revised table export

new version
feat: updated operators for creating new variables
2025-12-15 00:52:09 +01:00 · 2025-12-12 18:09:06 +01:00 · 2025-12-12 17:52:27 +01:00 · 2025-12-12 17:52:10 +01:00 · 2025-12-12 17:51:43 +01:00 · 2025-12-11 22:48:30 +01:00
60 changed files with 4778 additions and 1996 deletions
--- a/CITATION.cff
+++ b/CITATION.cff
@ -8,7 +8,7 @@ message: 'To cite package "FreesearchR" in publications use:'
 type: software
 license: AGPL-3.0-or-later
 title: 'FreesearchR: Easy data analysis for clinicians'
-version: 25.11.1
+version: 25.12.6
 doi: 10.5281/zenodo.14527429
 identifiers:
 - type: url
@ -143,7 +143,7 @@ references:
  authors:
  - family-names: Müller
    given-names: Kirill
-    email: krlmlr+r@mailbox.org
+    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  year: '2025'
  doi: 10.32614/CRAN.package.here
@ -250,6 +250,10 @@ references:
    given-names: Barret
    email: barret@posit.co
    orcid: https://orcid.org/0000-0001-9986-114X
+  - family-names: Aden-Buie
+    given-names: Garrick
+    email: garrick@adenbuie.com
+    orcid: https://orcid.org/0000-0002-7111-0077
  - family-names: Xie
    given-names: Yihui
    email: yihui@posit.co
@ -312,6 +316,10 @@ references:
    given-names: Simon
    email: simon.couch@posit.co
    orcid: https://orcid.org/0000-0001-5676-5107
+  - family-names: Hvitfeldt
+    given-names: Emil
+    email: emil.hvitfeldt@posit.co
+    orcid: https://orcid.org/0000-0002-0679-1945
  year: '2025'
  doi: 10.32614/CRAN.package.broom
 - type: software
@ -397,6 +405,10 @@ references:
    email: joe@posit.co
  - family-names: Tan
    given-names: Xianying
+  - family-names: Aden-Buie
+    given-names: Garrick
+    email: garrick@posit.co
+    orcid: https://orcid.org/0000-0002-7111-0077
  year: '2025'
  doi: 10.32614/CRAN.package.DT
 - type: software
@ -480,6 +492,10 @@ references:
    given-names: Brenton M.
    email: brenton@wiernik.org
    orcid: https://orcid.org/0000-0001-9560-6336
+  - family-names: Thériault
+    given-names: Rémi
+    email: remi.theriault@mail.mcgill.ca
+    orcid: https://orcid.org/0000-0003-4315-6788
  - family-names: Waggoner
    given-names: Philip
    email: philip.waggoner@gmail.com
@ -659,7 +675,7 @@ references:
  authors:
  - family-names: Wickham
    given-names: Hadley
-    email: h.wickham@gmail.com
+    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.reshape2
 - type: software
@ -999,6 +1015,9 @@ references:
  - family-names: Lenth
    given-names: Russell V.
    email: russell-lenth@uiowa.edu
+  - family-names: Piaskowski
+    given-names: Julia
+    email: julia.piask@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.emmeans
 - type: software
@ -1063,6 +1082,127 @@ references:
    orcid: https://orcid.org/0000-0002-7559-1154
  year: '2025'
  doi: 10.32614/CRAN.package.stRoke
+- type: software
+  title: data.table
+  abstract: 'data.table: Extension of `data.frame`'
+  notes: Imports
+  url: https://r-datatable.com
+  repository: https://CRAN.R-project.org/package=data.table
+  authors:
+  - family-names: Barrett
+    given-names: Tyson
+    email: t.barrett88@gmail.com
+    orcid: https://orcid.org/0000-0002-2137-1391
+  - family-names: Dowle
+    given-names: Matt
+    email: mattjdowle@gmail.com
+  - family-names: Srinivasan
+    given-names: Arun
+    email: asrini@pm.me
+  - family-names: Gorecki
+    given-names: Jan
+  - family-names: Chirico
+    given-names: Michael
+    orcid: https://orcid.org/0000-0003-0787-087X
+  - family-names: Hocking
+    given-names: Toby
+    orcid: https://orcid.org/0000-0002-3146-0865
+  - family-names: Schwendinger
+    given-names: Benjamin
+    orcid: https://orcid.org/0000-0003-3315-8114
+  - family-names: Krylov
+    given-names: Ivan
+    email: ikrylov@disroot.org
+    orcid: https://orcid.org/0000-0002-0172-3812
+  year: '2025'
+  doi: 10.32614/CRAN.package.data.table
+- type: software
+  title: viridis
+  abstract: 'viridis: Colorblind-Friendly Color Maps for R'
+  notes: Imports
+  url: https://sjmgarnier.github.io/viridis/
+  repository: https://CRAN.R-project.org/package=viridis
+  authors:
+  - family-names: Garnier
+    given-names: Simon
+    email: garnier@njit.edu
+  year: '2025'
+  doi: 10.32614/CRAN.package.viridis
+- type: software
+  title: smd
+  abstract: 'smd: Compute Standardized Mean Differences'
+  notes: Imports
+  url: https://bsaul.github.io/smd/
+  repository: https://CRAN.R-project.org/package=smd
+  authors:
+  - family-names: Saul
+    given-names: Bradley
+    email: bradleysaul@fastmail.com
+  year: '2025'
+  doi: 10.32614/CRAN.package.smd
+- type: software
+  title: doconv
+  abstract: 'doconv: Document Conversion to ''PDF'' or ''PNG'''
+  notes: Imports
+  url: https://github.com/ardata-fr/doconv
+  repository: https://CRAN.R-project.org/package=doconv
+  authors:
+  - family-names: Gohel
+    given-names: David
+    email: david.gohel@ardata.fr
+  year: '2025'
+  doi: 10.32614/CRAN.package.doconv
+- type: software
+  title: locatexec
+  abstract: 'locatexec: Detection and Localization of Executable Files'
+  notes: Imports
+  url: https://github.com/ardata-fr/locatexec
+  repository: https://CRAN.R-project.org/package=locatexec
+  authors:
+  - family-names: Gohel
+    given-names: David
+    email: david.gohel@ardata.fr
+  year: '2025'
+  doi: 10.32614/CRAN.package.locatexec
+- type: software
+  title: magick
+  abstract: 'magick: Advanced Graphics and Image-Processing in R'
+  notes: Imports
+  url: https://docs.ropensci.org/magick/
+  repository: https://CRAN.R-project.org/package=magick
+  authors:
+  - family-names: Ooms
+    given-names: Jeroen
+    email: jeroenooms@gmail.com
+    orcid: https://orcid.org/0000-0002-4035-0289
+  year: '2025'
+  doi: 10.32614/CRAN.package.magick
+- type: software
+  title: pdftools
+  abstract: 'pdftools: Text Extraction, Rendering and Converting of PDF Documents'
+  notes: Imports
+  url: https://ropensci.r-universe.dev/pdftools
+  repository: https://CRAN.R-project.org/package=pdftools
+  authors:
+  - family-names: Ooms
+    given-names: Jeroen
+    email: jeroenooms@gmail.com
+    orcid: https://orcid.org/0000-0002-4035-0289
+  year: '2025'
+  doi: 10.32614/CRAN.package.pdftools
+- type: software
+  title: qpdf
+  abstract: 'qpdf: Split, Combine and Compress PDF Files'
+  notes: Imports
+  url: https://docs.ropensci.org/qpdf/
+  repository: https://CRAN.R-project.org/package=qpdf
+  authors:
+  - family-names: Ooms
+    given-names: Jeroen
+    email: jeroenooms@gmail.com
+    orcid: https://orcid.org/0000-0002-4035-0289
+  year: '2025'
+  doi: 10.32614/CRAN.package.qpdf
 - type: software
  title: styler
  abstract: 'styler: Non-Invasive Pretty Printing of R Code'
@ -1077,6 +1217,10 @@ references:
  - family-names: Walthert
    given-names: Lorenz
    email: lorenz.walthert@icloud.com
+  - family-names: Patil
+    given-names: Indrajeet
+    email: patilindrajeet.science@gmail.com
+    orcid: https://orcid.org/0000-0003-1995-6531
  year: '2025'
  doi: 10.32614/CRAN.package.styler
 - type: software
@ -1094,7 +1238,7 @@ references:
    given-names: Winston
  - family-names: Bryan
    given-names: Jennifer
-    email: jenny@rstudio.com
+    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2025'
  doi: 10.32614/CRAN.package.devtools
--- a/10
+++ b/10
@ -1,6 +1,6 @@
 Package: FreesearchR
 Title: Easy data analysis for clinicians
-Version: 25.11.1
+Version: 25.12.6
 Authors@R: c(
    person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-7559-1154")),
@ -11,7 +11,7 @@ Description: Easily evaluate and analyse clinical health data in your browser, e
 License: AGPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Imports: 
    assertthat,
    bslib,
@ -68,7 +68,10 @@ Imports:
    readxl,
    NHANES,
    shiny.i18n,
-    stRoke
+    stRoke,
+    data.table,
+    viridis,
+    smd
 Suggests: 
    styler,
    devtools,
@ -128,6 +131,7 @@ Collate:
    'report.R'
    'separate_string.R'
    'syntax_highlight.R'
+    'table-download-module.R'
    'theme.R'
    'translate.R'
    'ui_elements.R'
--- a/6
+++ b/6
@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand

+S3method(cut_var,character)
 S3method(cut_var,default)
 S3method(cut_var,factor)
 S3method(cut_var,hms)
@ -9,6 +10,7 @@ export(add_class_icon)
 export(add_sparkline)
 export(align_axes)
 export(all_but)
+export(allowed_operations)
 export(append_column)
 export(append_list)
 export(argsstring2list)
@ -51,6 +53,7 @@ export(default_parsing)
 export(detect_delimiter)
 export(drop_empty_event)
 export(expression_string)
+export(factor_new_levels_labels)
 export(factorize)
 export(file_export)
 export(format_writer)
@ -86,7 +89,6 @@ export(launch_FreesearchR)
 export(limit_data_size)
 export(limit_log)
 export(line_break)
-export(list_allowed_operations)
 export(list_pkg_data)
 export(m_redcap_readServer)
 export(m_redcap_readUI)
@ -97,6 +99,7 @@ export(merge_expression)
 export(merge_long)
 export(missing_fraction)
 export(missings_apex_plot)
+export(missings_logic_across)
 export(missings_validate)
 export(modal_create_column)
 export(modal_cut_variable)
@ -148,6 +151,7 @@ export(symmetrical_scale_x_log10)
 export(tbl_merge)
 export(type_icons)
 export(ui_elements)
+export(unique_names)
 export(unique_short)
 export(update_factor_server)
 export(update_factor_ui)
--- a/NEWS.md
+++ b/NEWS.md
@ -1,3 +1,41 @@
+# FreesearchR 25.12.6
+
+*NEW* Export missingness table directly.
+
+*NEW* Updated and slightly extended list of allowed operators for new variable creation.
+
+*FIX* The exported MS Word documents prompts a warning. The codebase now includes a fix, but it only works running locally, but was disabled.
+
+# FreesearchR 25.12.5
+
+*NEW* Added option to add pairwise differences in discriptive table.
+
+# FreesearchR 25.12.4
+
+Republish 25.12.3
+
+# FreesearchR 25.12.3
+
+*NEW* Extended missingness evaluation to include two different approaches. Docs will catch up and video tutorials are coming.
+
+# FreesearchR 25.12.2
+
+*FIX* Fixed hanging interface when splitting strings.
+
+*NEW* New option to shorten character variables to the first N words or characters. Shortening by characters could be useful working with eg. ICD-10 diagnostic codes.
+
+# FreesearchR 25.12.1
+
+*NEW* Option to edit factor label names in the "New factor" pop-up. This allows for easier naming for tables, but also to combine levels. A new variable is appended to the dataset if label names are changed. Code is now also exported.
+
+*FIX* Fixes a bug, where white space in code exported was removed. Now a little too many spaces are included. Fine tuning continues.
+
+*NEW* Easily copy code by just clicking "copy" in code blocks.
+
+# FreesearchR 25.11.2
+
+*NEW* Vignettes were moved to the [FreesearchR project knowledge base](https://freesearchr.github.io/FreesearchR-knowledge/). This was mainly to ease rendering and allow quick and easy updates as well as future translations.
+
 # FreesearchR 25.11.1

 *NEW* Added option to select extensive baseline table selecting between "Minimal" (current) or "Extensive" which adds mean/sd and min/max as well as plots all levels also for dichotomous variables.
--- a/R/app_version.R
+++ b/R/app_version.R
@ -1 +1 @@
-app_version <- function()'25.11.1'
+app_version <- function()'25.12.6'
--- a/R/baseline_table.R
+++ b/R/baseline_table.R
@ -37,7 +37,7 @@ baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary,
 #' mtcars |> create_baseline(by.var = "gear", detail_level = "extended",type = list(gtsummary::all_dichotomous() ~ "categorical"),theme="nejm")
 #'
 #' create_baseline(default_parsing(mtcars), by.var = "am", add.p = FALSE, add.overall = FALSE, theme = "lancet")
-create_baseline <- function(data, ..., by.var, add.p = FALSE, add.overall = FALSE, theme = c("jama", "lancet", "nejm", "qjecon"), detail_level = c("minimal", "extended")) {
+create_baseline <- function(data, ..., by.var, add.p = FALSE, add.diff=FALSE, add.overall = FALSE, theme = c("jama", "lancet", "nejm", "qjecon"), detail_level = c("minimal", "extended")) {
  theme <- match.arg(theme)

  detail_level <- match.arg(detail_level)
@ -100,6 +100,10 @@ create_baseline <- function(data, ..., by.var, add.p = FALSE, add.overall = FALS
        gtsummary::add_p() |>
        gtsummary::bold_p()
    }
+    if (isTRUE(add.diff)) {
+      out <- out |>
+        gtsummary::add_difference()
+    }
  }

  out
--- a/R/create-column-mod.R
+++ b/R/create-column-mod.R
@ -26,9 +26,9 @@ create_column_ui <- function(id) {
  htmltools::tagList(
    # datamods:::html_dependency_datamods(),
    # html_dependency_FreesearchR(),
-   shiny::tags$head(
-    shiny::tags$link(rel = "stylesheet", type = "text/css", href = "FreesearchR/inst/assets/css/FreesearchR.css")
-  ),
+    shiny::tags$head(
+      shiny::tags$link(rel = "stylesheet", type = "text/css", href = "FreesearchR/inst/assets/css/FreesearchR.css")
+    ),
    fluidRow(
      column(
        width = 6,
@ -184,35 +184,44 @@ create_column_server <- function(id,
 #'
 #' @rdname create-column
 # @importFrom methods getGroupMembers
-list_allowed_operations <- function() {
-  c(
-    "(", "c",
+allowed_operations <- function() {
+  list(
+    "Misc" = c("(", "c",":","~"),
    # getGroupMembers("Arith"),
-    c("+", "-", "*", "^", "%%", "%/%", "/"),
+    "Arithmetics" = c("+", "-", "*", "^", "%%", "%/%", "/"),
    # getGroupMembers("Compare"),
-    c("==", ">", "<", "!=", "<=", ">="),
+    "Compare" = c("==", ">", "<", "!=", "<=", ">="),
    # getGroupMembers("Logic"),
-    c("&", "|"),
+    "Logic" = c("&", "|", "is.na", "ifelse", "any", "all"),
    # getGroupMembers("Math"),
-    c(
+    "Math" = c(
      "abs", "sign", "sqrt", "ceiling", "floor", "trunc", "cummax",
      "cummin", "cumprod", "cumsum", "exp", "expm1", "log", "log10",
      "log2", "log1p", "cos", "cosh", "sin", "sinh", "tan", "tanh",
      "acos", "acosh", "asin", "asinh", "atan", "atanh", "cospi", "sinpi",
-      "tanpi", "gamma", "lgamma", "digamma", "trigamma"
+      "tanpi", "gamma", "lgamma", "digamma", "trigamma", "round", "signif"
    ),
    # getGroupMembers("Math2"),
-    c("round", "signif"),
+    # c("round", "signif"),
    # getGroupMembers("Summary"),
-    c("max", "min", "range", "prod", "sum", "any", "all"),
-    "pmin", "pmax", "mean",
-    "paste", "paste0", "substr", "nchar", "trimws",
-    "gsub", "sub", "grepl", "ifelse", "length",
-    "as.numeric", "as.character", "as.integer", "as.Date", "as.POSIXct",
-    "as.factor", "factor"
+    "Summary" = c(
+      "max", "min", "range", "prod", "sum", "length",
+      "pmin", "pmax", "mean"
+    ),
+    "Text" = c(
+      "paste", "paste0", "substr", "nchar", "trimws",
+      "gsub", "sub", "grepl"
+    ),
+    "Class" = c(
+      "as.numeric", "as.character", "as.integer", "as.Date", "as.POSIXct",
+      "as.factor", "factor"
+    )
  )
 }

+list_allowed_operations <- function(data=allowed_operations()) {
+  Reduce(c,data)
+}


