diff --git a/CITATION.cff b/CITATION.cff
index 2a3ec2e4..b3fc5ff0 100644
--- a/CITATION.cff
+++ b/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
diff --git a/DESCRIPTION b/DESCRIPTION
index d602b0a3..002733c6 100644
--- a/DESCRIPTION
+++ b/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")),
diff --git a/NAMESPACE b/NAMESPACE
index 34c6092e..de51a148 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/NEWS.md b/NEWS.md
index fd591139..cd8a6859 100644
--- a/NEWS.md
+++ b/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.
diff --git a/R/app_version.R b/R/app_version.R
index 151c1165..6a80b530 100644
--- a/R/app_version.R
+++ b/R/app_version.R
@@ -1 +1 @@
-app_version <- function()'25.6.4'
+app_version <- function()'25.7.2'
diff --git a/R/data_plots.R b/R/data_plots.R
index bed502fc..a751e609 100644
--- a/R/data_plots.R
+++ b/R/data_plots.R
@@ -11,97 +11,96 @@
 data_visuals_ui <- function(id, tab_title = "Plots", ...) {
   ns <- shiny::NS(id)
 
-  # bslib::navset_bar(
   list(
-
-    # Sidebar with a slider input
-    sidebar = bslib::sidebar(
-      bslib::accordion(
-        multiple = FALSE,
-        bslib::accordion_panel(
-          title = "Creating plot",
-          icon = bsicons::bs_icon("graph-up"),
-          shiny::uiOutput(outputId = ns("primary")),
-          shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'),
-          shiny::tags$br(),
-          shiny::uiOutput(outputId = ns("type")),
-          shiny::uiOutput(outputId = ns("secondary")),
-          shiny::uiOutput(outputId = ns("tertiary")),
-          shiny::br(),
-          shiny::actionButton(
-            inputId = ns("act_plot"),
-            label = "Plot",
-            width = "100%",
-            icon = shiny::icon("palette"),
-            disabled = FALSE
+    bslib::layout_sidebar(
+      sidebar = bslib::sidebar(
+        bslib::accordion(
+          multiple = FALSE,
+          bslib::accordion_panel(
+            title = "Creating plot",
+            icon = bsicons::bs_icon("graph-up"),
+            shiny::uiOutput(outputId = ns("primary")),
+            shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'),
+            shiny::tags$br(),
+            shiny::uiOutput(outputId = ns("type")),
+            shiny::uiOutput(outputId = ns("secondary")),
+            shiny::uiOutput(outputId = ns("tertiary")),
+            shiny::br(),
+            shiny::actionButton(
+              inputId = ns("act_plot"),
+              label = "Plot",
+              width = "100%",
+              icon = shiny::icon("palette"),
+              disabled = FALSE
+            ),
+            shiny::helpText('Adjust settings, then press "Plot".')
           ),
-          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"),
-          shinyWidgets::noUiSliderInput(
-            inputId = ns("height_slide"),
-            label = "Plot height (mm)",
-            min = 50,
-            max = 300,
-            value = 100,
-            step = 1,
-            format = shinyWidgets::wNumbFormat(decimals = 0),
-            color = datamods:::get_primary_color(),
-            inline = TRUE
-          ),
-          # shiny::numericInput(
-          #   inputId = ns("height_numeric"),
-          #   label = "Plot height (mm)",
-          #   min = 50,
-          #   max = 300,
-          #   value = 100
-          # ),
-          shinyWidgets::noUiSliderInput(
-            inputId = ns("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"
+          bslib::accordion_panel(
+            title = "Download",
+            icon = bsicons::bs_icon("download"),
+            shinyWidgets::noUiSliderInput(
+              inputId = ns("height_slide"),
+              label = "Plot height (mm)",
+              min = 50,
+              max = 300,
+              value = 100,
+              step = 1,
+              format = shinyWidgets::wNumbFormat(decimals = 0),
+              color = datamods:::get_primary_color(),
+              inline = TRUE
+            ),
+            # shiny::numericInput(
+            #   inputId = ns("height_numeric"),
+            #   label = "Plot height (mm)",
+            #   min = 50,
+            #   max = 300,
+            #   value = 100
+            # ),
+            shinyWidgets::noUiSliderInput(
+              inputId = ns("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")
             )
-          ),
-          shiny::br(),
-          # Button
-          shiny::downloadButton(
-            outputId = ns("download_plot"),
-            label = "Download plot",
-            icon = shiny::icon("download")
           )
-        )
-      )
-    ),
-    bslib::nav_panel(
-      title = tab_title,
+        ),
+        shiny::p("We have collected a few notes on visualising data and details on the options included in FreesearchR:", shiny::tags$a(
+          href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
+          "View notes in new tab",
+          target = "_blank",
+          rel = "noopener noreferrer"
+        ))
+      ),
       shiny::plotOutput(ns("plot"), height = "70vh"),
       shiny::tags$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) {
diff --git a/R/hosted_version.R b/R/hosted_version.R
index 17d0c52a..f6236bf0 100644
--- a/R/hosted_version.R
+++ b/R/hosted_version.R
@@ -1 +1 @@
-hosted_version <- function()'v25.6.4-250627'
+hosted_version <- function()'v25.7.2-250703'
diff --git a/R/missings-module.R b/R/missings-module.R
index 71791ac6..c04a2561 100644
--- a/R/missings-module.R
+++ b/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)) {
-              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)
-            }
+            out <- compare_missings(df_tbl,by_var)
           },
           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
+}
diff --git a/R/regression-module.R b/R/regression-module.R
index ee2eb9f0..78f459d9 100644
--- a/R/regression-module.R
+++ b/R/regression-module.R
@@ -44,155 +44,173 @@ regression_ui <- function(id, ...) {
   ns <- shiny::NS(id)
 
   shiny::tagList(
-    title = "",
-    sidebar = bslib::sidebar(
-      shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
-      bslib::accordion(
-        open = "acc_reg",
-        multiple = FALSE,
-        bslib::accordion_panel(
-          value = "acc_reg",
-          title = "Regression",
-          icon = bsicons::bs_icon("calculator"),
-          shiny::uiOutput(outputId = ns("outcome_var")),
-          # shiny::selectInput(
-          #   inputId = "design",
-          #   label = "Study design",
-          #   selected = "no",
-          #   inline = TRUE,
-          #   choices = list(
-          #     "Cross-sectional" = "cross-sectional"
-          #   )
-          # ),
-          shiny::uiOutput(outputId = ns("regression_type")),
-          shiny::radioButtons(
-            inputId = ns("all"),
-            label = "Specify covariables",
-            inline = TRUE, selected = 2,
-            choiceNames = c(
-              "Yes",
-              "No"
-            ),
-            choiceValues = c(1, 2)
-          ),
-          shiny::conditionalPanel(
-            condition = "input.all==1",
-            shiny::uiOutput(outputId = ns("regression_vars")),
-            shiny::helpText("If none are selected, all are included."),
-            shiny::tags$br(),
-            ns = ns
-          ),
-          bslib::input_task_button(
-            id = ns("load"),
-            label = "Analyse",
-            icon = bsicons::bs_icon("pencil"),
-            label_busy = "Working...",
-            icon_busy = fontawesome::fa_i("arrows-rotate",
-              class = "fa-spin",
-              "aria-hidden" = "true"
-            ),
-            type = "secondary",
-            auto_reset = TRUE
-          ),
-          shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
-          shiny::tags$br(),
-          shiny::radioButtons(
-            inputId = ns("add_regression_p"),
-            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"),
+    # title = "",
+    bslib::nav_panel(
+      title = "Regression table",
+      bslib::layout_sidebar(
+        sidebar = bslib::sidebar(
+          shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
+          bslib::accordion(
+            open = "acc_reg",
+            multiple = FALSE,
+            bslib::accordion_panel(
+              value = "acc_reg",
+              title = "Regression",
+              icon = bsicons::bs_icon("calculator"),
+              shiny::uiOutput(outputId = ns("outcome_var")),
+              # shiny::selectInput(
+              #   inputId = "design",
+              #   label = "Study design",
+              #   selected = "no",
+              #   inline = TRUE,
+              #   choices = list(
+              #     "Cross-sectional" = "cross-sectional"
+              #   )
+              # ),
+              shiny::uiOutput(outputId = ns("regression_type")),
+              shiny::radioButtons(
+                inputId = ns("all"),
+                label = "Specify covariables",
+                inline = TRUE, selected = 2,
+                choiceNames = c(
+                  "Yes",
+                  "No"
+                ),
+                choiceValues = c(1, 2)
+              ),
+              shiny::conditionalPanel(
+                condition = "input.all==1",
+                shiny::uiOutput(outputId = ns("regression_vars")),
+                shiny::helpText("If none are selected, all are included."),
+                shiny::tags$br(),
+                ns = ns
+              ),
+              bslib::input_task_button(
+                id = ns("load"),
+                label = "Analyse",
+                icon = bsicons::bs_icon("pencil"),
+                label_busy = "Working...",
+                icon_busy = fontawesome::fa_i("arrows-rotate",
+                  class = "fa-spin",
+                  "aria-hidden" = "true"
+                ),
+                type = "secondary",
+                auto_reset = TRUE
+              ),
+              shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
               shiny::tags$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",
+              shiny::radioButtons(
+                inputId = ns("add_regression_p"),
+                label = "Show p-value",
+                inline = TRUE,
+                selected = "yes",
                 choices = list(
-                  "png",
-                  "tiff",
-                  "eps",
-                  "pdf",
-                  "jpeg",
-                  "svg"
+                  "Yes" = "yes",
+                  "No" = "no"
                 )
               ),
-              shiny::br(),
-              # Button
-              shiny::downloadButton(
-                outputId = ns("download_plot"),
-                label = "Download plot",
-                icon = shiny::icon("download")
+              # 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()
+            )
+          )
+        ),
+        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(
-          value = "acc_checks",
-          title = "Checks",
-          icon = bsicons::bs_icon("clipboard-check"),
-          shiny::uiOutput(outputId = ns("plot_checks"))
-        )
+        shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
       )
     ),
-    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")
+      )
     )
   )
 }
diff --git a/R/sysdata.rda b/R/sysdata.rda
index ff32e166..252c2f42 100644
Binary files a/R/sysdata.rda and b/R/sysdata.rda differ
diff --git a/SESSION.md b/SESSION.md
index efcc1d93..1e585990 100644
--- a/SESSION.md
+++ b/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) |
diff --git a/app_docker/app.R b/app_docker/app.R
index db2ebed5..b3b5a1bf 100644
--- a/app_docker/app.R
+++ b/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'
 
