer = shiny::tags$footer(
           style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
@@ -10452,7 +10535,7 @@ ui <- bslib::page_fixed(
           ),
           shiny::p(
             style = "margin: 1; color: #888;",
-            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")
+            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")
           ),
         )
       )
@@ -11164,7 +11247,7 @@ server <- function(input, output, session) {
   ##############################################################################
 
   shiny::observeEvent(input$act_start, {
-    bslib::nav_select(id = "main_panel", selected = "Data")
+    bslib::nav_select(id = "main_panel", selected = "nav_prepare_overview")
   })
 
   ##############################################################################

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
+}