 #' @inheritParams shiny::modalDialog
--- a/R/custom_SelectInput.R
+++ b/R/custom_SelectInput.R
@ -20,8 +20,18 @@
 #' @importFrom shiny selectizeInput
 #' @export
 #'
-columnSelectInput <- function(inputId, label, data, selected = "", ...,
-                              col_subset = NULL, placeholder = "", onInitialize, none_label="No variable selected",maxItems=NULL) {
+columnSelectInput <- function(
+  inputId,
+  label,
+  data,
+  selected = "",
+  ...,
+  col_subset = NULL,
+  placeholder = "",
+  onInitialize,
+  none_label = "No variable selected",
+  maxItems = NULL
+) {
  datar <- if (is.reactive(data)) data else reactive(data)
  col_subsetr <- if (is.reactive(col_subset)) col_subset else reactive(col_subset)

@ -41,8 +51,8 @@ columnSelectInput <- function(inputId, label, data, selected = "", ...,
    )
  }, col = names(datar()))

-  if (!"none" %in% names(datar())){
-    labels <- c("none"=list(sprintf('\n    {\n      \"name\": \"none\",\n      \"label\": \"%s\",\n      \"dataclass\": \"\",\n      \"datatype\": \"\"\n    }',none_label)),labels)
+  if (!"none" %in% names(datar())) {
+    labels <- c("none" = list(sprintf('\n    {\n      \"name\": \"none\",\n      \"label\": \"%s\",\n      \"dataclass\": \"\",\n      \"datatype\": \"\"\n    }', none_label)), labels)
    choices <- setNames(names(labels), labels)
    choices <- choices[match(if (length(col_subsetr()) == 0 || isTRUE(col_subsetr() == "")) names(datar()) else col_subsetr(), choices)]
  } else {
@ -86,7 +96,7 @@ columnSelectInput <- function(inputId, label, data, selected = "", ...,
               '</div>';
        }
      }")),
-      if (!is.null(maxItems)) list(maxItems=maxItems)
+      if (!is.null(maxItems)) list(maxItems = maxItems)
    )
  )
 }
@ -107,31 +117,31 @@ columnSelectInput <- function(inputId, label, data, selected = "", ...,
 #'
 #' @examples
 #' if (shiny::interactive()) {
-#' shinyApp(
-#'   ui = fluidPage(
-#'     shiny::uiOutput("select"),
-#'     tableOutput("data")
-#'   ),
-#'   server = function(input, output) {
-#'     output$select <- shiny::renderUI({
-#'       vectorSelectInput(
-#'         inputId = "variable", label = "Variable:",
-#'         data = c(
-#'           "Cylinders" = "cyl",
-#'           "Transmission" = "am",
-#'           "Gears" = "gear"
+#'   shinyApp(
+#'     ui = fluidPage(
+#'       shiny::uiOutput("select"),
+#'       tableOutput("data")
+#'     ),
+#'     server = function(input, output) {
+#'       output$select <- shiny::renderUI({
+#'         vectorSelectInput(
+#'           inputId = "variable", label = "Variable:",
+#'           data = c(
+#'             "Cylinders" = "cyl",
+#'             "Transmission" = "am",
+#'             "Gears" = "gear"
+#'           )
 #'         )
-#'       )
-#'     })
+#'       })
 #'
-#'     output$data <- renderTable(
-#'       {
-#'         mtcars[, c("mpg", input$variable), drop = FALSE]
-#'       },
-#'       rownames = TRUE
-#'     )
-#'   }
-#' )
+#'       output$data <- renderTable(
+#'         {
+#'           mtcars[, c("mpg", input$variable), drop = FALSE]
+#'         },
+#'         rownames = TRUE
+#'       )
+#'     }
+#'   )
 #' }
 vectorSelectInput <- function(inputId,
                              label,
@ -184,5 +194,3 @@ vectorSelectInput <- function(inputId,
    )
  )
 }
-
-
--- a/R/cut-variable-ext.R
+++ b/R/cut-variable-ext.R
@ -40,7 +40,7 @@ cut_variable_ui <- function(id) {
      column(
        width = 3,
        shiny::conditionalPanel(
-          condition = "input.method != 'top' && input.method != 'bottom'",
+          condition = "input.method != 'top' && input.method != 'bottom' && input.method != 'words' && input.method != 'characters'",
          ns = ns,
          checkboxInput(
            inputId = ns("right"),
@ -94,7 +94,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
        data <- data_r()
        rv$data <- data
        vars_num <- vapply(data, \(.x){
-          is.numeric(.x) || is_datetime(.x) || (is.factor(.x) && length(levels(.x)) > 2)
+          is.numeric(.x) || is_datetime(.x) || (is.factor(.x) && length(levels(.x)) > 2) || is.character(.x)
        }, logical(1))
        vars_num <- names(vars_num)[vars_num]

@ -216,6 +216,12 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
            "top",
            "bottom"
          )
+        } else if ("character" %in% class(data[[variable]])) {
+          choices <- c(
+            choices,
+            "characters",
+            "words"
+          )
        } else {
          choices <- c(
            choices,
@ -294,7 +300,9 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
          list(var = f, brks = levels(f))
        } else if (input$method %in% c(
          "top",
-          "bottom"
+          "bottom",
+          "characters",
+          "words"
        )) {
          # This allows factor simplification to get the top or bottom count
          f <- cut_var(data[[variable]], breaks = input$n_breaks)
@ -374,7 +382,11 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
          }
        )

-        data <- append_column(data, column = new_variable, name = paste0(variable, "_cut"), index = "right")
+        data <- append_column(data,
+                              column = new_variable,
+                              name = unique_names(paste0(variable, "_cut"),
+                                                  existing = names(data)),
+                              index = "right")

        code <- rlang::call2(
          "append_column",
@ -405,7 +417,6 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
          responseName = "count"
        )
        count_data$freq <- paste(signif(count_data$count / nrow(data) * 100, 3), "%")
-        # browser()
        gridTheme <- getOption("datagrid.theme")
        if (length(gridTheme) < 1) {
          datamods:::apply_grid_theme()
@ -472,6 +483,9 @@ plot_histogram <- function(data, column = NULL, bins = 30, breaks = NULL, color
  } else {
    x <- data[[column]]
  }
+  if (is.character(x)){
+    x <- REDCapCAST::as_factor(x)
+  }
  x <- as.numeric(x)
  op <- par(mar = rep(1.5, 4))
  on.exit(par(op))
@ -547,6 +561,18 @@ cut_methods <- function() {
      min = 1,
      max = 50
    ),
+    "characters" = list(
+      descr = i18n$t("Shorten to first letters"),
+      breaks = i18n$t("Letters"),
+      min = 1,
+      max = 20
+    ),
+    "words" = list(
+      descr = i18n$t("Shorten to first words"),
+      breaks = i18n$t("Words"),
+      min = 1,
+      max = 50
+    ),
    "fixed" = list(
      descr = i18n$t("By specified numbers"),
      breaks = i18n$t("Breaks"),
--- a/R/cut_var.R
+++ b/R/cut_var.R
@ -184,21 +184,24 @@ cut_var.factor <- function(x, breaks = NULL, type = c("top", "bottom"), other =
  tbl <- sort(table(x), decreasing = TRUE)

  if (type == "top") {
-    if (length(levels(x)) <= breaks){
+    if (length(levels(x)) <= breaks) {
      return(x)
    }
    lvls <- names(tbl[seq_len(breaks)])
  } else if (type == "bottom") {
    freqs_check <- tbl / NROW(x) * 100 < breaks
-    if (!any(freqs_check)){
+    if (!any(freqs_check)) {
      return(x)
    }
    lvls <- names(tbl)[!freqs_check]
  }

-  if (other %in% lvls) {
-    other <- paste(other, "_freesearchr")
-  }
+  # if (other %in% lvls) {
+  #   other <- paste(other, "_freesearchr")
+  # }
+
+  # Ensure unique new level name
+  other <- unique_names(other, lvls)

  ## Relabel and relevel
  out <- forcats::fct_relabel(
@ -214,6 +217,41 @@ cut_var.factor <- function(x, breaks = NULL, type = c("top", "bottom"), other =
 }


+#' Subset first part of string to factor
+#'
+#' @name cut_var
+#'
+#' @returns factor
+#' @export
+#'
+#' @examples
+#' c("Sunday", "This week is short") |> cut_var(breaks = 3)
+cut_var.character <- function(x, breaks = NULL, type = c("characters", "words"), ...) {
+  args <- list(...)
+
+  if (is.null(breaks)) {
+    return(x)
+  }
+
+  type <- match.arg(type)
+
+  if (type == "characters") {
+    out <- substr(x, start = 1, stop = breaks)
+  } else if (type == "words") {
+    out <- strsplit(x, " ") |>
+      sapply(\(.x){
+        if (length(.x) > breaks) {
+          paste(.x[seq_len(breaks)], collapse = " ")
+        } else {
+          paste(.x, collapse = " ")
+        }
+      })
+  }
+
+  attr(out, which = "brks") <- breaks
+  REDCapCAST::as_factor(out)
+}
+
 #' Test class
 #'
 #' @param data data
--- a/R/data_plots.R
+++ b/R/data_plots.R
@ -709,7 +709,7 @@ create_plot <- function(data, type, pri, sec, ter = NULL, ...) {
  out
 }

-#' Print label, and if missing print variable name
+#' Print label, and if missing print variable name for plots
 #'
 #' @param data vector or data frame
 #' @param var variable name. Optional.
--- a/R/helpers.R
+++ b/R/helpers.R
@ -515,18 +515,82 @@ pipe_string <- function(data, collapse = "|>\n") {
 #' @examples
 #' list(
 #'   as.symbol(paste0("mtcars$", "mpg")),
-#'   rlang::call2(.fn = "select", !!!list(c("cyl", "disp")), .ns = "dplyr"),
+#'   rlang::call2(.fn = "select", !!!list(c("cyl", "di  sp")), .ns = "dplyr"),
 #'   rlang::call2(.fn = "default_parsing", .ns = "FreesearchR")
 #' ) |>
 #'   merge_expression() |>
 #'   expression_string()
 expression_string <- function(data, assign.str = "") {
  exp.str <- if (is.call(data)) deparse(data) else data
-  # browser()
+
  out <- paste0(assign.str, gsub("%>%", "|>\n", paste(gsub('"', "'", paste(exp.str, collapse = "")), collapse = "")))
-  gsub(" |`", "", out)
+  out <- collapse_spaces(out,preserve_newlines = FALSE)
+  gsub("`", "", out)
 }

+#' Substitue spaces/tabs with single space excluding text within quotes
+#'
+#' @description
+#' Written assisted by Claude.ai. It is long and possibly too complicated,
+#' but it works
+#'
+#'
+#' @param x character string
+#' @param preserve_newlines flag to preserve new lines
+#'
+#' @returns character string
+#'
+#' @examples
+#' collapse_spaces(c("cyl", "di sp","s e   d","d  e'dl  e'"))
+collapse_spaces <- function(x, preserve_newlines = TRUE) {
+  # Function to process a single string
+  process_string <- function(text) {
+    # Pattern to match single-quoted strings
+    quote_pattern <- "'[^']*'"
+
+    # Find all quoted strings and their positions
+    quotes <- gregexpr(quote_pattern, text, perl = TRUE)[[1]]
+
+    if (quotes[1] == -1) {
+      # No quoted strings, process entire text
+      if (preserve_newlines) {
+        return(gsub("[ \\t]{1,}", " ", text))
+      } else {
+        return(gsub("\\s{1,}", " ", text))
+      }
+    }
+
+    # Extract quoted strings
+    quote_lengths <- attr(quotes, "match.length")
+    quoted_parts <- substring(text, quotes, quotes + quote_lengths - 1)
+
+    # Create placeholders
+    placeholders <- paste0("__QUOTE_", seq_along(quoted_parts), "__")
+
+    # Replace quoted strings with placeholders
+    result <- text
+    for (i in seq_along(quoted_parts)) {
+      result <- sub(quote_pattern, placeholders[i], result, perl = TRUE)
+    }
+
+    # Collapse spaces in non-quoted parts
+    if (preserve_newlines) {
+      result <- gsub("[ \\t]{2,}", "", result)
+    } else {
+      result <- gsub("\\s{2,}", "", result)
+    }
+
+    # Restore quoted strings
+    for (i in seq_along(quoted_parts)) {
+      result <- sub(placeholders[i], quoted_parts[i], result, fixed = TRUE)
+    }
+
+    return(result)
+  }
+
+  # Apply to each element of vector
+  sapply(x, process_string, USE.NAMES = FALSE)
+}

 #' Very simple function to remove nested lists, like when uploading .rds
 #'
--- a/R/hosted_version.R
+++ b/R/hosted_version.R
@ -1 +1 @@
-hosted_version <- function()'v25.11.1-251109'
+hosted_version <- function()'v25.12.6-251212'
--- a/R/missings-module.R
+++ b/R/missings-module.R
@ -1,18 +1,56 @@
 #' Data correlations evaluation module
 #'
 #' @param id Module id
+#' @param ... additional UI elements to show before the table overview
 #'
 #' @name data-missings
 #' @returns Shiny ui module
 #' @export
-data_missings_ui <- function(id) {
+data_missings_ui <- function(id, ...) {
  ns <- shiny::NS(id)

-  shiny::tagList(
-    gt::gt_output(outputId = ns("missings_table"))
+  list(
+    bslib::layout_sidebar(
+      sidebar = bslib::sidebar(
+        bslib::accordion(
+          id = ns("acc_mis"),
+          open = "acc_chars",
+          multiple = FALSE,
+          bslib::accordion_panel(
+            value = "acc_pan_mis",
+            title = "Settings",
+            icon = bsicons::bs_icon("gear"),
+            shiny::uiOutput(ns("missings_method")),
+            shiny::uiOutput(ns("missings_var")),
+            shiny::helpText(i18n$t("Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random.")),
+            shiny::br(),
+            shiny::actionButton(
+              inputId = ns("act_miss"),
+              label = i18n$t("Evaluate"),
+              width = "100%",
+              icon = shiny::icon("calculator"),
+              disabled = FALSE
+            )
+          ),
+          do.call(
+            bslib::accordion_panel,
+            c(
+              list(
+                title = "Download",
+                icon = bsicons::bs_icon("file-earmark-arrow-down")
+              ),
+              table_download_ui(id = ns("tbl_dwn"), title = NULL)
+            )
+          )
+        )
+      ),
+      ...,
+      gt::gt_output(outputId = ns("missings_table"))
+    )
  )
 }

+## This should really just be rebuild to only contain a function

 #'
 #' @param data data
@ -23,108 +61,216 @@ data_missings_ui <- function(id) {
 #' @export
 data_missings_server <- function(id,
                                 data,
-                                 variable,
-                                 max_level=20,
+                                 max_level = 20,
                                 ...) {
  shiny::moduleServer(
    id = id,
    module = function(input, output, session) {
-      # ns <- session$ns
+      ns <- session$ns

      datar <- if (is.reactive(data)) data else reactive(data)
-      variabler <- if (is.reactive(variable)) variable else reactive(variable)

      rv <- shiny::reactiveValues(
        data = NULL,
        table = NULL
      )

-      rv$data <- shiny::reactive({
-        df_tbl <- datar()
-        by_var <- variabler()
+      ## Notes
+      ##
+      ## Code export is still missing
+      ## Direct table export would be nice

-        tryCatch(
-          {
-            out <- compare_missings(df_tbl,by_var,max_level = max_level)
-          },
-          error = function(err) {
-            showNotification(paste0("Error: ", err), type = "err")
-          }
-        )
+      shiny::observe(
+        output$missings_method <- shiny::renderUI({
+          shiny::req(data())
+          vectorSelectInput(
+            inputId = ns("missings_method"),
+            label = i18n$t("Analysis method for missingness overview"),
+            choices = setNames(
+              c(
+                "predictors",
+                "outcome"
+              ),
+              c(
+                i18n$t("Overview of missings across variables"),
+                i18n$t("Overview of difference in variables by missing status in outcome")
+              )
+            )
+          )
+        })
+      )

-        out
-      })
-
-      output$missings_table <- gt::render_gt({
-        shiny::req(datar)
-        shiny::req(variabler)
-
-        if (is.null(variabler()) || variabler() == "" || !variabler() %in% names(datar())) {
-          tbl <- rv$data()
-          if (anyNA(datar())){
-            title <- i18n$t("No variable chosen for analysis")
+      shiny::observe({
+        output$missings_var <- shiny::renderUI({
+          shiny::req(datar())
+          shiny::req(input$missings_method)
+          # browser()
+          if (input$missings_method == "predictors") {
+            label <- i18n$t("Select a variable for grouped overview")
+            df <- data_type_filter(data(), type = c("categorical", "dichotomous"))
+            col_subset <- c("none", names(df))
          } else {
-          title <- i18n$t("No missing observations")
+            label <- i18n$t("Select outcome variable for overview")
+            df <- datar()[apply(datar(), 2, anyNA)]
+            col_subset <- names(df)
          }
-        } else {
-          tbl <- rv$data()|>
-            gtsummary::bold_p()
-          title <- glue::glue(i18n$t("Missing vs non-missing observations in the variable **'{variabler()}'**"))
-        }
-
-        out <-  tbl |>
-          gtsummary::as_gt() |>
-          gt::tab_header(title = gt::md(title))
-
-        rv$table <- out
-
-        out
+          columnSelectInput(
+            inputId = ns("missings_var"),
+            label = label,
+            data = df,
+            col_subset = col_subset,
+            none_label = i18n$t("No variable")
+          )
+        })
      })