 
 ########
@@ -1611,97 +1611,96 @@ 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(
-
-    # Sidebar with a slider input
-    sidebar = bslib::sidebar(
-      bslib::accordion(
-        multiple = FALSE,
-        bslib::accordion_panel(
-          title = "Creating plot",
-          icon = bsicons::bs_icon("graph-up"),
-          shiny::uiOutput(outputId = ns("primary")),
-          shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'),
-          shiny::tags$br(),
-          shiny::uiOutput(outputId = ns("type")),
-          shiny::uiOutput(outputId = ns("secondary")),
-          shiny::uiOutput(outputId = ns("tertiary")),
-          shiny::br(),
-          shiny::actionButton(
-            inputId = ns("act_plot"),
-            label = "Plot",
-            width = "100%",
-            icon = shiny::icon("palette"),
-            disabled = FALSE
+    bslib::layout_sidebar(
+      sidebar = bslib::sidebar(
+        bslib::accordion(
+          multiple = FALSE,
+          bslib::accordion_panel(
+            title = "Creating plot",
+            icon = bsicons::bs_icon("graph-up"),
+            shiny::uiOutput(outputId = ns("primary")),
+            shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'),
+            shiny::tags$br(),
+            shiny::uiOutput(outputId = ns("type")),
+            shiny::uiOutput(outputId = ns("secondary")),
+            shiny::uiOutput(outputId = ns("tertiary")),
+            shiny::br(),
+            shiny::actionButton(
+              inputId = ns("act_plot"),
+              label = "Plot",
+              width = "100%",
+              icon = shiny::icon("palette"),
+              disabled = FALSE
+            ),
+            shiny::helpText('Adjust settings, then press "Plot".')
           ),
-          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"),
-          shinyWidgets::noUiSliderInput(
-            inputId = ns("height_slide"),
-            label = "Plot height (mm)",
-            min = 50,
-            max = 300,
-            value = 100,
-            step = 1,
-            format = shinyWidgets::wNumbFormat(decimals = 0),
-            color = datamods:::get_primary_color(),
-            inline = TRUE
-          ),
-          # shiny::numericInput(
-          #   inputId = ns("height_numeric"),
-          #   label = "Plot height (mm)",
-          #   min = 50,
-          #   max = 300,
-          #   value = 100
-          # ),
-          shinyWidgets::noUiSliderInput(
-            inputId = ns("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"
+          bslib::accordion_panel(
+            title = "Download",
+            icon = bsicons::bs_icon("download"),
+            shinyWidgets::noUiSliderInput(
+              inputId = ns("height_slide"),
+              label = "Plot height (mm)",
+              min = 50,
+              max = 300,
+              value = 100,
+              step = 1,
+              format = shinyWidgets::wNumbFormat(decimals = 0),
+              color = datamods:::get_primary_color(),
+              inline = TRUE
+            ),
+            # shiny::numericInput(
+            #   inputId = ns("height_numeric"),
+            #   label = "Plot height (mm)",
+            #   min = 50,
+            #   max = 300,
+            #   value = 100
+            # ),
+            shinyWidgets::noUiSliderInput(
+              inputId = ns("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")
             )
-          ),
-          shiny::br(),
-          # Button
-          shiny::downloadButton(
-            outputId = ns("download_plot"),
-            label = "Download plot",
-            icon = shiny::icon("download")
           )
-        )
-      )
-    ),
-    bslib::nav_panel(
-      title = tab_title,
+        ),
+        shiny::p("We have collected a few notes on visualising data and details on the options included in FreesearchR:", shiny::tags$a(
+          href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
+          "View notes in new tab",
+          target = "_blank",
+          rel = "noopener noreferrer"
+        ))
+      ),
       shiny::plotOutput(ns("plot"), height = "70vh"),
       shiny::tags$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)) {
-              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)
-            }
+            out <- compare_missings(df_tbl,by_var)
           },
           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")
 }
 
@@ -7372,155 +7420,173 @@ regression_ui <- function(id, ...) {
   ns <- shiny::NS(id)
 
   shiny::tagList(
-    title = "",
-    sidebar = bslib::sidebar(
-      shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
-      bslib::accordion(
-        open = "acc_reg",
-        multiple = FALSE,
-        bslib::accordion_panel(
-          value = "acc_reg",
-          title = "Regression",
-          icon = bsicons::bs_icon("calculator"),
-          shiny::uiOutput(outputId = ns("outcome_var")),
-          # shiny::selectInput(
-          #   inputId = "design",
-          #   label = "Study design",
-          #   selected = "no",
-          #   inline = TRUE,
-          #   choices = list(
-          #     "Cross-sectional" = "cross-sectional"
-          #   )
-          # ),
-          shiny::uiOutput(outputId = ns("regression_type")),
-          shiny::radioButtons(
-            inputId = ns("all"),
-            label = "Specify covariables",
-            inline = TRUE, selected = 2,
-            choiceNames = c(
-              "Yes",
-              "No"
-            ),
-            choiceValues = c(1, 2)
-          ),
-          shiny::conditionalPanel(
-            condition = "input.all==1",
-            shiny::uiOutput(outputId = ns("regression_vars")),
-            shiny::helpText("If none are selected, all are included."),
-            shiny::tags$br(),
-            ns = ns
-          ),
-          bslib::input_task_button(
-            id = ns("load"),
-            label = "Analyse",
-            icon = bsicons::bs_icon("pencil"),
-            label_busy = "Working...",
-            icon_busy = fontawesome::fa_i("arrows-rotate",
-              class = "fa-spin",
-              "aria-hidden" = "true"
-            ),
-            type = "secondary",
-            auto_reset = TRUE
-          ),
-          shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
-          shiny::tags$br(),
-          shiny::radioButtons(
-            inputId = ns("add_regression_p"),
-            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"),
+    # title = "",
+    bslib::nav_panel(
+      title = "Regression table",
+      bslib::layout_sidebar(
+        sidebar = bslib::sidebar(
+          shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
+          bslib::accordion(
+            open = "acc_reg",
+            multiple = FALSE,
+            bslib::accordion_panel(
+              value = "acc_reg",
+              title = "Regression",
+              icon = bsicons::bs_icon("calculator"),
+              shiny::uiOutput(outputId = ns("outcome_var")),
+              # shiny::selectInput(
+              #   inputId = "design",
+              #   label = "Study design",
+              #   selected = "no",
+              #   inline = TRUE,
+              #   choices = list(
+              #     "Cross-sectional" = "cross-sectional"
+              #   )
+              # ),
+              shiny::uiOutput(outputId = ns("regression_type")),
+              shiny::radioButtons(
+                inputId = ns("all"),
+                label = "Specify covariables",
+                inline = TRUE, selected = 2,
+                choiceNames = c(
+                  "Yes",
+                  "No"
+                ),
+                choiceValues = c(1, 2)
+              ),
+              shiny::conditionalPanel(
+                condition = "input.all==1",
+                shiny::uiOutput(outputId = ns("regression_vars")),
+                shiny::helpText("If none are selected, all are included."),
+                shiny::tags$br(),
+                ns = ns
+              ),
+              bslib::input_task_button(
+                id = ns("load"),
+                label = "Analyse",
+                icon = bsicons::bs_icon("pencil"),
+                label_busy = "Working...",
+                icon_busy = fontawesome::fa_i("arrows-rotate",
+                  class = "fa-spin",
+                  "aria-hidden" = "true"
+                ),
+                type = "secondary",
+                auto_reset = TRUE
+              ),
+              shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
               shiny::tags$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",
+              shiny::radioButtons(
+                inputId = ns("add_regression_p"),
+                label = "Show p-value",
+                inline = TRUE,
+                selected = "yes",
                 choices = list(
-                  "png",
-                  "tiff",
-                  "eps",
-                  "pdf",
-                  "jpeg",
-                  "svg"
+                  "Yes" = "yes",
+                  "No" = "no"
                 )
               ),
-              shiny::br(),
-              # Button
-              shiny::downloadButton(
-                outputId = ns("download_plot"),
-                label = "Download plot",
-                icon = shiny::icon("download")
+              # 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()
+            )
+          )
+        ),
+        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(
-          value = "acc_checks",
-          title = "Checks",
-          icon = bsicons::bs_icon("clipboard-check"),
-          shiny::uiOutput(outputId = ns("plot_checks"))
-        )
+        shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
       )
     ),
-    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")
+      )
     )
   )
 }
@@ -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(
@@ -9907,13 +9975,13 @@ ui_elements <- list(
         shiny::conditionalPanel(
           condition = "output.data_loaded == true",
           shiny::br(),
-            shiny::actionButton(
-              inputId = "modal_initial_view",
-              label = "Quick overview",
-              width = "100%",
-              icon = shiny::icon("binoculars"),
-              disabled = FALSE
-            ),
+          shiny::actionButton(
+            inputId = "modal_initial_view",
+            label = "Quick overview",
+            width = "100%",
+            icon = shiny::icon("binoculars"),
+            disabled = FALSE
+          ),
           shiny::br(),
           shiny::br(),
           shiny::h5("Select variables for final import"),
@@ -9969,272 +10037,273 @@ ui_elements <- list(
   #########  Data overview panel
   #########
   ##############################################################################
-  "overview" =
-  # bslib::nav_panel_hidden(
+  "prepare" = bslib::nav_menu(
+    title = "Prepare",
+    icon = shiny::icon("pen-to-square"),
     bslib::nav_panel(
-      # value = "overview",
-      title = "Data",
-      bslib::navset_bar(
-        fillable = TRUE,
-        bslib::nav_panel(
-          title = "Overview",
-          tags$h3("Overview and filtering"),
-          fluidRow(
-            shiny::column(
-              width = 9,
-              shiny::uiOutput(outputId = "data_info", inline = TRUE),
-              shiny::tags$p(
-                "Below is a short summary table, on the right you can click to visualise data classes or browse data and create different data filters."
-              )
-            ),
-            shiny::column(
-              width = 3,
-              shiny::actionButton(
-                inputId = "modal_visual_overview",
-                label = "Visual overview",
-                width = "100%",
-                disabled = TRUE
-              ),
-              shiny::br(),
-              shiny::br(),
-              shiny::actionButton(
-                inputId = "modal_browse",
-                label = "Browse data",
-                width = "100%",
-                disabled = TRUE
-              ),
-              shiny::br(),
-              shiny::br()
-            )
-          ),
-          fluidRow(
-            shiny::column(
-              width = 9,
-              data_summary_ui(id = "data_summary"),
-              shiny::br(),
-              shiny::br(),
-              shiny::br(),
-              shiny::br(),
-              shiny::br()
-            ),
-            shiny::column(
-              width = 3,
-              # shiny::actionButton(
-              #   inputId = "modal_missings",
-              #   label = "Visual overview",
-              #   width = "100%",
-              #   disabled = TRUE
-              # ),
-              # shiny::br(),
-              # shiny::br(),
-              # shiny::actionButton(
-              #   inputId = "modal_browse",
-              #   label = "Browse data",
-              #   width = "100%",
-              #   disabled = TRUE
-              # ),
-              # shiny::br(),
-              # shiny::br(),
-              shiny::tags$h6("Filter data types"),
-              shiny::uiOutput(
-                outputId = "column_filter"
-              ),
-              shiny::helpText("Read more on how ", tags$a(
-                "data types",
-                href = "https://agdamsbo.github.io/FreesearchR/articles/data-types.html",
-                target = "_blank",
-                rel = "noopener noreferrer"
-              ), " are defined."),
-              shiny::br(),
-              shiny::br(),
-              shiny::tags$h6("Filter observations"),
-              shiny::tags$p("Filter on observation level"),
-              IDEAFilter::IDEAFilter_ui("data_filter"),
-              shiny::br(),
-              shiny::br()
-            )
+      title = "Overview",
+      icon = shiny::icon("eye"),
+      value = "nav_prepare_overview",
+      tags$h3("Overview and filtering"),
+      fluidRow(
+        shiny::column(
+          width = 9,
+          shiny::uiOutput(outputId = "data_info", inline = TRUE),
+          shiny::tags$p(
+            "Below is a short summary table, on the right you can click to visualise data classes or browse data and create different data filters."
+          )
+        ),
+        shiny::column(
+          width = 3,
+          shiny::actionButton(
+            inputId = "modal_visual_overview",
+            label = "Visual overview",
+            width = "100%",
+            disabled = TRUE
           ),
           shiny::br(),
           shiny::br(),
-          # shiny::br(),
-          # shiny::br(),
+          shiny::actionButton(
+            inputId = "modal_browse",
+            label = "Browse data",
+            width = "100%",
+            disabled = TRUE
+          ),
+          shiny::br(),
+          shiny::br()
+        )
+      ),
+      fluidRow(
+        shiny::column(
+          width = 9,
+          data_summary_ui(id = "data_summary"),
+          shiny::br(),
+          shiny::br(),
+          shiny::br(),
+          shiny::br(),
           shiny::br()
         ),
-        bslib::nav_panel(
-          title = "Modify",
-          tags$h3("Subset, rename and convert variables"),
-          fluidRow(
-            shiny::column(
-              width = 9,
-              shiny::tags$p(
-                shiny::markdown("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."),
-                shiny::markdown("There are more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."),
-                shiny::markdown("Please note that data modifications are applied before any filtering.")
-              )
-            )
+        shiny::column(
+          width = 3,
+          shiny::tags$h6("Filter data types"),
+          shiny::uiOutput(
+            outputId = "column_filter"
           ),
-          # shiny::tags$br(),
-          update_variables_ui("modal_variables"),
-          shiny::tags$br(),
-          shiny::tags$br(),
-          shiny::tags$h4("Advanced data manipulation"),
-          shiny::tags$p("Below options allow more advanced varaible manipulations."),
-          shiny::tags$br(),
-          shiny::tags$br(),
-          shiny::fluidRow(
-            shiny::column(
-              width = 4,
-              shiny::actionButton(
-                inputId = "modal_update",
-                label = "Reorder factor levels",
-                width = "100%"
-              ),
-              shiny::tags$br(),
-              shiny::helpText("Reorder the levels of factor/categorical variables."),
-              shiny::tags$br(),
-              shiny::tags$br()
-            ),
-            shiny::column(
-              width = 4,
-              shiny::actionButton(
-                inputId = "modal_cut",
-                label = "New factor",
-                width = "100%"
-              ),
-              shiny::tags$br(),
-              shiny::helpText("Create factor/categorical variable from a continous variable (number/date/time)."),
-              shiny::tags$br(),
-              shiny::tags$br()
-            ),
-            shiny::column(
-              width = 4,
-              shiny::actionButton(
-                inputId = "modal_column",
-                label = "New variable",
-                width = "100%"
-              ),
-              shiny::tags$br(),
-              shiny::helpText(shiny::markdown("Create a new variable/column based on an *R*-expression.")),
-              shiny::tags$br(),
-              shiny::tags$br()
-            )
-          ),
-          tags$h4("Compare modified data to original"),
-          shiny::tags$br(),
+          shiny::helpText("Read more on how ", tags$a(
+            "data types",
+            href = "https://agdamsbo.github.io/FreesearchR/articles/data-types.html",
+            target = "_blank",
+            rel = "noopener noreferrer"
+          ), " are defined."),
+          shiny::br(),
+          shiny::br(),
+          shiny::tags$h6("Filter observations"),
+          shiny::tags$p("Filter on observation level"),
+          IDEAFilter::IDEAFilter_ui("data_filter"),
+          shiny::br(),
+          shiny::br()
+        )
+      ),
+      shiny::br(),
+      shiny::br(),
+      shiny::br()
+    ),
+    bslib::nav_panel(
+      title = "Modify",
+      icon = shiny::icon("file-pen"),
+      tags$h3("Subset, rename and convert variables"),
+      fluidRow(
+        shiny::column(
+          width = 9,
           shiny::tags$p(
-            "Raw print of the original vs the modified data."
-          ),
-          shiny::tags$br(),
-          shiny::fluidRow(
-            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")
-            )
-          ),
-          shiny::tags$br(),
+            shiny::markdown("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."),
+            shiny::markdown("There are more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."),
+            shiny::markdown("Please note that data modifications are applied before any filtering.")
+          )
+        )
+      ),
+      update_variables_ui("modal_variables"),
+      shiny::tags$br(),
+      shiny::tags$br(),
+      shiny::tags$h4("Advanced data manipulation"),
+      shiny::tags$p("Below options allow more advanced varaible manipulations."),
+      shiny::tags$br(),
+      shiny::tags$br(),
+      shiny::fluidRow(
+        shiny::column(
+          width = 4,
           shiny::actionButton(
-            inputId = "data_reset",
-            label = "Restore original data",
+            inputId = "modal_update",
+            label = "Reorder factor levels",
             width = "100%"
           ),
           shiny::tags$br(),
-          shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
+          shiny::helpText("Reorder the levels of factor/categorical variables."),
+          shiny::tags$br(),
+          shiny::tags$br()
+        ),
+        shiny::column(
+          width = 4,
+          shiny::actionButton(
+            inputId = "modal_cut",
+            label = "New factor",
+            width = "100%"
+          ),
+          shiny::tags$br(),
+          shiny::helpText("Create factor/categorical variable from a continous variable (number/date/time)."),
+          shiny::tags$br(),
+          shiny::tags$br()
+        ),
+        shiny::column(
+          width = 4,
+          shiny::actionButton(
+            inputId = "modal_column",
+            label = "New variable",
+            width = "100%"
+          ),
+          shiny::tags$br(),
+          shiny::helpText(shiny::markdown("Create a new variable/column based on an *R*-expression.")),
+          shiny::tags$br(),
           shiny::tags$br()
         )
-      )
-    ),
+      ),
+      tags$h4("Compare modified data to original"),
+      shiny::tags$br(),
+      shiny::tags$p(
+        "Raw print of the original vs the modified data."
+      ),
+      shiny::tags$br(),
+      shiny::fluidRow(
+        shiny::column(
+          width = 6,
+          shiny::tags$b("Original data:"),
+          shiny::verbatimTextOutput("original_str")
+        ),
+        shiny::column(
+          width = 6,
+          shiny::tags$b("Modified data:"),
+          shiny::verbatimTextOutput("modified_str")
+        )
+      ),
+      shiny::tags$br(),
+      shiny::actionButton(
+        inputId = "data_reset",
+        label = "Restore original data",
+        width = "100%"
+      ),
+      shiny::tags$br(),
+      shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
+      shiny::tags$br()
+    )
+    # )
+  ),
   ##############################################################################
   #########
   #########  Descriptive analyses panel
   #########
   ##############################################################################
   "describe" =
-    bslib::nav_panel(
+    bslib::nav_menu(
       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(
-              value = "acc_chars",
-              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 'Data' tab to reclass a variable if it's not on the list."),
-              shiny::conditionalPanel(
-                condition = "input.strat_var!='none'",
-                shiny::radioButtons(
-                  inputId = "add_p",
-                  label = "Compare strata?",
-                  selected = "no",
-                  inline = TRUE,
-                  choices = list(
-                    "No" = "no",
-                    "Yes" = "yes"
-                  )
+      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(
+          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",
+                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::conditionalPanel(
+                  condition = "input.strat_var!='none'",
+                  shiny::radioButtons(
+                    inputId = "add_p",
+                    label = "Compare strata?",
+                    selected = "no",
+                    inline = TRUE,
+                    choices = list(
+                      "No" = "no",
+                      "Yes" = "yes"
+                    )
+                  ),
+                  shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
                 ),
-                shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
-              ),
-              shiny::br(),
-              shiny::br(),
-              shiny::actionButton(
-                inputId = "act_eval",
-                label = "Evaluate",
-                width = "100%",
-                icon = shiny::icon("calculator"),
-                disabled = TRUE
+                shiny::br(),
+                shiny::br(),
+                shiny::actionButton(
+                  inputId = "act_eval",
+                  label = "Evaluate",
+                  width = "100%",
+                  icon = shiny::icon("calculator"),
+                  disabled = TRUE
+                )
               )
-            ),
-            bslib::accordion_panel(
-              vlaue = "acc_cor",
-              title = "Correlations",
-              icon = bsicons::bs_icon("bounding-box"),
-              shiny::uiOutput("outcome_var_cor"),
-              shiny::helpText("To avoid evaluating the correlation of the outcome variable, this can be excluded from the plot or select 'none'."),
-              shiny::br(),
-              shinyWidgets::noUiSliderInput(
-                inputId = "cor_cutoff",
-                label = "Correlation cut-off",
-                min = 0,
-                max = 1,
-                step = .01,
-                value = .8,
-                format = shinyWidgets::wNumbFormat(decimals = 2),
-                color = datamods:::get_primary_color()
-              ),
-              shiny::helpText("Set the cut-off for considered 'highly correlated'.")
-            ),
-            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.")
             )
-          )
-        ),
-        bslib::nav_panel(
-          title = "Characteristics",
+          ),
           gt::gt_output(outputId = "table1")
-        ),
-        bslib::nav_panel(
-          title = "Correlations",
+        )
+      ),
+      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",
+                title = "Correlations",
+                icon = bsicons::bs_icon("bounding-box"),
+                shiny::uiOutput("outcome_var_cor"),
+                shiny::helpText("To avoid evaluating the correlation of the outcome variable, this can be excluded from the plot or select 'none'."),
+                shiny::br(),
+                shinyWidgets::noUiSliderInput(
+                  inputId = "cor_cutoff",
+                  label = "Correlation cut-off",
+                  min = 0,
+                  max = 1,
+                  step = .01,
+                  value = .8,
+                  format = shinyWidgets::wNumbFormat(decimals = 2),
+                  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",
+        )
+      ),
+      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.")
+              )
+            )
+          ),
           data_missings_ui(id = "missingness")
         )
       )
@@ -10244,27 +10313,23 @@ ui_elements <- list(
   #########  Download panel
   #########
   ##############################################################################
-  "visuals" = bslib::nav_panel(
-    title = "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"
-            )
-          )
-        )
-      )
+  "visuals" = do.call(
+    bslib::nav_panel,
+    c(
+      list(
+        title = "Visuals",
+        icon = shiny::icon("chart-line"),
+        id = "navvisuals"
+      ),
+      data_visuals_ui("visuals")
     )
+    # 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$docs,
+        # ui_elements$feedback,
+        # ui_elements$docs,
         fillable = FALSE,
         footer = shiny::tags$footer(
           style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
@@ -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")
   })
 