-      return(reactive(rv$table))
+
+      shiny::observeEvent(
+        list(input$act_miss),
+        {
+          shiny::req(datar())
+          shiny::req(input$missings_var)
+          # browser()
+          df_tbl <- datar()
+          by_var <- input$missings_var
+
+          parameters <- list(
+            by_var = by_var,
+            max_level = max_level,
+            type = input$missings_method
+          )
+
+          tryCatch(
+            {
+              shiny::withProgress(message = i18n$t("Calculating. Hold tight for a moment.."), {
+                out <- do.call(
+                  compare_missings,
+                  modifyList(parameters, list(data = df_tbl))
+                )
+              })
+            },
+            error = function(err) {
+              showNotification(paste0("Error: ", err), type = "err")
+            }
+          )
+
+          if (is.null(input$missings_var) || input$missings_var == "" || !input$missings_var %in% names(datar()) || input$missings_var == "none") {
+            # if (is.null(variabler()) || variabler() == "" || !variabler() %in% names(data()) || variabler() == "none") {
+            # tbl <- rv$data()
+            if (anyNA(datar())) {
+              if (input$missings_method == "predictors") {
+                title <- i18n$t("Overview of missing observations")
+              } else {
+                title <- i18n$t("No outcome measure chosen")
+              }
+            } else {
+              title <- i18n$t("No missing observations")
+            }
+          } else {
+            ## Due to reactivity, the table updates too quickly. this mitigates that issue..
+
+
+            if (input$missings_var == "predictors") {
+              title <- glue::glue(i18n$t("Missings across variables by the variable **'{input$missings_var}'**"))
+            } else {
+              title <- glue::glue(i18n$t("Missing vs non-missing observations in the variable **'{input$missings_var}'**"))
+            }
+          }
+
+          attr(out, "tbl_title") <- title
+
+          rv$data <- shiny::reactive(out)
+        }
+      )
+
+      shiny::observeEvent(
+        list(
+          # input$act_miss
+          rv$data
+        ),
+        {
+          output$missings_table <- gt::render_gt({
+            shiny::req(rv$data)
+            # shiny::req(input$missings_var)
+            # browser()
+            if ("p.value" %in% names(rv$data()[["table_body"]])) {
+              tbl <- rv$data() |>
+                gtsummary::bold_p()
+            } else {
+              tbl <- rv$data()
+            }
+
+
+            out <- tbl |>
+              gtsummary::as_gt() |>
+              gt::tab_header(title = gt::md(attr(tbl, "tbl_title")))
+
+            attr(out, "strat_var") <- input$missings_var
+
+            rv$table <- out
+
+            out
+          })
+        }
+      )
+
+
+      table_download_server(
+        id = "tbl_dwn",
+        data = shiny::reactive(rv$table),
+        file_name = "missings_table"
+      )
+
+      return(shiny::reactive(rv$table))
    }
  )
 }


 missing_demo_app <- function() {
-  ui <- shiny::fluidPage(
-    shiny::actionButton(
-      inputId = "modal_missings",
-      label = "Browse data",
-      width = "100%",
-      disabled = FALSE
-    ),
-    shiny::selectInput(
-      inputId = "missings_var",
-      label = "Select variable to stratify analysis", choices = c("cyl", "vs")
-    ),
-    data_missings_ui("data")
+  ui <- do.call(
+    bslib::page,
+    c(
+      list(
+        title = i18n$t("Missings"),
+        icon = bsicons::bs_icon("x-circle")
+      ),
+      data_missings_ui(id = "data"),
+      gt::gt_output("table_p")
+    )
  )
  server <- function(input, output, session) {
    data_demo <- mtcars
    data_demo[sample(1:32, 10), "cyl"] <- NA
    data_demo[sample(1:32, 8), "vs"] <- NA

-    data_missings_server(id = "data", data = data_demo, variable = shiny::reactive(input$missings_var))
+    rv <- shiny::reactiveValues(
+      table = NULL
+    )

-    visual_summary_server(id = "visual", data = data_demo)
+    rv$table <- data_missings_server(id = "data", data = data_demo)

-    observeEvent(input$modal_missings, {
-      tryCatch(
-        {
-          modal_visual_summary(id = "visual")
-        },
-        error = function(err) {
-          showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err")
-        }
-      )
+    output$table_p <- gt::render_gt({
+      rv$table
    })
+
+    # visual_summary_server(id = "visual", data = data_demo)
+
+    # observeEvent(input$modal_missings, {
+    #   tryCatch(
+    #     {
+    #       modal_visual_summary(id = "visual")
+    #     },
+    #     error = function(err) {
+    #       showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err")
+    #     }
+    #   )
+    # })
  }
  shiny::shinyApp(ui, server)
 }

-missing_demo_app()
+# missing_demo_app()

 #' Pairwise comparison of missings across covariables
 #'
@ -134,24 +280,76 @@ missing_demo_app()
 #' @returns gtsummary list object
 #' @export
 #'
-compare_missings <- function(data,by_var,max_level=20){
+compare_missings <- function(
+  data,
+  by_var,
+  max_level = 20,
+  type = c("predictors", "outcome")
+) {
+  type <- match.arg(type)
+
  if (!is.null(by_var) && by_var != "" && by_var %in% names(data)) {
    data <- data |>
      lapply(\(.x){
-        # browser()
-        if (is.factor(.x)){
-          cut_var(.x,breaks=20,type="top")
+        if (is.factor(.x)) {
+          cut_var(.x, breaks = 20, type = "top")
        } else {
          .x
        }
-      }) |> dplyr::bind_cols()
+      }) |>
+      dplyr::bind_cols()

-    data[[by_var]] <- ifelse(is.na(data[[by_var]]), "Missing", "Non-missing")
+    if (type == "predictors") {
+      data <- missings_logic_across(data, exclude = by_var)
+    } else {
+      data[[by_var]] <- ifelse(is.na(data[[by_var]]), "Missing", "Non-missing")
+    }

    out <- gtsummary::tbl_summary(data, by = by_var) |>
      gtsummary::add_p()
  } else {
+    if (type == "predictors") {
+      data <- missings_logic_across(data)
+    }
+
    out <- gtsummary::tbl_summary(data)
  }
+
  out
 }
+
+#' Converting all variables to logicals by missing status
+#'
+#' @param data data
+#' @param exclude character vector of variable names to be excluded
+#'
+#' @returns data frame
+#' @export
+#'
+#' @examples
+#' mtcars |> missings_logic_across("cyl")
+#' ## gtsummary::trial |>
+#' ##   missings_logic_across() |>
+#' ##   gtsummary::tbl_summary()
+missings_logic_across <- function(data, exclude = NULL) {
+  # This function includes a approach way to preserve variable labels
+  names(data) |>
+    lapply(\(.x){
+      # browser()
+      # Saving original labels
+      lab <- REDCapCAST::get_attr(data[[.x]], attr = "label")
+      if (!.x %in% exclude) {
+        out <- is.na(data[[.x]])
+      } else {
+        out <- data[[.x]]
+      }
+      if (!is.na(lab)) {
+        # Restoring original labels, if not NA
+        REDCapCAST::set_attr(data = out, label = lab, attr = "label", overwrite = TRUE)
+      } else {
+        out
+      }
+    }) |>
+    dplyr::bind_cols(.name_repair = "unique_quiet") |>
+    setNames(names(data))
+}
--- a/R/plot-download-module.R
+++ b/R/plot-download-module.R
@ -51,12 +51,10 @@ plot_download_server <- function(id,
  shiny::moduleServer(
    id = id,
    module = function(input, output, session) {
-      # ns <- session$ns
-
-
-
      output$download_plot <- shiny::downloadHandler(
-        filename = paste0(file_name, ".", input$plot_type),
+        filename = function() {
+          paste0(file_name, ".", input$plot_type)
+        },
        content = function(file) {
          shiny::withProgress(message = "Saving the plot. Hold on for a moment..", {
            ggplot2::ggsave(
@ -65,7 +63,8 @@ plot_download_server <- function(id,
              width = input$plot_width,
              height = input$plot_height,
              dpi = 300,
-              units = "mm", scale = 2
+              units = "mm",
+              scale = 2
            )
          })
        }
@ -73,3 +72,57 @@ plot_download_server <- function(id,
    }
  )
 }
+
+
+plot_download_demo_app <- function() {
+
+  ui <- bslib::page_fillable(
+    title = "Plot Download Demo",
+    bslib::layout_sidebar(
+      sidebar = bslib::sidebar(
+        title = "Download Settings",
+        plot_download_ui(id = "plot_dwn")
+      ),
+      bslib::card(
+        bslib::card_header("Sample Plot"),
+        shiny::plotOutput("demo_plot", height = "500px")
+      )
+    )
+  )
+
+  server <- function(input, output, session) {
+
+    # Create a sample ggplot
+    sample_plot <- ggplot2::ggplot(mtcars, ggplot2::aes(x = wt, y = mpg, color = factor(cyl))) +
+      ggplot2::geom_point(size = 3) +
+      ggplot2::geom_smooth(method = "lm", se = TRUE) +
+      ggplot2::labs(
+        title = "Car Weight vs MPG",
+        x = "Weight (1000 lbs)",
+        y = "Miles per Gallon",
+        color = "Cylinders"
+      ) +
+      ggplot2::theme_minimal() +
+      ggplot2::theme(
+        plot.title = ggplot2::element_text(size = 16, face = "bold"),
+        legend.position = "bottom"
+      )
+
+    # Display the plot
+    output$demo_plot <- shiny::renderPlot({
+      sample_plot
+    })
+
+    # Connect to download module
+    plot_download_server(
+      id = "plot_dwn",
+      data = sample_plot,
+      file_name = "mtcars_plot"
+    )
+  }
+
+  shiny::shinyApp(ui, server)
+}
+
+# Run the demo
+# plot_download_demo_app()
--- a/R/syntax_highlight.R
+++ b/R/syntax_highlight.R
@ -11,15 +11,25 @@ prismCodeBlock <- function(code) {

 prismDependencies <- tags$head(
  tags$script(src = "https://cdnjs.cloudflare.com/ajax/libs/prism/1.8.4/prism.min.js"),
-  tags$link(rel = "stylesheet", type = "text/css",
-            href = "https://cdnjs.cloudflare.com/ajax/libs/prism/1.8.4/themes/prism.min.css")
+  tags$link(
+    rel = "stylesheet", type = "text/css",
+    href = "https://cdnjs.cloudflare.com/ajax/libs/prism/1.8.4/themes/prism.min.css"
+  ),
+  tags$script(src = "https://cdnjs.cloudflare.com/ajax/libs/prism/1.8.4/components/prism-r.min.js"),
+  tags$link(
+    rel = "stylesheet",
+    href = "https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/plugins/toolbar/prism-toolbar.min.css"
+  ),
+  tags$script(
+    src = "https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/plugins/toolbar/prism-toolbar.min.js"
+  ),
+  tags$script(
+    src = "https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/plugins/copy-to-clipboard/prism-copy-to-clipboard.min.js"
+  )
 )

-prismRDependency <- tags$head(
-  tags$script(src = "https://cdnjs.cloudflare.com/ajax/libs/prism/1.8.4/components/prism-r.min.js")
-)

-html_code_wrap <- function(string,lang="r"){
+html_code_wrap <- function(string, lang = "r") {
  glue::glue("<pre><code class='language-{lang}'>{string}
  </code></pre>")
 }
--- a/R/sysdata.rda
+++ b/R/sysdata.rda
--- a/R/table-download-module.R
+++ b/R/table-download-module.R
@ -0,0 +1,115 @@
+table_download_ui <- function(id, title = "Table", ...) {
+  ns <- shiny::NS(id)
+  shiny::tagList(
+    shiny::h4(title),
+    shiny::helpText(i18n$t("Choose your favourite output file format for further work, and download, when the analyses are done.")),
+    shiny::br(),
+    shiny::br(),
+    shiny::selectInput(
+      inputId = ns("output_format"),
+      label = "Output format",
+      selected = NULL,
+      choices = list(
+        "MS Word" = "docx",
+        "Compatible (rtf)" = "rtf"
+      )
+    ),
+    shiny::br(),
+    shiny::uiOutput(ns("download_button_container")),
+    # shiny::downloadButton(
+    #   outputId = ns("act_table"),
+    #   label = "Download table",
+    #   icon = shiny::icon("download")
+    # ),
+    shiny::br()
+  )
+}
+
+table_download_server <- function(id, data, file_name = "table", ...) {
+  shiny::moduleServer(
+    id = id,
+    module = function(input, output, session) {
+      ns <- session$ns
+
+      output$download_button_container <- shiny::renderUI({
+        # Check if data exists and is valid
+        if (!is.null(data()) && (inherits(data(), "gt_tbl") || inherits(data(), "gtsummary"))) {
+          shiny::downloadButton(
+            outputId = ns("act_table"),
+            label = i18n$t("Download table"),
+            icon = shiny::icon("download")
+          )
+        } else {
+          # Return NULL to show nothing
+          NULL
+        }
+      })
+
+
+      output$act_table <- shiny::downloadHandler(
+        filename = function() {
+          paste0("report.", input$output_format)
+        },
+        content = function(file) {
+          shiny::req(data())
+          type <- input$output_format
+          table <- data()
+
+          shiny::withProgress(message = i18n$t("Generating the report. Hold on for a moment.."), {
+            tryCatch(
+              {
+                # browser()
+                if (inherits(table, "gtsummary")) {
+                  table <- gtsummary::as_gt(table)
+                }
+                out <- gt::gtsave(
+                  data = table,
+                  filename = file # Save to the file path provided by downloadHandler
+                )
+                # This only works locally and was disabled
+                # if (type == "docx") {
+                #   out |> doconv::docx_update()
+                # } else {
+                #   out
+                # }
+
+                out
+              },
+              error = function(err) {
+                shiny::showNotification(paste0(i18n$t("Error: "), err), type = "error")
+              }
+            )
+          })
+        }
+      )
+    }
+  )
+}
+
+
+# In your UI
+table_download_demo <- function() {
+  ui <- fluidPage(
+    table_download_ui(id = "my_table", title = "Download Results")
+  )
+
+  # In your server
+  server <- function(input, output, session) {
+    # Your data as a reactive
+    my_table_data <- reactive({
+      # This should return a gt or gtsummary table
+      mtcars |>
+        gt::gt() |>
+        gt::tab_header("My Table")
+    })
+
+    # Call the module server - THIS IS CRITICAL
+    table_download_server(
+      id = "my_table", # Must match the UI id
+      data = my_table_data # Pass the reactive (without parentheses)
+    )
+  }
+  shiny::shinyApp(ui, server)
+}
+
+# table_download_demo()
--- a/R/ui_elements.R
+++ b/R/ui_elements.R
@ -400,10 +400,20 @@ ui_elements <- function(selection) {
                        "Yes" = "yes"
                      )
                    ),
-                    shiny::helpText(i18n$t("Option to perform statistical comparisons between strata in baseline table."))
+                    # shiny::helpText(i18n$t("Option to perform statistical comparisons between strata in baseline table.")),
+                    shiny::br(),
+                    shiny::radioButtons(
+                      inputId = "add_diff",
+                      label = i18n$t("Include group differences"),
+                      selected = "no",
+                      inline = TRUE,
+                      choices = list(
+                        "No" = "no",
+                        "Yes" = "yes"
+                      )
+                    )
                  ),
                  shiny::br(),
-                  shiny::br(),
                  shiny::actionButton(
                    inputId = "act_eval",
                    label = i18n$t("Evaluate"),
@ -452,26 +462,15 @@ ui_elements <- function(selection) {
            data_correlations_ui(id = "correlations", height = 600)
          )
        ),
-        bslib::nav_panel(
-          title = i18n$t("Missings"),
-          icon = bsicons::bs_icon("x-circle"),
-          bslib::layout_sidebar(
-            sidebar = bslib::sidebar(
-              bslib::accordion(
-                id = "acc_mis",
-                open = "acc_chars",
-                multiple = FALSE,
-                bslib::accordion_panel(
-                  value = "acc_pan_mis",
-                  title = "Settings",
-                  icon = bsicons::bs_icon("x-circle"),
-                  shiny::uiOutput("missings_var"),
-                  shiny::helpText(i18n$t("To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random."))
-                )
-              )
+        do.call(
+          bslib::nav_panel,
+          c(
+            list(
+              title = i18n$t("Missings"),
+              icon = bsicons::bs_icon("x-circle")
            ),
-            validation_ui("validation_mcar"),
-            data_missings_ui(id = "missingness")
+            data_missings_ui(id = "missingness",
+                             validation_ui("validation_mcar"))
          )
        )
      ),
--- a/R/update-factor-ext.R
+++ b/R/update-factor-ext.R
@ -1,4 +1,3 @@
-
 ## Works, but not implemented
 ##
 ## These edits mainly allows for
@ -101,7 +100,6 @@ update_factor_server <- function(id, data_r = reactive(NULL)) {
  moduleServer(
    id,
    function(input, output, session) {
-
      rv <- reactiveValues(data = NULL, data_grid = NULL)

      bindEvent(observe({
@ -207,19 +205,37 @@ update_factor_server <- function(id, data_r = reactive(NULL)) {
        data <- req(data_r())
        variable <- req(input$variable)
        grid <- req(input$grid_data)
-        name_var <- if (isTRUE(input$new_var)) {
-          paste0(variable, "_updated")
-        } else {
-          variable
-        }
-        data[[name_var]] <- factor(
-          as.character(data[[variable]]),
-          levels = grid[["Var1"]]
+
+        parameters <- list(
+          variable = variable,
+          new_variable = isTRUE(input$new_var) | any(grid[["Var1_toset"]] == "New label"),
+          new_levels = as.character(grid[["Var1"]]),
+          new_labels = as.character(grid[["Var1_toset"]]),
+          ignore = "New label"
        )
-        data[[name_var]] <- factor(
-          data[[variable]],
-          labels = ifelse(grid[["Var1_toset"]]=="New label",grid[["Var1"]],grid[["Var1_toset"]])
+
+        data <- tryCatch(
+          {
+            rlang::exec(
+              factor_new_levels_labels,
+              !!!modifyList(parameters,
+                val = list(data = data)
+              )
+            )
+          },
+          error = function(err) {
+            showNotification(paste("We encountered the following error creating the new factor:", err), type = "err")
+          }
        )
+
+        # browser()
+        code <- rlang::call2(
+          "factor_new_levels_labels",
+          !!!parameters,
+          .ns = "FreesearchR"
+        )
+        attr(data, "code") <- code
+
        data
      })