   ##############################################################################
diff --git a/app_docker/www/FreesearchR-logo-black-nobg.png b/app_docker/www/FreesearchR-logo-black-nobg.png
new file mode 100644
index 00000000..2b927071
Binary files /dev/null and b/app_docker/www/FreesearchR-logo-black-nobg.png differ
diff --git a/app_docker/www/FreesearchR-logo-blue-nobg.png b/app_docker/www/FreesearchR-logo-blue-nobg.png
new file mode 100644
index 00000000..0a0e5729
Binary files /dev/null and b/app_docker/www/FreesearchR-logo-blue-nobg.png differ
diff --git a/app_docker/www/FreesearchR-logo-white-nobg-h80.png b/app_docker/www/FreesearchR-logo-white-nobg-h80.png
new file mode 100644
index 00000000..2423010d
Binary files /dev/null and b/app_docker/www/FreesearchR-logo-white-nobg-h80.png differ
diff --git a/app_docker/www/FreesearchR-logo-white-nobg.png b/app_docker/www/FreesearchR-logo-white-nobg.png
new file mode 100644
index 00000000..d9a68834
Binary files /dev/null and b/app_docker/www/FreesearchR-logo-white-nobg.png differ
diff --git a/inst/apps/FreesearchR/app.R b/inst/apps/FreesearchR/app.R
index 28f5e3b6..a93a739c 100644
--- a/inst/apps/FreesearchR/app.R
+++ b/inst/apps/FreesearchR/app.R
@@ -1,11 +1,11 @@
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/app/libs.R 
+#### Current file: /Users/au301842/FreesearchR/app/libs.R
 ########
 
 library(shiny)
-# library(shinyjs)
+library(shinyjs)
 # library(methods)
 # library(readr)
 # library(MASS)
@@ -40,20 +40,20 @@ library(rlang)
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/app/functions.R 
+#### Current file: /Users/au301842/FreesearchR/app/functions.R
 ########
 
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//app_version.R 
+#### Current file: /Users/au301842/FreesearchR/R//app_version.R
 ########
 
-app_version <- function()'25.6.4'
+app_version <- function()'25.7.2'
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//baseline_table.R 
+#### Current file: /Users/au301842/FreesearchR/R//baseline_table.R
 ########
 
 #' Print a flexible baseline characteristics table
@@ -138,7 +138,7 @@ create_baseline <- function(data, ..., by.var, add.p = FALSE, add.overall = FALS
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//contrast_text.R 
+#### Current file: /Users/au301842/FreesearchR/R//contrast_text.R
 ########
 
 #' @title Contrast Text Color
@@ -194,7 +194,7 @@ contrast_text <- function(background,
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//correlations-module.R 
+#### Current file: /Users/au301842/FreesearchR/R//correlations-module.R
 ########
 
 #' Data correlations evaluation module
@@ -339,7 +339,7 @@ sentence_paste <- function(data, and.str = "and") {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//create-column-mod.R 
+#### Current file: /Users/au301842/FreesearchR/R//create-column-mod.R
 ########
 