@ -231,6 +247,62 @@ update_factor_server <- function(id, data_r = reactive(NULL)) {
  )
 }

+#' Simple function to apply new levels and/or labels to factor
+#'
+#' @param variable factor variable
+#' @param new_level new levels, same length as original
+#' @param new_label new labels, same length as original
+#' @param ignore character string to ignore in new labels
+#'
+#' @returns factor
+#' @export
+#'
+#' @examples
+#' data_n <- mtcars
+#' data_n$cyl <- factor(data_n$cyl)
+#' factor_new_levels_labels(data_n, "cyl", new_labels = c("four", "New label", "New label"))
+factor_new_levels_labels <- function(
+    data,
+    variable,
+    new_variable = TRUE,
+    new_levels = NULL,
+    new_labels = NULL,
+    ignore = "New label") {
+  if (!is.factor(data[[variable]])) {
+    return(data)
+  }
+
+  if (is.null(new_levels)) {
+    new_levels <- levels(data[[variable]])
+  }
+
+  if (is.null(new_labels)) {
+    new_labels <- labels(data[[variable]])
+  }
+
+  with_level <- factor(
+    as.character(data[[variable]]),
+    levels = new_levels
+  )
+  with_label <- factor(
+    with_level,
+    labels = ifelse(new_labels == "New label", new_levels, new_labels)
+  )
+
+  # browser()
+
+  if (isTRUE(new_variable)) {
+    append_column(
+      data = data,
+      column = with_label,
+      name = unique_names(new = paste0(variable, "_updated"), existing = names(data))
+    )
+  } else {
+    data[[variable]] <- new_variable
+    data
+  }
+}
+


 #' @inheritParams shiny::modalDialog
@ -289,3 +361,22 @@ winbox_update_factor <- function(id,
  )
 }

+
+#' Make unique variable names
+#'
+#' Helper function to create new variable names that are unique
+#' given a set of existing names (in a data set, for example).
+#' If a variable name already exists, a number will be appended.
+#'
+#' @param new a vector of proposed new variable names
+#' @param existing a vector of existing variable names
+#' @return a vector of unique new variable names
+#' @examples
+#' unique_names(c("var_x", "var_y", "var_x"), c("var_x", "var_z"))
+#'
+#' @export
+unique_names <- function(new, existing = character()) {
+  new_names <- make.unique(c(existing, new), sep = "_")
+
+  new_names[-seq_along(existing)]
+}
--- a/R/update-variables-ext.R
+++ b/R/update-variables-ext.R
@ -688,7 +688,7 @@ convert_to <- function(data,

 #' Get variable(s) to convert
 #'
-#' @param vars Output of [summary_vars()]
+#' @param vars variables, output from summary_vars() function
 #' @param classes_input List of inputs containing new classes
 #'
 #' @return a `data.table`.
--- a/R/validation.R
+++ b/R/validation.R
@ -109,6 +109,9 @@ validation_server <- function(id,
              purrr::list_flatten()
          } else if (length(to_validate) > 0) {
            out <- make_validation_alerts(to_validate)
+          } else {
+            ## Defaulting to an emptu output vector
+            out <- character()
          }
          valid_ui$x <- tagList(out)
        }
@ -332,7 +335,7 @@ validation_lib <- function(name = NULL) {
    "mcar" = function(x, y) {
      ### Placeholder for missingness validation
      list(
-        string = i18n$t("There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}."),
+        string = i18n$t("There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."),
        summary.fun = mcar_validate,
        summary.fun.args = list(
          data = x,
--- a/R/visual_summary.R
+++ b/R/visual_summary.R
@ -6,7 +6,6 @@
 #' @returns Shiny ui module
 #' @export
 #'
-#' @example examples/visual_summary_demo.R
 visual_summary_ui <- function(id) {
  ns <- shiny::NS(id)

@ -100,14 +99,6 @@ modal_visual_summary <- function(id,
 #' @returns An [apexchart()] `htmlwidget` object.
 #' @export
 #'
-#' @examples
-#' data_demo <- mtcars
-#' data_demo[2:4, "cyl"] <- NA
-#' rbind(data_demo, data_demo, data_demo, data_demo) |> missings_apex_plot()
-#' data_demo |> missings_apex_plot()
-#' mtcars |> missings_apex_plot(animation = TRUE)
-#' # dplyr::storms |> missings_apex_plot()
-#' visdat::vis_dat(dplyr::storms)
 missings_apex_plot <- function(data, animation = FALSE, ...) {
  l <- data_summary_gather(data, ...)

@ -158,14 +149,6 @@ missings_apex_plot <- function(data, animation = FALSE, ...) {
 #' @returns ggplot2 object
 #' @export
 #'
-#' @examples
-#' data_demo <- mtcars
-#' data_demo[sample(1:32, 10), "cyl"] <- NA
-#' data_demo[sample(1:32, 8), "vs"] <- NA
-#' visual_summary(data_demo)
-#' visual_summary(data_demo, palette.fun = scales::hue_pal())
-#' visual_summary(dplyr::storms, summary.fun = data_type)
-#' visual_summary(dplyr::storms, summary.fun = data_type, na.label = "Missings", legend.title = "Class")
 visual_summary <- function(data, legend.title = NULL, ylab = "Observations", ...) {
  l <- data_summary_gather(data, ...)

@ -217,7 +200,7 @@ visual_summary <- function(data, legend.title = NULL, ylab = "Observations", ...
 #' @export
 #'
 #' @examples
-#' mtcars |> data_summary_gather()
+#' mtcars |> data_summary_gather() |> names()
 data_summary_gather <- function(data, summary.fun = class, palette.fun = viridisLite::viridis, na.label = "NA", ...) {
  df_plot <- setNames(data, unique_short(names(data))) |>
    purrr::map_df(\(x){
--- a/README.md
+++ b/README.md
@ -76,7 +76,7 @@ Thank you very much to all translators having helped to translate and validate t

 Like any other project, this project was never possible without the great work of others. These are some of the sources and packages I have used:

-   The ***FreesearchR*** app is build with [Shiny](https://shiny.posit.co/) and based on [*R*](https://www.r-project.org/).
+-   The ***FreesearchR*** app is built with [Shiny](https://shiny.posit.co/) and based on [*R*](https://www.r-project.org/).

 -   [gtsummary](https://www.danieldsjoberg.com/gtsummary/): superb and flexible way to create publication-ready analytical and summary tables.

--- a/SESSION.md
+++ b/SESSION.md
@ -1,21 +1,21 @@
 --------------------------------------------------------------------------------
 -------------------------------- R environment ---------------------------------
 --------------------------------------------------------------------------------
-|setting     |value                                      |
-|:-----------|:------------------------------------------|
-|version     |R version 4.4.1 (2024-06-14)               |
-|os          |macOS 15.7.1                               |
-|system      |aarch64, darwin20                          |
-|ui          |RStudio                                    |
-|language    |(EN)                                       |
-|collate     |en_US.UTF-8                                |
-|ctype       |en_US.UTF-8                                |
-|tz          |Europe/Copenhagen                          |
-|date        |2025-11-09                                 |
-|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 |25.11.1.251109                             |
+|setting     |value                                          |
+|:-----------|:----------------------------------------------|
+|version     |R version 4.4.1 (2024-06-14)                   |
+|os          |macOS 26.1                                     |
+|system      |aarch64, darwin20                              |
+|ui          |RStudio                                        |
+|language    |(EN)                                           |
+|collate     |en_US.UTF-8                                    |
+|ctype       |en_US.UTF-8                                    |
+|tz          |Europe/Copenhagen                              |
+|date        |2025-12-12                                     |
+|rstudio     |2025.09.2+418 Cucumberleaf Sunflower (desktop) |
+|pandoc      |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown)     |
+|quarto      |1.7.30 @ /usr/local/bin/quarto                 |
+|FreesearchR |25.12.6.251212                                 |
                                                                                