 #' @title Create new column
@@ -782,7 +782,7 @@ make_choices_with_infos <- function(data) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//custom_SelectInput.R 
+#### Current file: /Users/au301842/FreesearchR/R//custom_SelectInput.R
 ########
 
 #' A selectizeInput customized for data frames with column labels
@@ -976,7 +976,7 @@ vectorSelectInput <- function(inputId,
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//cut-variable-dates.R 
+#### Current file: /Users/au301842/FreesearchR/R//cut-variable-dates.R
 ########
 
 #' Extended cutting function with fall-back to the native base::cut
@@ -1595,7 +1595,7 @@ plot_histogram <- function(data, column=NULL, bins = 30, breaks = NULL, color =
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//data_plots.R 
+#### Current file: /Users/au301842/FreesearchR/R//data_plots.R
 ########
 
 # source(here::here("functions.R"))
@@ -1611,97 +1611,96 @@ 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(
-
-    # Sidebar with a slider input
-    sidebar = bslib::sidebar(
-      bslib::accordion(
-        multiple = FALSE,
-        bslib::accordion_panel(
-          title = "Creating plot",
-          icon = bsicons::bs_icon("graph-up"),
-          shiny::uiOutput(outputId = ns("primary")),
-          shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'),
-          shiny::tags$br(),
-          shiny::uiOutput(outputId = ns("type")),
-          shiny::uiOutput(outputId = ns("secondary")),
-          shiny::uiOutput(outputId = ns("tertiary")),
-          shiny::br(),
-          shiny::actionButton(
-            inputId = ns("act_plot"),
-            label = "Plot",
-            width = "100%",
-            icon = shiny::icon("palette"),
-            disabled = FALSE
+    bslib::layout_sidebar(
+      sidebar = bslib::sidebar(
+        bslib::accordion(
+          multiple = FALSE,
+          bslib::accordion_panel(
+            title = "Creating plot",
+            icon = bsicons::bs_icon("graph-up"),
+            shiny::uiOutput(outputId = ns("primary")),
+            shiny::helpText('Only non-text variables are available for plotting. Go the "Data" to reclass data to plot.'),
+            shiny::tags$br(),
+            shiny::uiOutput(outputId = ns("type")),
+            shiny::uiOutput(outputId = ns("secondary")),
+            shiny::uiOutput(outputId = ns("tertiary")),
+            shiny::br(),
+            shiny::actionButton(
+              inputId = ns("act_plot"),
+              label = "Plot",
+              width = "100%",
+              icon = shiny::icon("palette"),
+              disabled = FALSE
+            ),
+            shiny::helpText('Adjust settings, then press "Plot".')
           ),
-          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"),
-          shinyWidgets::noUiSliderInput(
-            inputId = ns("height_slide"),
-            label = "Plot height (mm)",
-            min = 50,
-            max = 300,
-            value = 100,
-            step = 1,
-            format = shinyWidgets::wNumbFormat(decimals = 0),
-            color = datamods:::get_primary_color(),
-            inline = TRUE
-          ),
-          # shiny::numericInput(
-          #   inputId = ns("height_numeric"),
-          #   label = "Plot height (mm)",
-          #   min = 50,
-          #   max = 300,
-          #   value = 100
-          # ),
-          shinyWidgets::noUiSliderInput(
-            inputId = ns("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"
+          bslib::accordion_panel(
+            title = "Download",
+            icon = bsicons::bs_icon("download"),
+            shinyWidgets::noUiSliderInput(
+              inputId = ns("height_slide"),
+              label = "Plot height (mm)",
+              min = 50,
+              max = 300,
+              value = 100,
+              step = 1,
+              format = shinyWidgets::wNumbFormat(decimals = 0),
+              color = datamods:::get_primary_color(),
+              inline = TRUE
+            ),
+            # shiny::numericInput(
+            #   inputId = ns("height_numeric"),
+            #   label = "Plot height (mm)",
+            #   min = 50,
+            #   max = 300,
+            #   value = 100
+            # ),
+            shinyWidgets::noUiSliderInput(
+              inputId = ns("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")
             )
-          ),
-          shiny::br(),
-          # Button
-          shiny::downloadButton(
-            outputId = ns("download_plot"),
-            label = "Download plot",
-            icon = shiny::icon("download")
           )
-        )
-      )
-    ),
-    bslib::nav_panel(
-      title = tab_title,
+        ),
+        shiny::p("We have collected a few notes on visualising data and details on the options included in FreesearchR:", shiny::tags$a(
+          href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
+          "View notes in new tab",
+          target = "_blank",
+          rel = "noopener noreferrer"
+        ))
+      ),
       shiny::plotOutput(ns("plot"), height = "70vh"),
       shiny::tags$br(),
       shiny::tags$br(),
       shiny::htmlOutput(outputId = ns("code_plot"))
     )
   )
+  # )
 }
 
 
@@ -2325,6 +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")
@@ -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) {
@@ -2445,7 +2445,7 @@ clean_common_axis <- function(p, axis) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//data-import.R 
+#### Current file: /Users/au301842/FreesearchR/R//data-import.R
 ########
 
 data_import_ui <- function(id) {
@@ -2602,7 +2602,7 @@ data_import_demo_app <- function() {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//data-summary.R 
+#### Current file: /Users/au301842/FreesearchR/R//data-summary.R
 ########
 
 #' Data summary module
@@ -3000,7 +3000,7 @@ get_var_icon <- function(data,class.type=c("class","type")){
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//datagrid-infos-mod.R 
+#### Current file: /Users/au301842/FreesearchR/R//datagrid-infos-mod.R
 ########
 
 
@@ -3349,7 +3349,7 @@ construct_col_summary <- function(data) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//helpers.R 
+#### Current file: /Users/au301842/FreesearchR/R//helpers.R
 ########
 
 #' Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()'
@@ -4023,14 +4023,14 @@ simple_snake <- function(data){
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R 
+#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R
 ########
 
-hosted_version <- function()'v25.6.4-250627'
+hosted_version <- function()'v25.7.2-250703'
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//html_dependency_freesearchr.R 
+#### Current file: /Users/au301842/FreesearchR/R//html_dependency_freesearchr.R
 ########
 
 html_dependency_FreesearchR <- function() {
@@ -4045,7 +4045,7 @@ html_dependency_FreesearchR <- function() {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//import-file-ext.R 
+#### Current file: /Users/au301842/FreesearchR/R//import-file-ext.R
 ########
 
 #' @title Import data from a file
@@ -4655,7 +4655,7 @@ import_file_demo_app <- function() {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//launch_FreesearchR.R 
+#### Current file: /Users/au301842/FreesearchR/R//launch_FreesearchR.R
 ########
 
 #' Easily launch the FreesearchR app
@@ -4686,7 +4686,7 @@ launch_FreesearchR <- function(...){
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//missings-module.R 
+#### Current file: /Users/au301842/FreesearchR/R//missings-module.R
 ########
 
 #' Data correlations evaluation module
@@ -4735,14 +4735,7 @@ data_missings_server <- function(id,
 
         tryCatch(
           {
-            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)
-            }
+            out <- compare_missings(df_tbl,by_var)
           },
           error = function(err) {
             showNotification(paste0("Error: ", err), type = "err")
@@ -4820,17 +4813,29 @@ 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
+}
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//plot_box.R 
+#### Current file: /Users/au301842/FreesearchR/R//plot_box.R
 ########
 
 #' Beautiful box plot(s)
@@ -4929,7 +4934,7 @@ plot_box_single <- function(data, pri, sec=NULL, seed = 2103) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//plot_euler.R 
+#### Current file: /Users/au301842/FreesearchR/R//plot_euler.R
 ########
 
 #' Area proportional venn diagrams
@@ -5070,7 +5075,7 @@ plot_euler_single <- function(data) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//plot_hbar.R 
+#### Current file: /Users/au301842/FreesearchR/R//plot_hbar.R
 ########
 
 #' Nice horizontal stacked bars (Grotta bars)
@@ -5170,7 +5175,7 @@ vertical_stacked_bars <- function(data,
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//plot_ridge.R 
+#### Current file: /Users/au301842/FreesearchR/R//plot_ridge.R
 ########
 
 #' Plot nice ridge plot
@@ -5204,7 +5209,7 @@ plot_ridge <- function(data, x, y, z = NULL, ...) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//plot_sankey.R 
+#### Current file: /Users/au301842/FreesearchR/R//plot_sankey.R
 ########
 
 #' Readying data for sankey plot
@@ -5437,7 +5442,7 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//plot_scatter.R 
+#### Current file: /Users/au301842/FreesearchR/R//plot_scatter.R
 ########
 
 #' Beautiful violin plot
@@ -5472,7 +5477,7 @@ plot_scatter <- function(data, pri, sec, ter = NULL) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//plot_violin.R 
+#### Current file: /Users/au301842/FreesearchR/R//plot_violin.R
 ########
 