                                                                                
 --------------------------------------------------------------------------------
@ -26,183 +26,205 @@
 |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        |0.16.1        |2025-07-01 |CRAN (R 4.4.1) |
+|bayestestR        |0.17.0        |2025-08-29 |CRAN (R 4.4.1) |
 |bit               |4.6.0         |2025-03-06 |CRAN (R 4.4.1) |
 |bit64             |4.6.0-1       |2025-01-16 |CRAN (R 4.4.1) |
 |bitops            |1.0-9         |2024-10-03 |CRAN (R 4.4.1) |
-|boot              |1.3-31        |2024-08-28 |RSPM (R 4.4.0) |
+|boot              |1.3-32        |2025-08-29 |CRAN (R 4.4.1) |
 |brio              |1.1.5         |2024-04-24 |CRAN (R 4.4.1) |
-|broom             |1.0.9         |2025-07-28 |CRAN (R 4.4.1) |
-|broom.helpers     |1.21.0        |2025-04-24 |CRAN (R 4.4.1) |
+|broom             |1.0.11        |2025-12-04 |CRAN (R 4.4.3) |
+|broom.helpers     |1.22.0        |2025-09-17 |CRAN (R 4.4.1) |
 |bsicons           |0.1.2         |2023-11-04 |CRAN (R 4.4.0) |
 |bslib             |0.9.0         |2025-01-30 |CRAN (R 4.4.1) |
 |cachem            |1.1.0         |2024-05-16 |CRAN (R 4.4.1) |
 |calendar          |0.2.0         |2024-08-20 |CRAN (R 4.4.1) |
-|cards             |0.6.1         |2025-07-03 |CRAN (R 4.4.1) |
-|cardx             |0.2.5         |2025-07-03 |CRAN (R 4.4.1) |
+|cards             |0.7.1         |2025-12-02 |CRAN (R 4.4.3) |
+|cardx             |0.3.1         |2025-12-04 |CRAN (R 4.4.3) |
 |caTools           |1.18.3        |2024-09-04 |CRAN (R 4.4.1) |
 |cellranger        |1.1.0         |2016-07-27 |CRAN (R 4.4.0) |
-|checkmate         |2.3.2         |2024-07-29 |RSPM (R 4.4.0) |
+|cffr              |1.2.0         |2025-01-25 |CRAN (R 4.4.1) |
+|checkmate         |2.3.3         |2025-08-18 |CRAN (R 4.4.1) |
 |class             |7.3-23        |2025-01-01 |CRAN (R 4.4.1) |
 |classInt          |0.4-11        |2025-01-08 |CRAN (R 4.4.1) |
 |cli               |3.6.5         |2025-04-23 |CRAN (R 4.4.1) |
 |cluster           |2.1.8.1       |2025-03-12 |CRAN (R 4.4.1) |
 |codetools         |0.2-20        |2024-03-31 |CRAN (R 4.4.1) |
-|colorspace        |2.1-1         |2024-07-26 |CRAN (R 4.4.1) |
+|colorspace        |2.1-2         |2025-09-22 |CRAN (R 4.4.1) |
 |commonmark        |2.0.0         |2025-07-07 |CRAN (R 4.4.1) |
 |crayon            |1.5.3         |2024-06-20 |CRAN (R 4.4.1) |
+|curl              |7.0.0         |2025-08-19 |CRAN (R 4.4.1) |
 |data.table        |1.17.8        |2025-07-10 |CRAN (R 4.4.1) |
 |datamods          |1.5.3         |2024-10-02 |CRAN (R 4.4.1) |
-|datawizard        |1.2.0         |2025-07-17 |CRAN (R 4.4.1) |
+|datawizard        |1.3.0         |2025-10-11 |CRAN (R 4.4.1) |
 |DEoptimR          |1.1-4         |2025-07-27 |CRAN (R 4.4.1) |
 |desc              |1.4.3         |2023-12-10 |CRAN (R 4.4.1) |
-|devtools          |2.4.5         |2022-10-11 |CRAN (R 4.4.0) |
+|devtools          |2.4.6         |2025-10-03 |CRAN (R 4.4.1) |
 |DHARMa            |0.4.7         |2024-10-18 |CRAN (R 4.4.1) |
-|digest            |0.6.37        |2024-08-19 |CRAN (R 4.4.1) |
+|digest            |0.6.39        |2025-11-19 |CRAN (R 4.4.3) |
+|dockerfiler       |0.2.5         |2025-05-07 |CRAN (R 4.4.1) |
+|doconv            |0.3.3         |2025-08-18 |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) |
+|DT                |0.34.0        |2025-09-02 |CRAN (R 4.4.1) |
 |e1071             |1.7-16        |2024-09-16 |CRAN (R 4.4.1) |
 |easystats         |0.7.5         |2025-07-11 |CRAN (R 4.4.1) |
 |ellipsis          |0.3.2         |2021-04-29 |CRAN (R 4.4.1) |
-|emmeans           |1.11.2        |2025-07-11 |CRAN (R 4.4.1) |
+|emmeans           |2.0.0         |2025-10-29 |CRAN (R 4.4.1) |
 |esquisse          |2.1.0         |2025-02-21 |CRAN (R 4.4.1) |
 |estimability      |1.5.1         |2024-05-12 |CRAN (R 4.4.1) |
-|eulerr            |7.0.2         |2024-03-28 |CRAN (R 4.4.0) |
-|evaluate          |1.0.4         |2025-06-18 |RSPM (R 4.4.0) |
+|eulerr            |7.0.4         |2025-09-24 |CRAN (R 4.4.1) |
+|evaluate          |1.0.5         |2025-08-27 |CRAN (R 4.4.1) |
 |farver            |2.1.2         |2024-05-13 |CRAN (R 4.4.1) |
 |fastmap           |1.2.0         |2024-05-15 |CRAN (R 4.4.1) |
-|flextable         |0.9.9         |2025-05-31 |CRAN (R 4.4.1) |
+|flextable         |0.9.10        |2025-08-24 |CRAN (R 4.4.1) |
 |fontawesome       |0.5.3         |2024-11-16 |CRAN (R 4.4.1) |
 |fontBitstreamVera |0.1.1         |2017-02-01 |CRAN (R 4.4.1) |
 |fontLiberation    |0.1.0         |2016-10-15 |CRAN (R 4.4.1) |
 |fontquiver        |0.2.1         |2017-02-01 |CRAN (R 4.4.0) |
-|forcats           |1.0.0         |2023-01-29 |RSPM (R 4.4.0) |
+|forcats           |1.0.1         |2025-09-25 |CRAN (R 4.4.1) |
 |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       |25.11.1       |NA         |NA             |
+|FreesearchR       |25.12.6       |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) |
+|gdtools           |0.4.4         |2025-10-06 |CRAN (R 4.4.1) |
 |generics          |0.1.4         |2025-05-09 |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           |0.5.0         |2025-06-18 |CRAN (R 4.4.1) |
-|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           |0.10.0        |2025-07-02 |CRAN (R 4.4.1) |
+|ggplot2           |4.0.1         |2025-11-14 |CRAN (R 4.4.1) |
+|ggridges          |0.5.7         |2025-08-27 |CRAN (R 4.4.1) |
+|ggstats           |0.11.0        |2025-09-15 |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) |
+|gt                |1.1.0         |2025-09-23 |CRAN (R 4.4.1) |
 |gtable            |0.3.6         |2024-10-25 |CRAN (R 4.4.1) |
-|gtsummary         |2.3.0         |2025-07-03 |CRAN (R 4.4.1) |
+|gtsummary         |2.5.0         |2025-12-05 |CRAN (R 4.4.3) |
 |haven             |2.5.5         |2025-05-30 |CRAN (R 4.4.1) |
-|here              |1.0.1         |2020-12-13 |CRAN (R 4.4.1) |
-|Hmisc             |5.2-3         |2025-03-16 |CRAN (R 4.4.1) |
-|hms               |1.1.3         |2023-03-21 |CRAN (R 4.4.0) |
+|here              |1.0.2         |2025-09-15 |CRAN (R 4.4.1) |
+|Hmisc             |5.2-4         |2025-10-05 |CRAN (R 4.4.1) |
+|hms               |1.1.4         |2025-10-17 |CRAN (R 4.4.1) |
 |htmlTable         |2.4.3         |2024-07-21 |CRAN (R 4.4.0) |
-|htmltools         |0.5.8.1       |2024-04-04 |CRAN (R 4.4.1) |
+|htmltools         |0.5.9         |2025-12-04 |CRAN (R 4.4.3) |
 |htmlwidgets       |1.6.4         |2023-12-06 |CRAN (R 4.4.0) |
 |httpuv            |1.6.16        |2025-04-16 |CRAN (R 4.4.1) |
 |IDEAFilter        |0.2.1         |2025-07-29 |CRAN (R 4.4.1) |
-|insight           |1.4.0         |2025-08-18 |CRAN (R 4.4.1) |
+|insight           |1.4.4         |2025-12-06 |CRAN (R 4.4.3) |
 |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           |1.4.1         |2025-06-15 |CRAN (R 4.4.1) |
 |knitr             |1.50          |2025-03-16 |CRAN (R 4.4.1) |
-|later             |1.4.2         |2025-04-08 |RSPM (R 4.4.0) |
+|labeling          |0.4.3         |2023-08-29 |CRAN (R 4.4.1) |
+|later             |1.4.4         |2025-08-27 |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) |
+|litedown          |0.8           |2025-11-02 |CRAN (R 4.4.1) |
+|lme4              |1.1-38        |2025-12-02 |CRAN (R 4.4.3) |
+|locatexec         |0.1.1         |2021-05-19 |CRAN (R 4.4.0) |
 |lubridate         |1.9.4         |2024-12-08 |CRAN (R 4.4.1) |
-|magrittr          |2.0.3         |2022-03-30 |RSPM (R 4.4.0) |
+|magick            |2.9.0         |2025-09-08 |CRAN (R 4.4.1) |
+|magrittr          |2.0.4         |2025-09-12 |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 |RSPM (R 4.4.0) |
+|Matrix            |1.7-4         |2025-08-28 |CRAN (R 4.4.1) |
 |memoise           |2.0.1         |2021-11-26 |CRAN (R 4.4.0) |
+|mgcv              |1.9-4         |2025-11-07 |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) |
 |mvtnorm           |1.3-3         |2025-01-10 |CRAN (R 4.4.1) |
 |NHANES            |2.1.0         |2015-07-02 |CRAN (R 4.4.0) |
 |nlme              |3.1-168       |2025-03-31 |CRAN (R 4.4.1) |
 |nloptr            |2.2.1         |2025-03-17 |CRAN (R 4.4.1) |
 |nnet              |7.3-20        |2025-01-01 |CRAN (R 4.4.1) |
-|officer           |0.6.10        |2025-05-30 |CRAN (R 4.4.1) |
+|officer           |0.7.2         |2025-12-04 |CRAN (R 4.4.3) |
 |opdisDownsampling |1.0.1         |2024-04-15 |CRAN (R 4.4.0) |
-|openssl           |2.3.3         |2025-05-26 |CRAN (R 4.4.1) |
-|openxlsx2         |1.18          |2025-07-29 |CRAN (R 4.4.1) |
-|parameters        |0.27.0        |2025-07-09 |CRAN (R 4.4.1) |
-|patchwork         |1.3.1         |2025-06-21 |RSPM (R 4.4.0) |
+|openssl           |2.3.4         |2025-09-30 |CRAN (R 4.4.1) |
+|openxlsx2         |1.22          |2025-12-07 |CRAN (R 4.4.3) |
+|otel              |0.2.0         |2025-08-29 |CRAN (R 4.4.1) |
+|pak               |0.9.1         |2025-12-01 |CRAN (R 4.4.3) |
+|parameters        |0.28.3        |2025-11-25 |CRAN (R 4.4.3) |
+|patchwork         |1.3.2         |2025-08-25 |CRAN (R 4.4.1) |
 |pbmcapply         |1.5.1         |2022-04-28 |CRAN (R 4.4.1) |
-|performance       |0.15.0        |2025-07-10 |CRAN (R 4.4.1) |
+|pdftools          |3.6.0         |2025-09-10 |CRAN (R 4.4.1) |
+|performance       |0.15.3        |2025-12-01 |CRAN (R 4.4.3) |
 |phosphoricons     |0.2.1         |2024-04-08 |CRAN (R 4.4.0) |
-|pillar            |1.11.0        |2025-07-04 |RSPM (R 4.4.0) |
+|pillar            |1.11.1        |2025-09-17 |CRAN (R 4.4.1) |
 |pkgbuild          |1.4.8         |2025-05-26 |CRAN (R 4.4.1) |
 |pkgconfig         |2.0.3         |2019-09-22 |CRAN (R 4.4.1) |
-|pkgload           |1.4.0         |2024-06-28 |RSPM (R 4.4.0) |
+|pkgload           |1.4.1         |2025-09-23 |CRAN (R 4.4.1) |
 |plyr              |1.8.9         |2023-10-02 |CRAN (R 4.4.1) |
 |polyclip          |1.10-7        |2024-07-23 |CRAN (R 4.4.1) |
-|pracma            |2.4.4         |2023-11-10 |CRAN (R 4.4.1) |
+|pracma            |2.4.6         |2025-10-22 |CRAN (R 4.4.1) |
 |processx          |3.8.6         |2025-02-21 |CRAN (R 4.4.1) |
-|profvis           |0.4.0         |2024-09-20 |CRAN (R 4.4.1) |
-|promises          |1.3.3         |2025-05-29 |CRAN (R 4.4.1) |
+|promises          |1.5.0         |2025-11-01 |CRAN (R 4.4.1) |
 |proxy             |0.4-27        |2022-06-09 |CRAN (R 4.4.1) |
 |ps                |1.9.1         |2025-04-12 |CRAN (R 4.4.1) |
-|purrr             |1.1.0         |2025-07-10 |CRAN (R 4.4.1) |
+|purrr             |1.2.0         |2025-11-04 |CRAN (R 4.4.1) |
+|qpdf              |1.4.1         |2025-07-02 |CRAN (R 4.4.1) |
 |qqconf            |1.3.2         |2023-04-14 |CRAN (R 4.4.0) |
-|qqplotr           |0.0.6         |2023-01-25 |CRAN (R 4.4.0) |
-|quarto            |1.5.0         |2025-07-28 |RSPM (R 4.4.0) |
+|qqplotr           |0.0.7         |2025-09-05 |CRAN (R 4.4.1) |
+|quarto            |1.5.1         |2025-09-04 |CRAN (R 4.4.1) |
+|R.cache           |0.17.0        |2025-05-02 |CRAN (R 4.4.1) |
+|R.methodsS3       |1.8.2         |2022-06-13 |CRAN (R 4.4.1) |
+|R.oo              |1.27.1        |2025-05-02 |CRAN (R 4.4.1) |
+|R.utils           |2.13.0        |2025-02-24 |CRAN (R 4.4.1) |
 |R6                |2.6.1         |2025-02-15 |CRAN (R 4.4.1) |
-|ragg              |1.4.0         |2025-04-10 |RSPM (R 4.4.0) |
+|ragg              |1.5.0         |2025-09-02 |CRAN (R 4.4.1) |
 |rankinPlot        |1.1.0         |2023-01-30 |CRAN (R 4.4.0) |
-|rbibutils         |2.3           |2024-10-04 |CRAN (R 4.4.1) |
+|rappdirs          |0.3.3         |2021-01-31 |CRAN (R 4.4.1) |
+|rbibutils         |2.4           |2025-11-07 |CRAN (R 4.4.1) |
 |RColorBrewer      |1.1-3         |2022-04-03 |CRAN (R 4.4.1) |
 |Rcpp              |1.1.0         |2025-07-02 |CRAN (R 4.4.1) |
-|RcppArmadillo     |14.6.0-1      |2025-07-02 |CRAN (R 4.4.1) |
+|RcppArmadillo     |15.2.2-1      |2025-11-22 |CRAN (R 4.4.3) |
 |Rdpack            |2.6.4         |2025-04-09 |CRAN (R 4.4.1) |
-|reactable         |0.4.4         |2023-03-12 |CRAN (R 4.4.0) |
+|reactable         |0.4.5         |2025-12-01 |CRAN (R 4.4.3) |
 |readODS           |2.3.2         |2025-01-13 |CRAN (R 4.4.1) |
-|readr             |2.1.5         |2024-01-10 |CRAN (R 4.4.0) |
+|readr             |2.1.6         |2025-11-14 |CRAN (R 4.4.3) |
 |readxl            |1.4.5         |2025-03-07 |CRAN (R 4.4.1) |
 |REDCapCAST        |25.3.2        |2025-03-10 |CRAN (R 4.4.1) |
-|REDCapR           |1.5.0         |2025-07-28 |CRAN (R 4.4.1) |
-|reformulas        |0.4.1         |2025-04-30 |CRAN (R 4.4.1) |
+|REDCapR           |1.6.0         |2025-10-08 |CRAN (R 4.4.1) |
+|reformulas        |0.4.2         |2025-10-28 |CRAN (R 4.4.1) |
 |remotes           |2.5.0         |2024-03-17 |CRAN (R 4.4.1) |
-|rempsyc           |0.1.9         |2025-02-01 |CRAN (R 4.4.1) |
+|rempsyc           |0.2.0         |2025-09-15 |CRAN (R 4.4.1) |
 |renv              |1.1.5         |2025-07-24 |CRAN (R 4.4.1) |
-|reshape2          |1.4.4         |2020-04-09 |CRAN (R 4.4.0) |
-|rio               |1.2.3         |2024-09-25 |CRAN (R 4.4.1) |
+|reshape2          |1.4.5         |2025-11-12 |CRAN (R 4.4.1) |
+|rio               |1.2.4         |2025-09-26 |CRAN (R 4.4.1) |
 |rlang             |1.1.6         |2025-04-11 |CRAN (R 4.4.1) |
-|rmarkdown         |2.29          |2024-11-04 |CRAN (R 4.4.1) |
-|robustbase        |0.99-4-1      |2024-09-27 |CRAN (R 4.4.1) |
-|roxygen2          |7.3.2         |2024-06-28 |RSPM (R 4.4.0) |
+|rmarkdown         |2.30          |2025-09-28 |CRAN (R 4.4.1) |
+|robustbase        |0.99-6        |2025-09-04 |CRAN (R 4.4.1) |
+|roxygen2          |7.3.3         |2025-09-03 |CRAN (R 4.4.1) |
 |rpart             |4.1.24        |2025-01-07 |CRAN (R 4.4.1) |
-|rprojroot         |2.1.0         |2025-07-12 |RSPM (R 4.4.0) |
-|rsconnect         |1.5.0         |2025-06-26 |CRAN (R 4.4.1) |
+|rprojroot         |2.1.1         |2025-08-26 |CRAN (R 4.4.1) |
+|rsconnect         |1.7.0         |2025-12-06 |CRAN (R 4.4.3) |
 |rstudioapi        |0.17.1        |2024-10-22 |CRAN (R 4.4.1) |
+|S7                |0.2.1         |2025-11-14 |CRAN (R 4.4.3) |
 |sass              |0.4.10        |2025-04-11 |CRAN (R 4.4.1) |
 |scales            |1.4.0         |2025-04-24 |CRAN (R 4.4.1) |
-|see               |0.11.0        |2025-03-11 |CRAN (R 4.4.1) |
+|see               |0.12.0        |2025-09-14 |CRAN (R 4.4.1) |
 |sessioninfo       |1.2.3         |2025-02-05 |CRAN (R 4.4.1) |
-|shiny             |1.11.1        |2025-07-03 |CRAN (R 4.4.1) |
+|shiny             |1.12.1        |2025-12-09 |CRAN (R 4.4.1) |
 |shiny.i18n        |0.3.0         |2023-01-16 |CRAN (R 4.4.0) |
+|shiny2docker      |0.0.3         |2025-06-28 |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) |
+|smd               |0.8.0         |2025-02-12 |CRAN (R 4.4.1) |
 |stringi           |1.8.7         |2025-03-27 |CRAN (R 4.4.1) |
-|stringr           |1.5.1         |2023-11-14 |RSPM (R 4.4.0) |
+|stringr           |1.6.0         |2025-11-04 |CRAN (R 4.4.1) |
 |stRoke            |25.9.2        |2025-09-30 |CRAN (R 4.4.1) |
-|systemfonts       |1.2.3         |2025-04-30 |CRAN (R 4.4.1) |
-|testthat          |3.2.3         |2025-01-13 |CRAN (R 4.4.1) |
-|textshaping       |1.0.1         |2025-05-01 |RSPM (R 4.4.0) |
-|thematic          |0.1.7         |2025-06-19 |CRAN (R 4.4.1) |
+|styler            |1.11.0        |2025-10-13 |CRAN (R 4.4.1) |
+|systemfonts       |1.3.1         |2025-10-01 |CRAN (R 4.4.1) |
+|testthat          |3.3.1         |2025-11-25 |CRAN (R 4.4.3) |
+|textshaping       |1.0.4         |2025-10-10 |CRAN (R 4.4.1) |
+|thematic          |0.1.8         |2025-09-29 |CRAN (R 4.4.1) |
 |tibble            |3.3.0         |2025-06-08 |CRAN (R 4.4.1) |
 |tidyr             |1.3.1         |2024-01-24 |CRAN (R 4.4.1) |
 |tidyselect        |1.2.1         |2024-03-11 |CRAN (R 4.4.0) |
@ -211,15 +233,18 @@
 |tweenr            |2.0.3         |2024-02-26 |CRAN (R 4.4.0) |
 |twosamples        |2.0.1         |2023-06-23 |CRAN (R 4.4.1) |
 |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 |RSPM (R 4.4.0) |
+|usethis           |3.2.1         |2025-09-06 |CRAN (R 4.4.1) |
 |uuid              |1.2-1         |2024-07-29 |CRAN (R 4.4.1) |
+|V8                |8.0.1         |2025-10-10 |CRAN (R 4.4.1) |
 |vctrs             |0.6.5         |2023-12-01 |CRAN (R 4.4.0) |
-|vroom             |1.6.5         |2023-12-05 |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             |1.6.7         |2025-11-28 |CRAN (R 4.4.3) |
 |withr             |3.0.2         |2024-10-28 |CRAN (R 4.4.1) |
 |writexl           |1.5.4         |2025-04-15 |CRAN (R 4.4.1) |
-|xfun              |0.52          |2025-04-02 |RSPM (R 4.4.0) |
-|xml2              |1.3.8         |2025-03-14 |RSPM (R 4.4.0) |
+|xfun              |0.54          |2025-10-30 |CRAN (R 4.4.1) |
+|xml2              |1.5.1         |2025-12-01 |CRAN (R 4.4.3) |
 |xtable            |1.8-4         |2019-04-21 |CRAN (R 4.4.1) |
-|yaml              |2.3.10        |2024-07-26 |CRAN (R 4.4.1) |
+|yaml              |2.3.11        |2025-11-28 |CRAN (R 4.4.3) |
+|yesno             |0.1.3         |2024-07-26 |CRAN (R 4.4.1) |
 |zip               |2.3.3         |2025-05-13 |CRAN (R 4.4.1) |
--- a/app_docker/Dockerfile
+++ b/app_docker/Dockerfile
@ -1,5 +1,5 @@
 FROM rocker/geospatial:4.4.1
-RUN apt-get update -y && apt-get install -y  cmake make libcurl4-openssl-dev libicu-dev libssl-dev pandoc zlib1g-dev libsecret-1-dev libxml2-dev libx11-dev libcairo2-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libjpeg-dev libpng-dev libtiff-dev libwebp-dev libfftw3-dev && rm -rf /var/lib/apt/lists/*
+RUN apt-get update -y && apt-get install -y  cmake make libcurl4-openssl-dev libicu-dev libssl-dev pandoc zlib1g-dev libsecret-1-dev libxml2-dev libx11-dev libmagick++-dev gsfonts libjpeg-dev libpoppler-cpp-dev libcairo2-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libpng-dev libtiff-dev libwebp-dev libfftw3-dev && rm -rf /var/lib/apt/lists/*
 RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
 RUN echo "options(renv.config.pak.enabled = FALSE, repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site
 RUN R -e 'install.packages("remotes")'
--- a/app_docker/app.R
+++ b/app_docker/app.R
--- a/app_docker/renv.lock
+++ b/app_docker/renv.lock
--- a/app_docker/translations/translation_da.csv
+++ b/app_docker/translations/translation_da.csv
@ -150,10 +150,7 @@
 "Settings","Indstillinger"
 "The following error occured on determining correlations:","Følgende fejl opstod i forbindelse med korrelationsanalysen:"
 "We encountered the following error creating your report:","Følgende fejl opstod, da rapporten blev dannet:"
-"No variable chosen for analysis","Ingen variabel er valgt til analysen"
 "No missing observations","Ingen manglende observationer"
-"Missing vs non-missing observations in the variable **'{variabler()}'**","Manglende vs ikke-manglende observationer i variablen **'{variabler()}'**"
-"There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}.","Der er en betydelig korrelation blandt {n_nonmcar} variabler sammenlignet efter manglende observationer i {outcome}."
 "There is a total of {p_miss} % missing observations.","Der er i alt {p_miss} % manglende observationer."
 "Median:","Median:"
 "Restore original data","Gendan originale data"
@ -246,11 +243,9 @@
 "Data characteristics table","Oversigtstabel"
 "The dataset without text variables","Datasættet uden variabler formateret som tekst"
 "Creating the table. Hold on for a moment..","Opretter tabellen. Vent et øjeblik.."
-"Select variable to stratify analysis","Vælg variabler til at stratificere analysen"
 "Generating the report. Hold on for a moment..","Opretter rapporten. Vent et øjeblik.."
 "We encountered the following error showing missingness:","Under analysen af manglende observationer opstod følgende fejl:"
 "We encountered the following error browsing your data:","I forsøget på at vise en dataoversigt opstod følgende fejl:"
-"To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random.","Vælg svarvariablen, for at få hjælp til at vurdere om manglende observationer manglende tilfældigt eller ej (kun variabler med manglende data kan vælges). Hvis der er statistisk signifikant forskel mellem nogle af de øvrige variabler i forhold til manglende data i den valgte variable kan det være et udtryk for at data ikke mangler tilfældigt."
 "Choose a name for the column to be created or modified, then enter an expression before clicking on the button below to create the variable, or cancel to exit without saving anything.","Vælg et navn til den nye variabel, skriv din formel og tryk så på knappen for at gemme variablen, eller annuler for at lukke uden at gemme."
 "Please fill in web address and API token, then press 'Connect'.","Udfyld serveradresse og API-nøgle, og tryk så 'Fobind'."
 "Other","Other"
@ -295,3 +290,22 @@
 "Level of detail","Level of detail"
 "Minimal","Minimal"
 "Extensive","Extensive"
+"Letters","Letters"
+"Words","Words"
+"Shorten to first letters","Shorten to first letters"
+"Shorten to first words","Shorten to first words"
+"Missings across variables by the variable **'{input$missings_var}'**","Missings across variables by the variable **'{input$missings_var}'**"
+"Missing vs non-missing observations in the variable **'{input$missings_var}'**","Missing vs non-missing observations in the variable **'{input$missings_var}'**"
+"Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random.","Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random."
+"Calculating. Hold tight for a moment..","Calculating. Hold tight for a moment.."
+"Overview of missing observations","Overview of missing observations"
+"Analysis method for missingness overview","Analysis method for missingness overview"
+"Overview of missings across variables","Overview of missings across variables"
+"Overview of difference in variables by missing status in outcome","Overview of difference in variables by missing status in outcome"
+"Select a variable for grouped overview","Select a variable for grouped overview"
+"Select outcome variable for overview","Select outcome variable for overview"
+"No outcome measure chosen","No outcome measure chosen"
+"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"Include group differences","Include group differences"
+"Error:","Error:"
+"Download table","Download table"
--- a/app_docker/translations/translation_de.csv
+++ b/app_docker/translations/translation_de.csv
@ -103,9 +103,7 @@
 "You can choose between these file types:","You can choose between these file types:"
 "You can import {file_extensions_text} files","You can import {file_extensions_text} files"
 "First five rows are shown below:","First five rows are shown below:"
-"No variable chosen for analysis","No variable chosen for analysis"
 "No missing observations","No missing observations"
-"Missing vs non-missing observations in the variable **'{variabler()}'**","Missing vs non-missing observations in the variable **'{variabler()}'**"
 "Grouped by {get_label(data,ter)}","Grouped by {get_label(data,ter)}"
 "Import data from REDCap","Import data from REDCap"
 "REDCap server","REDCap server"
@ -207,7 +205,6 @@
 "Correlation cut-off","Correlation cut-off"
 "Set the cut-off for considered 'highly correlated'.","Set the cut-off for considered 'highly correlated'."
 "Missings","Missings"
-"To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random.","To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random."
 "Visuals","Visuals"
 "Analysis validation","Analysis validation"
 "Report","Report"
@ -230,7 +227,6 @@
 "You removed {p_out} % of observations.","You removed {p_out} % of observations."
 "You removed {p_out} % of variables.","You removed {p_out} % of variables."
 "There is a total of {p_miss} % missing observations.","There is a total of {p_miss} % missing observations."
-"There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}.","There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}."
 "Data includes {n_pairs} pairs of highly correlated variables.","Data includes {n_pairs} pairs of highly correlated variables."
 "Class","Class"
 "Observations","Observations"
@ -267,7 +263,6 @@
 "The dataset without text variables","The dataset without text variables"
 "The data includes {n_col} variables. Please limit to 100.","The data includes {n_col} variables. Please limit to 100."
 "Creating the table. Hold on for a moment..","Creating the table. Hold on for a moment.."
-"Select variable to stratify analysis","Select variable to stratify analysis"
 "Generating the report. Hold on for a moment..","Generating the report. Hold on for a moment.."
 "We encountered the following error creating your report:","We encountered the following error creating your report:"
 "There are more advanced options to modify factor/categorical variables as well as create new factor from an existing variable or new variables with R code. At the bottom you can restore the original data.","There are more advanced options to modify factor/categorical variables as well as create new factor from an existing variable or new variables with R code. At the bottom you can restore the original data."
@ -295,3 +290,22 @@
 "Level of detail","Level of detail"
 "Minimal","Minimal"
 "Extensive","Extensive"
+"Letters","Letters"
+"Words","Words"
+"Shorten to first letters","Shorten to first letters"
+"Shorten to first words","Shorten to first words"
+"Missings across variables by the variable **'{input$missings_var}'**","Missings across variables by the variable **'{input$missings_var}'**"
+"Missing vs non-missing observations in the variable **'{input$missings_var}'**","Missing vs non-missing observations in the variable **'{input$missings_var}'**"
+"Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random.","Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random."
+"Calculating. Hold tight for a moment..","Calculating. Hold tight for a moment.."
+"Overview of missing observations","Overview of missing observations"
+"Analysis method for missingness overview","Analysis method for missingness overview"
+"Overview of missings across variables","Overview of missings across variables"
+"Overview of difference in variables by missing status in outcome","Overview of difference in variables by missing status in outcome"
+"Select a variable for grouped overview","Select a variable for grouped overview"
+"Select outcome variable for overview","Select outcome variable for overview"
+"No outcome measure chosen","No outcome measure chosen"
+"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"Include group differences","Include group differences"
+"Error:","Error:"
+"Download table","Download table"
--- a/app_docker/translations/translation_sv.csv
+++ b/app_docker/translations/translation_sv.csv
@ -103,9 +103,7 @@
 "You can choose between these file types:","You can choose between these file types:"
 "You can import {file_extensions_text} files","You can import {file_extensions_text} files"
 "First five rows are shown below:","First five rows are shown below:"
-"No variable chosen for analysis","No variable chosen for analysis"
 "No missing observations","No missing observations"
-"Missing vs non-missing observations in the variable **'{variabler()}'**","Missing vs non-missing observations in the variable **'{variabler()}'**"
 "Grouped by {get_label(data,ter)}","Grouped by {get_label(data,ter)}"
 "Import data from REDCap","Import data from REDCap"
 "REDCap server","REDCap server"
@ -207,7 +205,6 @@
 "Correlation cut-off","Correlation cut-off"
 "Set the cut-off for considered 'highly correlated'.","Set the cut-off for considered 'highly correlated'."
 "Missings","Missings"
-"To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random.","To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random."
 "Visuals","Visuals"
 "Analysis validation","Analysis validation"
 "Report","Report"
@ -230,7 +227,6 @@
 "You removed {p_out} % of observations.","You removed {p_out} % of observations."
 "You removed {p_out} % of variables.","You removed {p_out} % of variables."
 "There is a total of {p_miss} % missing observations.","There is a total of {p_miss} % missing observations."
-"There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}.","There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}."
 "Data includes {n_pairs} pairs of highly correlated variables.","Data includes {n_pairs} pairs of highly correlated variables."
 "Class","Class"
 "Observations","Observations"
@ -267,7 +263,6 @@
 "The dataset without text variables","The dataset without text variables"
 "The data includes {n_col} variables. Please limit to 100.","The data includes {n_col} variables. Please limit to 100."
 "Creating the table. Hold on for a moment..","Creating the table. Hold on for a moment.."
-"Select variable to stratify analysis","Select variable to stratify analysis"
 "Generating the report. Hold on for a moment..","Generating the report. Hold on for a moment.."
 "We encountered the following error creating your report:","We encountered the following error creating your report:"
 "There are more advanced options to modify factor/categorical variables as well as create new factor from an existing variable or new variables with R code. At the bottom you can restore the original data.","There are more advanced options to modify factor/categorical variables as well as create new factor from an existing variable or new variables with R code. At the bottom you can restore the original data."
@ -295,3 +290,22 @@
 "Level of detail","Level of detail"
 "Minimal","Minimal"
 "Extensive","Extensive"
+"Letters","Letters"
+"Words","Words"
+"Shorten to first letters","Shorten to first letters"
+"Shorten to first words","Shorten to first words"
+"Missings across variables by the variable **'{input$missings_var}'**","Missings across variables by the variable **'{input$missings_var}'**"
+"Missing vs non-missing observations in the variable **'{input$missings_var}'**","Missing vs non-missing observations in the variable **'{input$missings_var}'**"
+"Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random.","Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random."
+"Calculating. Hold tight for a moment..","Calculating. Hold tight for a moment.."
+"Overview of missing observations","Overview of missing observations"
+"Analysis method for missingness overview","Analysis method for missingness overview"
+"Overview of missings across variables","Overview of missings across variables"
+"Overview of difference in variables by missing status in outcome","Overview of difference in variables by missing status in outcome"
+"Select a variable for grouped overview","Select a variable for grouped overview"
+"Select outcome variable for overview","Select outcome variable for overview"
+"No outcome measure chosen","No outcome measure chosen"
+"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"Include group differences","Include group differences"
+"Error:","Error:"
+"Download table","Download table"
--- a/app_docker/translations/translation_sw.csv
+++ b/app_docker/translations/translation_sw.csv
@ -150,10 +150,7 @@
 "Settings","Settings"
 "The following error occured on determining correlations:","The following error occured on determining correlations:"
 "We encountered the following error creating your report:","We encountered the following error creating your report:"
-"No variable chosen for analysis","No variable chosen for analysis"
 "No missing observations","No missing observations"
-"Missing vs non-missing observations in the variable **'{variabler()}'**","Missing vs non-missing observations in the variable **'{variabler()}'**"
-"There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}.","There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}."
 "There is a total of {p_miss} % missing observations.","There is a total of {p_miss} % missing observations."
 "Median:","Median:"
 "Restore original data","Restore original data"
@ -246,11 +243,9 @@
 "Data characteristics table","Data characteristics table"
 "The dataset without text variables","The dataset without text variables"
 "Creating the table. Hold on for a moment..","Creating the table. Hold on for a moment.."
-"Select variable to stratify analysis","Select variable to stratify analysis"
 "Generating the report. Hold on for a moment..","Generating the report. Hold on for a moment.."
 "We encountered the following error showing missingness:","We encountered the following error showing missingness:"
 "We encountered the following error browsing your data:","We encountered the following error browsing your data:"
-"To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random.","To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random."
 "Choose a name for the column to be created or modified, then enter an expression before clicking on the button below to create the variable, or cancel to exit without saving anything.","Choose a name for the column to be created or modified, then enter an expression before clicking on the button below to create the variable, or cancel to exit without saving anything."
 "Other","Other"
 "Hour of the day","Hour of the day"
@ -295,3 +290,22 @@
 "Level of detail","Level of detail"
 "Minimal","Minimal"
 "Extensive","Extensive"
+"Letters","Letters"
+"Words","Words"
+"Shorten to first letters","Shorten to first letters"
+"Shorten to first words","Shorten to first words"
+"Missings across variables by the variable **'{input$missings_var}'**","Missings across variables by the variable **'{input$missings_var}'**"
+"Missing vs non-missing observations in the variable **'{input$missings_var}'**","Missing vs non-missing observations in the variable **'{input$missings_var}'**"
+"Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random.","Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random."
+"Calculating. Hold tight for a moment..","Calculating. Hold tight for a moment.."
+"Overview of missing observations","Overview of missing observations"
+"Analysis method for missingness overview","Analysis method for missingness overview"
+"Overview of missings across variables","Overview of missings across variables"
+"Overview of difference in variables by missing status in outcome","Overview of difference in variables by missing status in outcome"
+"Select a variable for grouped overview","Select a variable for grouped overview"
+"Select outcome variable for overview","Select outcome variable for overview"
+"No outcome measure chosen","No outcome measure chosen"
+"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"Include group differences","Include group differences"
+"Error:","Error:"
+"Download table","Download table"
--- a/app_docker/www/scripts.js
+++ b/app_docker/www/scripts.js
@ -91,3 +91,12 @@ $(document).on('focus', '.smart-dropdown .selectize-control input', function() {
      }
    });