 #' Beatiful violin plot
@@ -5507,7 +5512,7 @@ plot_violin <- function(data, pri, sec, ter = NULL) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//plot-download-module.R 
+#### Current file: /Users/au301842/FreesearchR/R//plot-download-module.R
 ########
 
 plot_download_ui <- regression_ui <- function(id, ...) {
@@ -5588,7 +5593,7 @@ plot_download_server <- function(id,
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//redcap_read_shiny_module.R 
+#### Current file: /Users/au301842/FreesearchR/R//redcap_read_shiny_module.R
 ########
 
 #' Shiny module to browser and export REDCap data
@@ -6284,7 +6289,7 @@ redcap_demo_app <- function() {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//regression_model.R 
+#### Current file: /Users/au301842/FreesearchR/R//regression_model.R
 ########
 
 #' Create a regression model programatically
@@ -7011,7 +7016,7 @@ regression_model_uv_list <- function(data,
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//regression_plot.R 
+#### Current file: /Users/au301842/FreesearchR/R//regression_plot.R
 ########
 
 #' Regression coef plot from gtsummary. Slightly modified to pass on arguments
@@ -7177,7 +7182,7 @@ symmetrical_scale_x_log10 <- function(plot, breaks = c(1, 2, 3, 5, 10), ...) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//regression_table.R 
+#### Current file: /Users/au301842/FreesearchR/R//regression_table.R
 ########
 
 #' Create table of regression model
@@ -7366,7 +7371,7 @@ tbl_merge <- function(data) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//regression-module.R 
+#### Current file: /Users/au301842/FreesearchR/R//regression-module.R
 ########
 
 ### On rewriting this module
@@ -7415,155 +7420,173 @@ regression_ui <- function(id, ...) {
   ns <- shiny::NS(id)
 
   shiny::tagList(
-    title = "",
-    sidebar = bslib::sidebar(
-      shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
-      bslib::accordion(
-        open = "acc_reg",
-        multiple = FALSE,
-        bslib::accordion_panel(
-          value = "acc_reg",
-          title = "Regression",
-          icon = bsicons::bs_icon("calculator"),
-          shiny::uiOutput(outputId = ns("outcome_var")),
-          # shiny::selectInput(
-          #   inputId = "design",
-          #   label = "Study design",
-          #   selected = "no",
-          #   inline = TRUE,
-          #   choices = list(
-          #     "Cross-sectional" = "cross-sectional"
-          #   )
-          # ),
-          shiny::uiOutput(outputId = ns("regression_type")),
-          shiny::radioButtons(
-            inputId = ns("all"),
-            label = "Specify covariables",
-            inline = TRUE, selected = 2,
-            choiceNames = c(
-              "Yes",
-              "No"
-            ),
-            choiceValues = c(1, 2)
-          ),
-          shiny::conditionalPanel(
-            condition = "input.all==1",
-            shiny::uiOutput(outputId = ns("regression_vars")),
-            shiny::helpText("If none are selected, all are included."),
-            shiny::tags$br(),
-            ns = ns
-          ),
-          bslib::input_task_button(
-            id = ns("load"),
-            label = "Analyse",
-            icon = bsicons::bs_icon("pencil"),
-            label_busy = "Working...",
-            icon_busy = fontawesome::fa_i("arrows-rotate",
-              class = "fa-spin",
-              "aria-hidden" = "true"
-            ),
-            type = "secondary",
-            auto_reset = TRUE
-          ),
-          shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
-          shiny::tags$br(),
-          shiny::radioButtons(
-            inputId = ns("add_regression_p"),
-            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"),
+    # title = "",
+    bslib::nav_panel(
+      title = "Regression table",
+      bslib::layout_sidebar(
+        sidebar = bslib::sidebar(
+          shiny::uiOutput(outputId = ns("data_info"), inline = TRUE),
+          bslib::accordion(
+            open = "acc_reg",
+            multiple = FALSE,
+            bslib::accordion_panel(
+              value = "acc_reg",
+              title = "Regression",
+              icon = bsicons::bs_icon("calculator"),
+              shiny::uiOutput(outputId = ns("outcome_var")),
+              # shiny::selectInput(
+              #   inputId = "design",
+              #   label = "Study design",
+              #   selected = "no",
+              #   inline = TRUE,
+              #   choices = list(
+              #     "Cross-sectional" = "cross-sectional"
+              #   )
+              # ),
+              shiny::uiOutput(outputId = ns("regression_type")),
+              shiny::radioButtons(
+                inputId = ns("all"),
+                label = "Specify covariables",
+                inline = TRUE, selected = 2,
+                choiceNames = c(
+                  "Yes",
+                  "No"
+                ),
+                choiceValues = c(1, 2)
+              ),
+              shiny::conditionalPanel(
+                condition = "input.all==1",
+                shiny::uiOutput(outputId = ns("regression_vars")),
+                shiny::helpText("If none are selected, all are included."),
+                shiny::tags$br(),
+                ns = ns
+              ),
+              bslib::input_task_button(
+                id = ns("load"),
+                label = "Analyse",
+                icon = bsicons::bs_icon("pencil"),
+                label_busy = "Working...",
+                icon_busy = fontawesome::fa_i("arrows-rotate",
+                  class = "fa-spin",
+                  "aria-hidden" = "true"
+                ),
+                type = "secondary",
+                auto_reset = TRUE
+              ),
+              shiny::helpText("Press 'Analyse' to create the regression model and after changing parameters."),
               shiny::tags$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",
+              shiny::radioButtons(
+                inputId = ns("add_regression_p"),
+                label = "Show p-value",
+                inline = TRUE,
+                selected = "yes",
                 choices = list(
-                  "png",
-                  "tiff",
-                  "eps",
-                  "pdf",
-                  "jpeg",
-                  "svg"
+                  "Yes" = "yes",
+                  "No" = "no"
                 )
               ),
-              shiny::br(),
-              # Button
-              shiny::downloadButton(
-                outputId = ns("download_plot"),
-                label = "Download plot",
-                icon = shiny::icon("download")
+              # 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()
+            )
+          )
+        ),
+        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(
-          value = "acc_checks",
-          title = "Checks",
-          icon = bsicons::bs_icon("clipboard-check"),
-          shiny::uiOutput(outputId = ns("plot_checks"))
-        )
+        shiny::plotOutput(outputId = ns("regression_plot"), height = "80vh")
       )
     ),
-    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")
+      )
     )
   )
 }
@@ -8036,7 +8059,7 @@ regression_server <- function(id,
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//report.R 
+#### Current file: /Users/au301842/FreesearchR/R//report.R
 ########
 
 #' Split vector by an index and embed addition
@@ -8124,7 +8147,7 @@ modify_qmd <- function(file, format) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//syntax_highlight.R 
+#### Current file: /Users/au301842/FreesearchR/R//syntax_highlight.R
 ########
 
 ## Inpiration:
@@ -8155,7 +8178,7 @@ html_code_wrap <- function(string,lang="r"){
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//theme.R 
+#### Current file: /Users/au301842/FreesearchR/R//theme.R
 ########
 
 #' Custom theme based on unity
@@ -8274,7 +8297,7 @@ gg_theme_export <- function() {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//update-factor-ext.R 
+#### Current file: /Users/au301842/FreesearchR/R//update-factor-ext.R
 ########
 
 
@@ -8571,7 +8594,7 @@ winbox_update_factor <- function(id,
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//update-variables-ext.R 
+#### Current file: /Users/au301842/FreesearchR/R//update-variables-ext.R
 ########
 
 #' Select, rename and convert variables
@@ -9383,7 +9406,7 @@ clean_date <- function(data) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//visual_summary.R 
+#### Current file: /Users/au301842/FreesearchR/R//visual_summary.R
 ########
 
 #' Data correlations evaluation module
@@ -9680,7 +9703,7 @@ unique_short <- function(data, max = 15) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/R//wide2long.R 
+#### Current file: /Users/au301842/FreesearchR/R//wide2long.R
 ########
 
 #' Alternative pivoting method for easily pivoting based on name pattern
@@ -9839,17 +9862,18 @@ grepl_fix <- function(data, pattern, type = c("prefix", "infix", "suffix")) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/dev/header_include.R 
+#### Current file: /Users/au301842/FreesearchR/dev/header_include.R
 ########
 
 header_include <- function(){
   shiny::tags$head(
-    tags$link(rel = "stylesheet", type = "text/css", href = "style.css"))
+    tags$link(rel = "stylesheet", type = "text/css", href = "style.css"),
+    tags$script(src="scripts.js"))
 }
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/dev/dev_banner.R 
+#### Current file: /Users/au301842/FreesearchR/dev/dev_banner.R
 ########
 
 dev_banner <- function(){
@@ -9858,7 +9882,7 @@ dev_banner <- function(){
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/app/ui.R 
+#### Current file: /Users/au301842/FreesearchR/app/ui.R
 ########
 
 # ns <- NS(id)
@@ -9873,6 +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"
@@ -9884,8 +9910,7 @@ ui_elements <- list(
         shiny::markdown(readLines("www/intro.md")),
         shiny::column(width = 2)
       )
-    ),
-    icon = shiny::icon("home")
+    )
   ),
   ##############################################################################
   #########
@@ -9893,7 +9918,8 @@ ui_elements <- list(
   #########
   ##############################################################################
   "import" = bslib::nav_panel(
-    title = "Import",
+    title = "Get started",
+    icon = shiny::icon("play"),
     shiny::fluidRow(
       shiny::column(width = 2),
       shiny::column(
@@ -9949,13 +9975,13 @@ ui_elements <- list(
         shiny::conditionalPanel(
           condition = "output.data_loaded == true",
           shiny::br(),
-            shiny::actionButton(
-              inputId = "modal_initial_view",
-              label = "Quick overview",
-              width = "100%",
-              icon = shiny::icon("binoculars"),
-              disabled = FALSE
-            ),
+          shiny::actionButton(
+            inputId = "modal_initial_view",
+            label = "Quick overview",
+            width = "100%",
+            icon = shiny::icon("binoculars"),
+            disabled = FALSE
+          ),
           shiny::br(),
           shiny::br(),
           shiny::h5("Select variables for final import"),
@@ -10011,272 +10037,273 @@ ui_elements <- list(
   #########  Data overview panel
   #########
   ##############################################################################
-  "overview" =
-  # bslib::nav_panel_hidden(
+  "prepare" = bslib::nav_menu(
+    title = "Prepare",
+    icon = shiny::icon("pen-to-square"),
     bslib::nav_panel(
-      # value = "overview",
-      title = "Data",
-      bslib::navset_bar(
-        fillable = TRUE,
-        bslib::nav_panel(
-          title = "Overview",
-          tags$h3("Overview and filtering"),
-          fluidRow(
-            shiny::column(
-              width = 9,
-              shiny::uiOutput(outputId = "data_info", inline = TRUE),
-              shiny::tags$p(
-                "Below is a short summary table, on the right you can click to visualise data classes or browse data and create different data filters."
-              )
-            ),
-            shiny::column(
-              width = 3,
-              shiny::actionButton(
-                inputId = "modal_visual_overview",
-                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()
-            )
-          ),
-          fluidRow(
-            shiny::column(
-              width = 9,
-              data_summary_ui(id = "data_summary"),
-              shiny::br(),
-              shiny::br(),
-              shiny::br(),
-              shiny::br(),
-              shiny::br()
-            ),
-            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$h6("Filter data types"),
-              shiny::uiOutput(
-                outputId = "column_filter"
-              ),
-              shiny::helpText("Read more on how ", tags$a(
-                "data types",
-                href = "https://agdamsbo.github.io/FreesearchR/articles/data-types.html",
-                target = "_blank",
-                rel = "noopener noreferrer"
-              ), " are defined."),
-              shiny::br(),
-              shiny::br(),
-              shiny::tags$h6("Filter observations"),
-              shiny::tags$p("Filter on observation level"),
-              IDEAFilter::IDEAFilter_ui("data_filter"),
-              shiny::br(),
-              shiny::br()
-            )
+      title = "Overview",
+      icon = shiny::icon("eye"),
+      value = "nav_prepare_overview",
+      tags$h3("Overview and filtering"),
+      fluidRow(
+        shiny::column(
+          width = 9,
+          shiny::uiOutput(outputId = "data_info", inline = TRUE),
+          shiny::tags$p(
+            "Below is a short summary table, on the right you can click to visualise data classes or browse data and create different data filters."
+          )
+        ),
+        shiny::column(
+          width = 3,
+          shiny::actionButton(
+            inputId = "modal_visual_overview",
+            label = "Visual overview",
+            width = "100%",
+            disabled = TRUE
           ),
           shiny::br(),
           shiny::br(),
-          # shiny::br(),
-          # shiny::br(),
+          shiny::actionButton(
+            inputId = "modal_browse",
+            label = "Browse data",
+            width = "100%",
+            disabled = TRUE
+          ),
+          shiny::br(),
+          shiny::br()
+        )
+      ),
+      fluidRow(
+        shiny::column(
+          width = 9,
+          data_summary_ui(id = "data_summary"),
+          shiny::br(),
+          shiny::br(),
+          shiny::br(),
+          shiny::br(),
           shiny::br()
         ),
-        bslib::nav_panel(
-          title = "Modify",
-          tags$h3("Subset, rename and convert variables"),
-          fluidRow(
-            shiny::column(
-              width = 9,
-              shiny::tags$p(
-                shiny::markdown("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."),
-                shiny::markdown("There are more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."),
-                shiny::markdown("Please note that data modifications are applied before any filtering.")
-              )
-            )
+        shiny::column(
+          width = 3,
+          shiny::tags$h6("Filter data types"),
+          shiny::uiOutput(
+            outputId = "column_filter"
           ),
-          # shiny::tags$br(),
-          update_variables_ui("modal_variables"),
-          shiny::tags$br(),
-          shiny::tags$br(),
-          shiny::tags$h4("Advanced data manipulation"),
-          shiny::tags$p("Below options allow more advanced varaible manipulations."),
-          shiny::tags$br(),
-          shiny::tags$br(),
-          shiny::fluidRow(
-            shiny::column(
-              width = 4,
-              shiny::actionButton(
-                inputId = "modal_update",
-                label = "Reorder factor levels",
-                width = "100%"
-              ),
-              shiny::tags$br(),
-              shiny::helpText("Reorder the levels of factor/categorical variables."),
-              shiny::tags$br(),
-              shiny::tags$br()
-            ),
-            shiny::column(
-              width = 4,
-              shiny::actionButton(
-                inputId = "modal_cut",
-                label = "New factor",
-                width = "100%"
-              ),
-              shiny::tags$br(),
-              shiny::helpText("Create factor/categorical variable from a continous variable (number/date/time)."),
-              shiny::tags$br(),
-              shiny::tags$br()
-            ),
-            shiny::column(
-              width = 4,
-              shiny::actionButton(
-                inputId = "modal_column",
-                label = "New variable",
-                width = "100%"
-              ),
-              shiny::tags$br(),
-              shiny::helpText(shiny::markdown("Create a new variable/column based on an *R*-expression.")),
-              shiny::tags$br(),
-              shiny::tags$br()
-            )
-          ),
-          tags$h4("Compare modified data to original"),
-          shiny::tags$br(),
+          shiny::helpText("Read more on how ", tags$a(
+            "data types",
+            href = "https://agdamsbo.github.io/FreesearchR/articles/data-types.html",
+            target = "_blank",
+            rel = "noopener noreferrer"
+          ), " are defined."),
+          shiny::br(),
+          shiny::br(),
+          shiny::tags$h6("Filter observations"),
+          shiny::tags$p("Filter on observation level"),
+          IDEAFilter::IDEAFilter_ui("data_filter"),
+          shiny::br(),
+          shiny::br()
+        )
+      ),
+      shiny::br(),
+      shiny::br(),
+      shiny::br()
+    ),
+    bslib::nav_panel(
+      title = "Modify",
+      icon = shiny::icon("file-pen"),
+      tags$h3("Subset, rename and convert variables"),
+      fluidRow(
+        shiny::column(
+          width = 9,
           shiny::tags$p(
-            "Raw print of the original vs the modified data."
-          ),
-          shiny::tags$br(),
-          shiny::fluidRow(
-            shiny::column(
-              width = 6,
-              shiny::tags$b("Original data:"),
-              # verbatimTextOutput("original"),
-              shiny::verbatimTextOutput("original_str")
-            ),
-            shiny::column(
-              width = 6,
-              shiny::tags$b("Modified data:"),
-              # verbatimTextOutput("modified"),
-              shiny::verbatimTextOutput("modified_str")
-            )
-          ),
-          shiny::tags$br(),
+            shiny::markdown("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."),
+            shiny::markdown("There are more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."),
+            shiny::markdown("Please note that data modifications are applied before any filtering.")
+          )
+        )
+      ),
+      update_variables_ui("modal_variables"),
+      shiny::tags$br(),
+      shiny::tags$br(),
+      shiny::tags$h4("Advanced data manipulation"),
+      shiny::tags$p("Below options allow more advanced varaible manipulations."),
+      shiny::tags$br(),
+      shiny::tags$br(),
+      shiny::fluidRow(
+        shiny::column(
+          width = 4,
           shiny::actionButton(
-            inputId = "data_reset",
-            label = "Restore original data",
+            inputId = "modal_update",
+            label = "Reorder factor levels",
             width = "100%"
           ),
           shiny::tags$br(),
-          shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
+          shiny::helpText("Reorder the levels of factor/categorical variables."),
+          shiny::tags$br(),
+          shiny::tags$br()
+        ),
+        shiny::column(
+          width = 4,
+          shiny::actionButton(
+            inputId = "modal_cut",
+            label = "New factor",
+            width = "100%"
+          ),
+          shiny::tags$br(),
+          shiny::helpText("Create factor/categorical variable from a continous variable (number/date/time)."),
+          shiny::tags$br(),
+          shiny::tags$br()
+        ),
+        shiny::column(
+          width = 4,
+          shiny::actionButton(
+            inputId = "modal_column",
+            label = "New variable",
+            width = "100%"
+          ),
+          shiny::tags$br(),
+          shiny::helpText(shiny::markdown("Create a new variable/column based on an *R*-expression.")),
+          shiny::tags$br(),
           shiny::tags$br()
         )
-      )
-    ),
+      ),
+      tags$h4("Compare modified data to original"),
+      shiny::tags$br(),
+      shiny::tags$p(
+        "Raw print of the original vs the modified data."
+      ),
+      shiny::tags$br(),
+      shiny::fluidRow(
+        shiny::column(
+          width = 6,
+          shiny::tags$b("Original data:"),
+          shiny::verbatimTextOutput("original_str")
+        ),
+        shiny::column(
+          width = 6,
+          shiny::tags$b("Modified data:"),
+          shiny::verbatimTextOutput("modified_str")
+        )
+      ),
+      shiny::tags$br(),
+      shiny::actionButton(
+        inputId = "data_reset",
+        label = "Restore original data",
+        width = "100%"
+      ),
+      shiny::tags$br(),
+      shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
+      shiny::tags$br()
+    )
+    # )
+  ),
   ##############################################################################
   #########
   #########  Descriptive analyses panel
   #########
   ##############################################################################
   "describe" =
-    bslib::nav_panel(
+    bslib::nav_menu(
       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(
-              value = "acc_chars",
-              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 'Data' tab to reclass a variable if it's not on the list."),
-              shiny::conditionalPanel(
-                condition = "input.strat_var!='none'",
-                shiny::radioButtons(
-                  inputId = "add_p",
-                  label = "Compare strata?",
-                  selected = "no",
-                  inline = TRUE,
-                  choices = list(
-                    "No" = "no",
-                    "Yes" = "yes"
-                  )
+      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(
+          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",
+                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::conditionalPanel(
+                  condition = "input.strat_var!='none'",
+                  shiny::radioButtons(
+                    inputId = "add_p",
+                    label = "Compare strata?",
+                    selected = "no",
+                    inline = TRUE,
+                    choices = list(
+                      "No" = "no",
+                      "Yes" = "yes"
+                    )
+                  ),
+                  shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
                 ),
-                shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
-              ),
-              shiny::br(),
-              shiny::br(),
-              shiny::actionButton(
-                inputId = "act_eval",
-                label = "Evaluate",
-                width = "100%",
-                icon = shiny::icon("calculator"),
-                disabled = TRUE
+                shiny::br(),
+                shiny::br(),
+                shiny::actionButton(
+                  inputId = "act_eval",
+                  label = "Evaluate",
+                  width = "100%",
+                  icon = shiny::icon("calculator"),
+                  disabled = TRUE
+                )
               )
-            ),
-            bslib::accordion_panel(
-              vlaue = "acc_cor",
-              title = "Correlations",
-              icon = bsicons::bs_icon("bounding-box"),
-              shiny::uiOutput("outcome_var_cor"),
-              shiny::helpText("To avoid evaluating the correlation of the outcome variable, this can be excluded from the plot or select 'none'."),
-              shiny::br(),
-              shinyWidgets::noUiSliderInput(
-                inputId = "cor_cutoff",
-                label = "Correlation cut-off",
-                min = 0,
-                max = 1,
-                step = .01,
-                value = .8,
-                format = shinyWidgets::wNumbFormat(decimals = 2),
-                color = datamods:::get_primary_color()
-              ),
-              shiny::helpText("Set the cut-off for considered 'highly correlated'.")
-            ),
-            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.")
             )
-          )
-        ),
-        bslib::nav_panel(
-          title = "Characteristics",
+          ),
           gt::gt_output(outputId = "table1")
-        ),
-        bslib::nav_panel(
-          title = "Correlations",
+        )
+      ),
+      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",
+                title = "Correlations",
+                icon = bsicons::bs_icon("bounding-box"),
+                shiny::uiOutput("outcome_var_cor"),
+                shiny::helpText("To avoid evaluating the correlation of the outcome variable, this can be excluded from the plot or select 'none'."),
+                shiny::br(),
+                shinyWidgets::noUiSliderInput(
+                  inputId = "cor_cutoff",
+                  label = "Correlation cut-off",
+                  min = 0,
+                  max = 1,
+                  step = .01,
+                  value = .8,
+                  format = shinyWidgets::wNumbFormat(decimals = 2),
+                  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",
+        )
+      ),
+      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.")
+              )
+            )
+          ),
           data_missings_ui(id = "missingness")
         )
       )
@@ -10286,27 +10313,23 @@ ui_elements <- list(
   #########  Download panel
   #########
   ##############################################################################
-  "visuals" = bslib::nav_panel(
-    title = "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"
-            )
-          )
-        )
-      )
+  "visuals" = do.call(
+    bslib::nav_panel,
+    c(
+      list(
+        title = "Visuals",
+        icon = shiny::icon("chart-line"),
+        id = "navvisuals"
+      ),
+      data_visuals_ui("visuals")
     )
+    # do.call(
+    #   bslib::navset_bar,
+    #     data_visuals_ui("visuals")#,
+    # c(
+
+    # )
+    # )
   ),
   ##############################################################################
   #########
@@ -10316,9 +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")
       )
     ),
@@ -10330,6 +10354,7 @@ ui_elements <- list(
   "download" =
     bslib::nav_panel(
       title = "Download",
+      icon = shiny::icon("download"),
       id = "navdownload",
       shiny::fluidRow(
         shiny::column(width = 2),
@@ -10455,9 +10480,42 @@ 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$link(rel = "shortcut icon", href = "favicon.svg")),
@@ -10477,14 +10535,14 @@ ui <- bslib::page_fixed(
         id = "main_panel",
         ui_elements$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$docs,
+        # ui_elements$feedback,
+        # ui_elements$docs,
         fillable = FALSE,
         footer = shiny::tags$footer(
           style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
@@ -10494,7 +10552,7 @@ 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")
           ),
         )
       )
@@ -10504,7 +10562,7 @@ ui <- bslib::page_fixed(
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/app/server.R 
+#### Current file: /Users/au301842/FreesearchR/app/server.R
 ########
 