+// window.addEventListener('beforeunload', function (e) {
+//         // Cancel the event
+//         e.preventDefault();
+//         // Chrome requires returnValue to be set
+//         e.returnValue = '';
+//         // Some browsers display this message, others show a generic one
+//         return 'Are you sure you want to leave? Any unsaved changes will be lost.';
+//       });
+
--- a/inst/apps/FreesearchR/app.R
+++ b/inst/apps/FreesearchR/app.R
--- a/inst/apps/FreesearchR/www/scripts.js
+++ b/inst/apps/FreesearchR/www/scripts.js
@ -91,3 +91,12 @@ $(document).on('focus', '.smart-dropdown .selectize-control input', function() {
      }
    });

+// window.addEventListener('beforeunload', function (e) {
+//         // Cancel the event
+//         e.preventDefault();
+//         // Chrome requires returnValue to be set
+//         e.returnValue = '';
+//         // Some browsers display this message, others show a generic one
+//         return 'Are you sure you want to leave? Any unsaved changes will be lost.';
+//       });
+
--- a/inst/assets/js/FreesearchR.js
+++ b/inst/assets/js/FreesearchR.js
@ -91,3 +91,12 @@ $(document).on('focus', '.smart-dropdown .selectize-control input', function() {
      }
    });

+// window.addEventListener('beforeunload', function (e) {
+//         // Cancel the event
+//         e.preventDefault();
+//         // Chrome requires returnValue to be set
+//         e.returnValue = '';
+//         // Some browsers display this message, others show a generic one
+//         return 'Are you sure you want to leave? Any unsaved changes will be lost.';
+//       });
+
--- a/inst/translations/translation_da.csv
+++ b/inst/translations/translation_da.csv
@ -150,10 +150,7 @@
 "Settings","Indstillinger"
 "The following error occured on determining correlations:","Følgende fejl opstod i forbindelse med korrelationsanalysen:"
 "We encountered the following error creating your report:","Følgende fejl opstod, da rapporten blev dannet:"
-"No variable chosen for analysis","Ingen variabel er valgt til analysen"
 "No missing observations","Ingen manglende observationer"
-"Missing vs non-missing observations in the variable **'{variabler()}'**","Manglende vs ikke-manglende observationer i variablen **'{variabler()}'**"
-"There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}.","Der er en betydelig korrelation blandt {n_nonmcar} variabler sammenlignet efter manglende observationer i {outcome}."
 "There is a total of {p_miss} % missing observations.","Der er i alt {p_miss} % manglende observationer."
 "Median:","Median:"
 "Restore original data","Gendan originale data"
@ -246,11 +243,9 @@
 "Data characteristics table","Oversigtstabel"
 "The dataset without text variables","Datasættet uden variabler formateret som tekst"
 "Creating the table. Hold on for a moment..","Opretter tabellen. Vent et øjeblik.."
-"Select variable to stratify analysis","Vælg variabler til at stratificere analysen"
 "Generating the report. Hold on for a moment..","Opretter rapporten. Vent et øjeblik.."
 "We encountered the following error showing missingness:","Under analysen af manglende observationer opstod følgende fejl:"
 "We encountered the following error browsing your data:","I forsøget på at vise en dataoversigt opstod følgende fejl:"
-"To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random.","Vælg svarvariablen, for at få hjælp til at vurdere om manglende observationer manglende tilfældigt eller ej (kun variabler med manglende data kan vælges). Hvis der er statistisk signifikant forskel mellem nogle af de øvrige variabler i forhold til manglende data i den valgte variable kan det være et udtryk for at data ikke mangler tilfældigt."
 "Choose a name for the column to be created or modified, then enter an expression before clicking on the button below to create the variable, or cancel to exit without saving anything.","Vælg et navn til den nye variabel, skriv din formel og tryk så på knappen for at gemme variablen, eller annuler for at lukke uden at gemme."
 "Please fill in web address and API token, then press 'Connect'.","Udfyld serveradresse og API-nøgle, og tryk så 'Fobind'."
 "Other","Other"
@ -295,3 +290,22 @@
 "Level of detail","Level of detail"
 "Minimal","Minimal"
 "Extensive","Extensive"
+"Letters","Letters"
+"Words","Words"
+"Shorten to first letters","Shorten to first letters"
+"Shorten to first words","Shorten to first words"
+"Missings across variables by the variable **'{input$missings_var}'**","Missings across variables by the variable **'{input$missings_var}'**"
+"Missing vs non-missing observations in the variable **'{input$missings_var}'**","Missing vs non-missing observations in the variable **'{input$missings_var}'**"
+"Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random.","Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random."
+"Calculating. Hold tight for a moment..","Calculating. Hold tight for a moment.."
+"Overview of missing observations","Overview of missing observations"
+"Analysis method for missingness overview","Analysis method for missingness overview"
+"Overview of missings across variables","Overview of missings across variables"
+"Overview of difference in variables by missing status in outcome","Overview of difference in variables by missing status in outcome"
+"Select a variable for grouped overview","Select a variable for grouped overview"
+"Select outcome variable for overview","Select outcome variable for overview"
+"No outcome measure chosen","No outcome measure chosen"
+"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"Include group differences","Include group differences"
+"Error:","Error:"
+"Download table","Download table"
--- a/inst/translations/translation_de.csv
+++ b/inst/translations/translation_de.csv
@ -103,9 +103,7 @@
 "You can choose between these file types:","You can choose between these file types:"
 "You can import {file_extensions_text} files","You can import {file_extensions_text} files"
 "First five rows are shown below:","First five rows are shown below:"
-"No variable chosen for analysis","No variable chosen for analysis"
 "No missing observations","No missing observations"
-"Missing vs non-missing observations in the variable **'{variabler()}'**","Missing vs non-missing observations in the variable **'{variabler()}'**"
 "Grouped by {get_label(data,ter)}","Grouped by {get_label(data,ter)}"
 "Import data from REDCap","Import data from REDCap"
 "REDCap server","REDCap server"
@ -207,7 +205,6 @@
 "Correlation cut-off","Correlation cut-off"
 "Set the cut-off for considered 'highly correlated'.","Set the cut-off for considered 'highly correlated'."
 "Missings","Missings"
-"To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random.","To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random."
 "Visuals","Visuals"
 "Analysis validation","Analysis validation"
 "Report","Report"
@ -230,7 +227,6 @@
 "You removed {p_out} % of observations.","You removed {p_out} % of observations."
 "You removed {p_out} % of variables.","You removed {p_out} % of variables."
 "There is a total of {p_miss} % missing observations.","There is a total of {p_miss} % missing observations."
-"There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}.","There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}."
 "Data includes {n_pairs} pairs of highly correlated variables.","Data includes {n_pairs} pairs of highly correlated variables."
 "Class","Class"
 "Observations","Observations"
@ -267,7 +263,6 @@
 "The dataset without text variables","The dataset without text variables"
 "The data includes {n_col} variables. Please limit to 100.","The data includes {n_col} variables. Please limit to 100."
 "Creating the table. Hold on for a moment..","Creating the table. Hold on for a moment.."
-"Select variable to stratify analysis","Select variable to stratify analysis"
 "Generating the report. Hold on for a moment..","Generating the report. Hold on for a moment.."
 "We encountered the following error creating your report:","We encountered the following error creating your report:"
 "There are more advanced options to modify factor/categorical variables as well as create new factor from an existing variable or new variables with R code. At the bottom you can restore the original data.","There are more advanced options to modify factor/categorical variables as well as create new factor from an existing variable or new variables with R code. At the bottom you can restore the original data."
@ -295,3 +290,22 @@
 "Level of detail","Level of detail"
 "Minimal","Minimal"
 "Extensive","Extensive"
+"Letters","Letters"
+"Words","Words"
+"Shorten to first letters","Shorten to first letters"
+"Shorten to first words","Shorten to first words"
+"Missings across variables by the variable **'{input$missings_var}'**","Missings across variables by the variable **'{input$missings_var}'**"
+"Missing vs non-missing observations in the variable **'{input$missings_var}'**","Missing vs non-missing observations in the variable **'{input$missings_var}'**"
+"Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random.","Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random."
+"Calculating. Hold tight for a moment..","Calculating. Hold tight for a moment.."
+"Overview of missing observations","Overview of missing observations"
+"Analysis method for missingness overview","Analysis method for missingness overview"
+"Overview of missings across variables","Overview of missings across variables"
+"Overview of difference in variables by missing status in outcome","Overview of difference in variables by missing status in outcome"
+"Select a variable for grouped overview","Select a variable for grouped overview"
+"Select outcome variable for overview","Select outcome variable for overview"
+"No outcome measure chosen","No outcome measure chosen"
+"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"Include group differences","Include group differences"
+"Error:","Error:"
+"Download table","Download table"
--- a/inst/translations/translation_sv.csv
+++ b/inst/translations/translation_sv.csv
@ -103,9 +103,7 @@
 "You can choose between these file types:","You can choose between these file types:"
 "You can import {file_extensions_text} files","You can import {file_extensions_text} files"
 "First five rows are shown below:","First five rows are shown below:"
-"No variable chosen for analysis","No variable chosen for analysis"
 "No missing observations","No missing observations"
-"Missing vs non-missing observations in the variable **'{variabler()}'**","Missing vs non-missing observations in the variable **'{variabler()}'**"
 "Grouped by {get_label(data,ter)}","Grouped by {get_label(data,ter)}"
 "Import data from REDCap","Import data from REDCap"
 "REDCap server","REDCap server"
@ -207,7 +205,6 @@
 "Correlation cut-off","Correlation cut-off"
 "Set the cut-off for considered 'highly correlated'.","Set the cut-off for considered 'highly correlated'."
 "Missings","Missings"
-"To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random.","To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random."
 "Visuals","Visuals"
 "Analysis validation","Analysis validation"
 "Report","Report"
@ -230,7 +227,6 @@
 "You removed {p_out} % of observations.","You removed {p_out} % of observations."
 "You removed {p_out} % of variables.","You removed {p_out} % of variables."
 "There is a total of {p_miss} % missing observations.","There is a total of {p_miss} % missing observations."
-"There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}.","There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}."
 "Data includes {n_pairs} pairs of highly correlated variables.","Data includes {n_pairs} pairs of highly correlated variables."
 "Class","Class"
 "Observations","Observations"
@ -267,7 +263,6 @@
 "The dataset without text variables","The dataset without text variables"
 "The data includes {n_col} variables. Please limit to 100.","The data includes {n_col} variables. Please limit to 100."
 "Creating the table. Hold on for a moment..","Creating the table. Hold on for a moment.."
-"Select variable to stratify analysis","Select variable to stratify analysis"
 "Generating the report. Hold on for a moment..","Generating the report. Hold on for a moment.."
 "We encountered the following error creating your report:","We encountered the following error creating your report:"
 "There are more advanced options to modify factor/categorical variables as well as create new factor from an existing variable or new variables with R code. At the bottom you can restore the original data.","There are more advanced options to modify factor/categorical variables as well as create new factor from an existing variable or new variables with R code. At the bottom you can restore the original data."
@ -295,3 +290,22 @@
 "Level of detail","Level of detail"
 "Minimal","Minimal"
 "Extensive","Extensive"
+"Letters","Letters"
+"Words","Words"
+"Shorten to first letters","Shorten to first letters"
+"Shorten to first words","Shorten to first words"
+"Missings across variables by the variable **'{input$missings_var}'**","Missings across variables by the variable **'{input$missings_var}'**"
+"Missing vs non-missing observations in the variable **'{input$missings_var}'**","Missing vs non-missing observations in the variable **'{input$missings_var}'**"
+"Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random.","Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random."
+"Calculating. Hold tight for a moment..","Calculating. Hold tight for a moment.."
+"Overview of missing observations","Overview of missing observations"
+"Analysis method for missingness overview","Analysis method for missingness overview"
+"Overview of missings across variables","Overview of missings across variables"
+"Overview of difference in variables by missing status in outcome","Overview of difference in variables by missing status in outcome"
+"Select a variable for grouped overview","Select a variable for grouped overview"
+"Select outcome variable for overview","Select outcome variable for overview"
+"No outcome measure chosen","No outcome measure chosen"
+"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"Include group differences","Include group differences"
+"Error:","Error:"
+"Download table","Download table"
--- a/inst/translations/translation_sw.csv
+++ b/inst/translations/translation_sw.csv
@ -150,10 +150,7 @@
 "Settings","Settings"
 "The following error occured on determining correlations:","The following error occured on determining correlations:"
 "We encountered the following error creating your report:","We encountered the following error creating your report:"
-"No variable chosen for analysis","No variable chosen for analysis"
 "No missing observations","No missing observations"
-"Missing vs non-missing observations in the variable **'{variabler()}'**","Missing vs non-missing observations in the variable **'{variabler()}'**"
-"There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}.","There is a significant correlation between {n_nonmcar} variables and missing observations in the outcome variable {outcome}."
 "There is a total of {p_miss} % missing observations.","There is a total of {p_miss} % missing observations."
 "Median:","Median:"
 "Restore original data","Restore original data"
@ -246,11 +243,9 @@
 "Data characteristics table","Data characteristics table"
 "The dataset without text variables","The dataset without text variables"
 "Creating the table. Hold on for a moment..","Creating the table. Hold on for a moment.."
-"Select variable to stratify analysis","Select variable to stratify analysis"
 "Generating the report. Hold on for a moment..","Generating the report. Hold on for a moment.."
 "We encountered the following error showing missingness:","We encountered the following error showing missingness:"
 "We encountered the following error browsing your data:","We encountered the following error browsing your data:"
-"To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random.","To consider if data is missing by random, choose the outcome/dependent variable (only variables with any missings are available). If there is a significant difference across other variables depending on missing observations, it may not be missing at random."
 "Choose a name for the column to be created or modified, then enter an expression before clicking on the button below to create the variable, or cancel to exit without saving anything.","Choose a name for the column to be created or modified, then enter an expression before clicking on the button below to create the variable, or cancel to exit without saving anything."
 "Other","Other"
 "Hour of the day","Hour of the day"
@ -295,3 +290,22 @@
 "Level of detail","Level of detail"
 "Minimal","Minimal"
 "Extensive","Extensive"
+"Letters","Letters"
+"Words","Words"
+"Shorten to first letters","Shorten to first letters"
+"Shorten to first words","Shorten to first words"
+"Missings across variables by the variable **'{input$missings_var}'**","Missings across variables by the variable **'{input$missings_var}'**"
+"Missing vs non-missing observations in the variable **'{input$missings_var}'**","Missing vs non-missing observations in the variable **'{input$missings_var}'**"
+"Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random.","Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random."
+"Calculating. Hold tight for a moment..","Calculating. Hold tight for a moment.."
+"Overview of missing observations","Overview of missing observations"
+"Analysis method for missingness overview","Analysis method for missingness overview"
+"Overview of missings across variables","Overview of missings across variables"
+"Overview of difference in variables by missing status in outcome","Overview of difference in variables by missing status in outcome"
+"Select a variable for grouped overview","Select a variable for grouped overview"
+"Select outcome variable for overview","Select outcome variable for overview"
+"No outcome measure chosen","No outcome measure chosen"
+"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"Include group differences","Include group differences"
+"Error:","Error:"
+"Download table","Download table"
--- a/man/collapse_spaces.Rd
+++ b/man/collapse_spaces.Rd
@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{collapse_spaces}
+\alias{collapse_spaces}
+\title{Substitue spaces/tabs with single space excluding text within quotes}
+\usage{
+collapse_spaces(x, preserve_newlines = TRUE)
+}
+\arguments{
+\item{x}{character string}
+
+\item{preserve_newlines}{flag to preserve new lines}
+}
+\value{
+character string
+}
+\description{
+Written assisted by Claude.ai. It is long and possibly too complicated,
+but it works
+}
+\examples{
+collapse_spaces(c("cyl", "di sp","s e   d","d  e'dl  e'"))
+}
--- a/man/compare_missings.Rd
+++ b/man/compare_missings.Rd
@ -4,7 +4,12 @@
 \alias{compare_missings}
 \title{Pairwise comparison of missings across covariables}
 \usage{
-compare_missings(data, by_var, max_level = 20)
+compare_missings(
+  data,
+  by_var,
+  max_level = 20,
+  type = c("predictors", "outcome")
+)
 }
 \arguments{
 \item{data}{data frame}
--- a/man/create-column.Rd
+++ b/man/create-column.Rd
@ -4,7 +4,7 @@
 \alias{create-column}
 \alias{create_column_ui}
 \alias{create_column_server}
-\alias{list_allowed_operations}
+\alias{allowed_operations}
 \alias{modal_create_column}
 \alias{winbox_create_column}
 \title{Create new column}
@ -17,7 +17,7 @@ create_column_server(
  allowed_operations = list_allowed_operations()
 )

-list_allowed_operations()
+allowed_operations()

 modal_create_column(
  id,
@ -68,7 +68,7 @@ A \code{\link[shiny:reactive]{shiny::reactive()}} function returning the data.
 This module allow to enter an expression to create a new column in a \code{data.frame}.
 }
 \note{
-User can only use a subset of function: (, c, +, -, *, ^, \%\%, \%/\%, /, ==, >, <, !=, <=, >=, &, |, abs, sign, sqrt, ceiling, floor, trunc, cummax, cummin, cumprod, cumsum, exp, expm1, log, log10, log2, log1p, cos, cosh, sin, sinh, tan, tanh, acos, acosh, asin, asinh, atan, atanh, cospi, sinpi, tanpi, gamma, lgamma, digamma, trigamma, round, signif, max, min, range, prod, sum, any, all, pmin, pmax, mean, paste, paste0, substr, nchar, trimws, gsub, sub, grepl, ifelse, length, as.numeric, as.character, as.integer, as.Date, as.POSIXct, as.factor, factor.
+User can only use a subset of function: (, c, :, ~, +, -, *, ^, \%\%, \%/\%, /, ==, >, <, !=, <=, >=, &, |, is.na, ifelse, any, all, abs, sign, sqrt, ceiling, floor, trunc, cummax, cummin, cumprod, cumsum, exp, expm1, log, log10, log2, log1p, cos, cosh, sin, sinh, tan, tanh, acos, acosh, asin, asinh, atan, atanh, cospi, sinpi, tanpi, gamma, lgamma, digamma, trigamma, round, signif, max, min, range, prod, sum, length, pmin, pmax, mean, paste, paste0, substr, nchar, trimws, gsub, sub, grepl, as.numeric, as.character, as.integer, as.Date, as.POSIXct, as.factor, factor.
 You can add more operations using the \code{allowed_operations} argument, for  example if you want to allow to use package lubridate, you can do:

 \if{html}{\out{<div class="sourceCode r">}}\preformatted{c(list_allowed_operations(), getNamespaceExports("lubridate"))
--- a/man/create_baseline.Rd
+++ b/man/create_baseline.Rd
@ -9,6 +9,7 @@ create_baseline(
  ...,
  by.var,
  add.p = FALSE,
+  add.diff = FALSE,
  add.overall = FALSE,
  theme = c("jama", "lancet", "nejm", "qjecon"),
  detail_level = c("minimal", "extended")
--- a/man/cut_var.Rd
+++ b/man/cut_var.Rd
@ -8,6 +8,7 @@
 \alias{cut_var.POSIXct}
 \alias{cut_var.Date}
 \alias{cut_var.factor}
+\alias{cut_var.character}
 \title{Extended cutting function with fall-back to the native base::cut}
 \usage{
 cut_var(x, ...)
@ -37,6 +38,8 @@ cut_var(x, ...)
 \method{cut_var}{Date}(x, breaks = NULL, start.on.monday = TRUE, ...)

 \method{cut_var}{factor}(x, breaks = NULL, type = c("top", "bottom"), other = "Other", ...)
+
+\method{cut_var}{character}(x, breaks = NULL, type = c("characters", "words"), ...)
 }
 \arguments{
 \item{x}{an object inheriting from class "POSIXct"}
@ -48,12 +51,16 @@ cut_var(x, ...)
 \value{
 factor

+factor
+
 factor
 }
 \description{
 Extended cutting function with fall-back to the native base::cut

 Simplify a factor to only the top or bottom n levels
+
+Subset first part of string to factor
 }
 \examples{
 readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "08:20:20", "21:20:20", "03:02:20")) |> cut_var(2)
@ -80,4 +87,5 @@ mtcars$carb |>
  as.factor() |>
  cut_var(20, "bottom") |>
  table()
+c("Sunday", "This week is short") |> cut_var(breaks = 3)
 }
--- a/man/data-missings.Rd
+++ b/man/data-missings.Rd
@ -6,13 +6,15 @@
 \alias{data_missings_server}
 \title{Data correlations evaluation module}
 \usage{
-data_missings_ui(id)
+data_missings_ui(id, ...)