 data(mtcars)
@@ -11206,7 +11264,7 @@ 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")
   })
 
   ##############################################################################
@@ -11311,7 +11369,7 @@ server <- function(input, output, session) {
 
 
 ########
-#### Current file: /Users/au301842/FreesearchR/app/launch.R 
+#### Current file: /Users/au301842/FreesearchR/app/launch.R
 ########
 
 shinyApp(ui, server)
diff --git a/inst/apps/FreesearchR/www/FreesearchR-logo-black-nobg.png b/inst/apps/FreesearchR/www/FreesearchR-logo-black-nobg.png
new file mode 100644
index 00000000..2b927071
Binary files /dev/null and b/inst/apps/FreesearchR/www/FreesearchR-logo-black-nobg.png differ
diff --git a/inst/apps/FreesearchR/www/FreesearchR-logo-blue-nobg.png b/inst/apps/FreesearchR/www/FreesearchR-logo-blue-nobg.png
new file mode 100644
index 00000000..0a0e5729
Binary files /dev/null and b/inst/apps/FreesearchR/www/FreesearchR-logo-blue-nobg.png differ
diff --git a/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg-h80.png b/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg-h80.png
new file mode 100644
index 00000000..2423010d
Binary files /dev/null and b/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg-h80.png differ
diff --git a/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg.png b/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg.png
new file mode 100644
index 00000000..d9a68834
Binary files /dev/null and b/inst/apps/FreesearchR/www/FreesearchR-logo-white-nobg.png differ
diff --git a/inst/apps/FreesearchR/www/scripts.js b/inst/apps/FreesearchR/www/scripts.js
new file mode 100644
index 00000000..3382b4e4
--- /dev/null
+++ b/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
+  $(document).on('click', '.navbar-nav .nav-link', function() {
+    setTimeout(collapseNavbar, 10);
+  });
+});
diff --git a/inst/assets/js/FreesearchR.js b/inst/assets/js/FreesearchR.js
new file mode 100644
index 00000000..3382b4e4
--- /dev/null
+++ b/inst/assets/js/FreesearchR.js
@@ -0,0 +1,29 @@
+// Automatically close drop-downs on navigation
+// Thanks to claude.ai
+$(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
+  $(document).on('click', '.navbar-nav .nav-link', function() {
+    setTimeout(collapseNavbar, 10);
+  });
+});
diff --git a/man/compare_missings.Rd b/man/compare_missings.Rd
new file mode 100644
index 00000000..8950200c
--- /dev/null
+++ b/man/compare_missings.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/missings-module.R
+\name{compare_missings}
+\alias{compare_missings}
+\title{Pairwise comparison of missings across covariables}
+\usage{
+compare_missings(data, by_var)
+}
+\arguments{
+\item{data}{data frame}
+
+\item{by_var}{variable to stratify by missingness}
+}
+\value{
+gtsummary list object
+}
+\description{
+Pairwise comparison of missings across covariables
+}
diff --git a/vignettes/missingness.Rmd b/vignettes/missingness.Rmd
new file mode 100644
index 00000000..b070878b
--- /dev/null
+++ b/vignettes/missingness.Rmd
@@ -0,0 +1,26 @@
+---
+title: "Missingness in data"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{missingness}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$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]().