-data_missings_server(id, data, variable, max_level = 20, ...)
+data_missings_server(id, data, max_level = 20, ...)
 }
 \arguments{
 \item{id}{Module id}

+\item{...}{additional UI elements to show before the table overview}
+
 \item{data}{data}

 \item{output.format}{output format}
--- a/man/data_summary_gather.Rd
+++ b/man/data_summary_gather.Rd
@ -31,5 +31,5 @@ data.frame
 Data summary for printing visual summary
 }
 \examples{
-mtcars |> data_summary_gather()
+mtcars |> data_summary_gather() |> names()
 }
--- a/man/expression_string.Rd
+++ b/man/expression_string.Rd
@ -18,7 +18,7 @@ Deparses expression as string, substitutes native pipe and adds assign
 \examples{
 list(
  as.symbol(paste0("mtcars$", "mpg")),
-  rlang::call2(.fn = "select", !!!list(c("cyl", "disp")), .ns = "dplyr"),
+  rlang::call2(.fn = "select", !!!list(c("cyl", "di  sp")), .ns = "dplyr"),
  rlang::call2(.fn = "default_parsing", .ns = "FreesearchR")
 ) |>
  merge_expression() |>
--- a/man/factor_new_levels_labels.Rd
+++ b/man/factor_new_levels_labels.Rd
@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/update-factor-ext.R
+\name{factor_new_levels_labels}
+\alias{factor_new_levels_labels}
+\title{Simple function to apply new levels and/or labels to factor}
+\usage{
+factor_new_levels_labels(
+  data,
+  variable,
+  new_variable = TRUE,
+  new_levels = NULL,
+  new_labels = NULL,
+  ignore = "New label"
+)
+}
+\arguments{
+\item{variable}{factor variable}
+
+\item{ignore}{character string to ignore in new labels}
+
+\item{new_level}{new levels, same length as original}
+
+\item{new_label}{new labels, same length as original}
+}
+\value{
+factor
+}
+\description{
+Simple function to apply new levels and/or labels to factor
+}
+\examples{
+data_n <- mtcars
+data_n$cyl <- factor(data_n$cyl)
+factor_new_levels_labels(data_n, "cyl", new_labels = c("four", "New label", "New label"))
+}
--- a/man/get_label.Rd
+++ b/man/get_label.Rd
@ -2,7 +2,7 @@
 % Please edit documentation in R/data_plots.R
 \name{get_label}
 \alias{get_label}
-\title{Print label, and if missing print variable name}
+\title{Print label, and if missing print variable name for plots}
 \usage{
 get_label(data, var = NULL)
 }
@ -15,7 +15,7 @@ get_label(data, var = NULL)
 character string
 }
 \description{
-Print label, and if missing print variable name
+Print label, and if missing print variable name for plots
 }
 \examples{
 mtcars |> get_label(var = "mpg")
--- a/man/missings_logic_across.Rd
+++ b/man/missings_logic_across.Rd
@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/missings-module.R
+\name{missings_logic_across}
+\alias{missings_logic_across}
+\title{Converting all variables to logicals by missing status}
+\usage{
+missings_logic_across(data, exclude = NULL)
+}
+\arguments{
+\item{data}{data}
+
+\item{exclude}{character vector of variable names to be excluded}
+}
+\value{
+data frame
+}
+\description{
+Converting all variables to logicals by missing status
+}
+\examples{
+mtcars |> missings_logic_across("cyl")
+## gtsummary::trial |>
+##   missings_logic_across() |>
+##   gtsummary::tbl_summary()
+}
--- a/man/unique_names.Rd
+++ b/man/unique_names.Rd
@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/update-factor-ext.R
+\name{unique_names}
+\alias{unique_names}
+\title{Make unique variable names}
+\usage{
+unique_names(new, existing = character())
+}
+\arguments{
+\item{new}{a vector of proposed new variable names}
+
+\item{existing}{a vector of existing variable names}
+}
+\value{
+a vector of unique new variable names
+}
+\description{
+Helper function to create new variable names that are unique
+given a set of existing names (in a data set, for example).
+If a variable name already exists, a number will be appended.
+}
+\examples{
+unique_names(c("var_x", "var_y", "var_x"), c("var_x", "var_z"))
+
+}
--- a/man/vectorSelectInput.Rd
+++ b/man/vectorSelectInput.Rd
@ -37,30 +37,30 @@ A selectizeInput customized for named vectors
 }
 \examples{
 if (shiny::interactive()) {
-shinyApp(
-  ui = fluidPage(
-    shiny::uiOutput("select"),
-    tableOutput("data")
-  ),
-  server = function(input, output) {
-    output$select <- shiny::renderUI({
-      vectorSelectInput(
-        inputId = "variable", label = "Variable:",
-        data = c(
-          "Cylinders" = "cyl",
-          "Transmission" = "am",
-          "Gears" = "gear"
+  shinyApp(
+    ui = fluidPage(
+      shiny::uiOutput("select"),
+      tableOutput("data")
+    ),
+    server = function(input, output) {
+      output$select <- shiny::renderUI({
+        vectorSelectInput(
+          inputId = "variable", label = "Variable:",
+          data = c(
+            "Cylinders" = "cyl",
+            "Transmission" = "am",
+            "Gears" = "gear"
+          )
        )
-      )
-    })
+      })

-    output$data <- renderTable(
-      {
-        mtcars[, c("mpg", input$variable), drop = FALSE]
-      },
-      rownames = TRUE
-    )
-  }
-)
+      output$data <- renderTable(
+        {
+          mtcars[, c("mpg", input$variable), drop = FALSE]
+        },
+        rownames = TRUE
+      )
+    }
+  )
 }
 }
--- a/man/visual-summary.Rd
+++ b/man/visual-summary.Rd
@ -54,7 +54,7 @@ shiny server

 shiny modal

-An \code{\link[=apexchart]{apexchart()}} \code{htmlwidget} object.
+An \code{\link[apexcharter:apexchart]{apexcharter::apexchart()}} \code{htmlwidget} object.

 ggplot2 object
 }
@ -69,51 +69,3 @@ Plot missings and class with apexcharter. Not in use with FreesearchR.

 Ggplot2 data summary visualisation based on visdat::vis_dat.
 }
-\examples{
-visual_summary_demo_app <- function() {
-  ui <- shiny::fluidPage(
-    shiny::actionButton(
-      inputId = "modal_missings",
-      label = "Visual summary",
-      width = "100\%",
-      disabled = FALSE
-    )
-  )
-  server <- function(input, output, session) {
-    data_demo <- mtcars
-    data_demo[sample(1:32, 10), "cyl"] <- NA
-    data_demo[sample(1:32, 8), "vs"] <- NA
-    data_demo$gear <- factor(data_demo$gear)
-
-    visual_summary_server(id = "data", data = shiny::reactive(data_demo),summary.fun=class)
-
-    observeEvent(input$modal_missings, {
-      tryCatch(
-        {
-          modal_visual_summary(id = "data")
-        },
-        error = function(err) {
-          showNotification(paste0("We encountered the following error browsing your data: ", err), type = "err")
-        }
-      )
-    })
-  }
-  shiny::shinyApp(ui, server)
-}
-
-visual_summary_demo_app()
-data_demo <- mtcars
-data_demo[2:4, "cyl"] <- NA
-rbind(data_demo, data_demo, data_demo, data_demo) |> missings_apex_plot()
-data_demo |> missings_apex_plot()
-mtcars |> missings_apex_plot(animation = TRUE)
-# dplyr::storms |> missings_apex_plot()
-visdat::vis_dat(dplyr::storms)
-data_demo <- mtcars
-data_demo[sample(1:32, 10), "cyl"] <- NA
-data_demo[sample(1:32, 8), "vs"] <- NA
-visual_summary(data_demo)
-visual_summary(data_demo, palette.fun = scales::hue_pal())
-visual_summary(dplyr::storms, summary.fun = data_type)
-visual_summary(dplyr::storms, summary.fun = data_type, na.label = "Missings", legend.title = "Class")
-}
--- a/renv.lock
+++ b/renv.lock
--- a/tests/testthat.R
+++ b/tests/testthat.R
@ -10,4 +10,9 @@ library(testthat)
 library(FreesearchR)
 library(shiny)

+
+i18n <- shiny.i18n::Translator$new(translation_csvs_path = here::here("inst/translations/"))
+i18n$set_translation_language("en")
+
+
 test_check("FreesearchR")
--- a/vignettes/FreesearchR.Rmd
+++ b/vignettes/FreesearchR.Rmd
@ -7,163 +7,6 @@ vignette: >
  %\VignetteEncoding{UTF-8}
 ---

-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE,eval = TRUE)
-library(FreesearchR)
-i18n_path <- system.file("translations", package = "FreesearchR")
-i18n <- shiny.i18n::Translator$new(translation_csvs_path = i18n_path)
-i18n$set_translation_language("en")
-```
+Documentation on getting started using the FreesearchR app can be found in the [FreesearchR project documentations (link)](https://freesearchr.github.io/FreesearchR-knowledge/app/app.html).

-# Getting started with ***FreesearchR***

-Below is a simple walk-trough and basic descriptions on the different features of the ***FreesearchR*** app.
-
-## Launching
-
-The easiest way to get started is to launch [the onlie version of the app (click this link)](https://app.freesearchr.org/). Please be aware not to upload sensitive data in this version as data security can not be guaranteed in this online environment. The app can easily be run from *R* on your own computer by running the code below ([read more on running locally here](https://agdamsbo.github.io/FreesearchR/#run-locally-on-your-own-machine)):
-
-```{r eval = FALSE}
-require("pak")
-pak::pak("agdamsbo/FreesearchR")
-library(FreesearchR)
-FreesearchR::launch_FreesearchR()
-```
-
-As a small note, a standalone Windows app version is on the drawing board as well, but no time frame is currently available.
-
-## Get started
-
-Once in the app, get started by loading your data. You have three options available for importing data: file upload, REDCap server export and local or sample data.
-
-After choosing a data source nad importing data, you can preview the basic data structure and missing observations, set a threshold to filter data by completeness and further manually specify variables to include for analyses.
-
-### File upload
-
-Several data file formats are supported for easy import (csv, txt, xls(x), ods, rds, dta). If importing workbooks (xls(x) or ods), you are prompted to specify sheet(s) to import. If choosing multiple sheets, these are automatically merged by common variable(s), so please make sure that key/ID variables are correctly named identically.
-
-### REDCap server export
-
-Export data directly from a REDCap server. You need to first generate an API-token ([see these instruction](https://confluence.research.cchmc.org/pages/viewpage.action?pageId=50987698)) in REDCap. Make sure you have the necessary rights to do so.
-
-Please don't store the API-key on your device unless encrypted or in a keyring, as this may compromise data safety. Log in to your REDCap server and retrieve the token when needed.
-
-Type the correct web address of your REDCap server.
-
-The module will validate the information and you can click "Connect".
-
-This will unfold options to preview your data dictionary (the main database metadata), choose fields/variables to download as well as filtering options.
-
-### Local or sample data
-
-When opening the online hosted app, you can load some sample data to try out the app. When running the app locally from *R* on your own computer, you will find all data frames loaded in your environment here. This extends the possible uses of this app to allow for quick and easy data insights and code generation.
-
-## Prepare
-
-This is the panel to prepare data for evaluation and analyses and get a good overview of your data, check data is classed and formatted correctly, perform simple modifications and filter data. 
-
-### Summary
-
-Here, the data variables can be inspected with a simple visualisation and a few key measures. Also, data filtering is available at two levels: 
-
-   - Data type filtering allows to filter by variable [data type](https://agdamsbo.github.io/FreesearchR/articles/data-types.html)
-   
-   - Observations level filtering allow to filter data by variable
-
-### Modify
-
-Re-class, rename, and relabel variables. Subset data, create new variables and reorder factor levels. Also, compare the modified dataset to the original and restore the original data.
-
-## Evaluate
-
-This panel allows for basic data evaluation.
-
-### Characteristics
-
-Create a classical baseline characteristics table with optional data stratification and comparisons.
-
-### Correlation matrix
-
-Visualise variable correlations and get suggestions to exclude highly correlated variables.
-
-## Visuals
-
-There are a number of plotting options to visualise different aspects of the data.
-
-Below are the available plot types listed.
-
-```{r echo = FALSE}
-c("continuous", "dichotomous", "categorical") |> 
-  lapply(\(.x){
-    dplyr::bind_cols(
-      dplyr::tibble("Data type"=.x),
-      supported_plots() |> 
-      lapply(\(.y){
-        if (.x %in% .y$primary.type){
-          .y[c("descr","note")]|> dplyr::bind_cols()
-        }
-})|> 
-  dplyr::bind_rows() |> 
-  setNames(c("Plot type","Description")))
-  }) |> 
-  dplyr::bind_rows() |> 
-  # toastui::datagrid(filters=TRUE,theme="striped") |> 
-  knitr::kable()
-```
-
-Export the plots directly from the sidebar with easily adjusted plot dimensions for your next publication.
-
-Also copy the code to generate the plot in your own R-environment and fine tune all the small details.
-
-## Regression
-
-This section is only intended for very simple explorative analyses and as a proof-of-concept for now. If you are doing complex regression analyses you should probably just write the code yourself.
-
-Below are the available regression types listed.
-
-```{r echo = FALSE}
-c("continuous", "dichotomous", "categorical") |> 
-  lapply(\(.x){
-    dplyr::bind_cols(
-      dplyr::tibble("Data type"=.x),
-      supported_functions()|> 
-      lapply(\(.y){
-        if (.x %in% .y$out.type){
-          .y[c("descr","fun","design")]|> dplyr::bind_cols()
-        }
-})|> 
-  dplyr::bind_rows() |> 
-  setNames(c("Regression model","Function","Study design")))
-  }) |> 
-  dplyr::bind_rows() |> 
-  # toastui::datagrid(filters=TRUE,theme="striped") |> 
-  knitr::kable()
-```
-
-### Table
-
-Generate simple regression models and get the results in a nice table. This will also be included in the exported report.
-
-This will generate a combined table with both univariate regression model results for each included variable and a multivariate model with all variables included for explorative analyses.
-
-### Plots
-
-Plot the coefficients from the regression models in a forest plot. Choose which model(s) to include.
-
-### Model checks
-
-Check model assumptions visually. Supported checks can be chosen.
-
-## Download
-
-### Report
-
-Download a nice report with baseline characteristics and regression model results. Choose between MS Word or LibreOffice format.
-
-### Data
-
-Export the modified dataset in different formats.
-
-### Code
-
-See all the code snippets from the different steps in your data evaluation.
--- a/vignettes/data-types.Rmd
+++ b/vignettes/data-types.Rmd
@ -16,23 +16,4 @@ knitr::opts_chunk$set(
 options(rmarkdown.html_vignette.check_title = FALSE)
 ```

-```{r setup}
-library(FreesearchR)
-i18n_path <- system.file("translations", package = "FreesearchR")
-i18n <- shiny.i18n::Translator$new(translation_csvs_path = i18n_path)
-i18n$set_translation_language("en")
-```
-
-## A clinical data class
-
-Traditionally in *R*, data is identified by classes, like numeric, integer, double, logical, factor etc. These classes can be a little confusing from a clinical or operational standpoint. In the ***FreesearchR*** app, these classes has been simplified and modified to the following data types, that are assigned on a prioritised order like the following:
-
-```{r echo = FALSE}
-data_types() |> purrr::imap(\(.x,.i){
-  dplyr::bind_cols("type"=.i,.x,.name_repair = "unique_quiet")
-  }) |> dplyr::bind_rows() |> 
-  setNames(c("Data type","Description","Data classes included")) |> 
-  knitr::kable()
-```
-
-Categorising data in this way makes sense when making choices on how to evaluate and analyse data. This is used throughout the ***FreesearchR*** app to simplify data handling.
+Documentation on the data types used in FreesearchR can be found in the [FreesearchR project documentations (link)](https://freesearchr.github.io/FreesearchR-knowledge/app/data_types.html).
--- a/vignettes/missingness.Rmd
+++ b/vignettes/missingness.Rmd
@ -15,12 +15,4 @@ knitr::opts_chunk$set(
 options(rmarkdown.html_vignette.check_title = FALSE)
 ```

-```{r setup}
-library(FreesearchR)
-```
-
-## Considering missing observations
-
-### Further reading
-
-The authors behind the [{finalfit}-package](https://finalfit.org/index.html) have shared a very comprehensive article on what to do and think about missing observations in your data. Please [have a look here](https://finalfit.org/articles/missing.html).
+Considerations of data missingness can be found in the [FreesearchR project documentations (link)](https://freesearchr.github.io/FreesearchR-knowledge/intro/missingness.html).
--- a/vignettes/visuals.Rmd
+++ b/vignettes/visuals.Rmd
@ -16,44 +16,4 @@ knitr::opts_chunk$set(
 options(rmarkdown.html_vignette.check_title = FALSE)
 ```

-```{r setup}
-library(FreesearchR)
-i18n_path <- system.file("translations", package = "FreesearchR")
-i18n <- shiny.i18n::Translator$new(translation_csvs_path = i18n_path)
-i18n$set_translation_language("en")
-```
-
-## Basic visualisations
-
-The goal of ***FreesearchR*** is to keep things simple. Visuals can get very complicated. We provide a selection of plots, that helps visualise typical clinical and will be enough for most use cases, and for publishing to most journals.
-
-If you want to go further, have a look at these sites with suggestions and sample code for data plotting:
-
-   [*R* Charts](https://r-charts.com/): Extensive gallery with great plots
-
-   [*R* Graph gallery](https://r-graph-gallery.com/): Another gallery with great graphs
-
-   [graphics principles](https://graphicsprinciples.github.io/): Easy to follow recommendations for clear visuals. 
-
-
-### Available plots
-
-Below are the available plot types listed.
-
-```{r echo = FALSE}
-c("continuous", "dichotomous", "categorical") |> 
-  lapply(\(.x){
-    dplyr::bind_cols(
-      dplyr::tibble("Data type"=.x),
-      supported_plots() |> 
-      lapply(\(.y){
-        if (.x %in% .y$primary.type){
-          .y[c("descr","note")]|> dplyr::bind_cols()
-        }
-})|> 
-  dplyr::bind_rows() |> 
-  setNames(c("Plot type","Description")))
-  }) |> 
-  dplyr::bind_rows() |> 
-  knitr::kable()
-```
+Documentation on visuals used in FreesearchR can be found in the [FreesearchR project documentations (link)](https://freesearchr.github.io/FreesearchR-knowledge/app/visuals.html).
Author	SHA1	Message	Date
Andreas Gammelgaard Damsbo	ed74e0492c	revised table export Some checks failed pkgdown.yaml / pkgdown (push) Has been cancelled Details	2025-12-12 18:09:06 +01:00
Andreas Gammelgaard Damsbo	d9614eb37f	new version	2025-12-12 17:52:27 +01:00
Andreas Gammelgaard Damsbo	30f13c7232	feat: updated operators for creating new variables	2025-12-12 17:52:10 +01:00
Andreas Gammelgaard Damsbo	f4f433ee84	feat: direct table download	2025-12-12 17:51:43 +01:00
Andreas Gammelgaard Damsbo	2a580965e3	feat: added add difference option to overview Some checks are pending pkgdown.yaml / pkgdown (push) Waiting to run Details	2025-12-11 22:48:30 +01:00
Andreas Gammelgaard Damsbo	208590e91f	republish	2025-12-11 17:24:09 +01:00
Andreas Gammelgaard Damsbo	35afbc1dc9	refined missingness evaluation	2025-12-11 17:22:47 +01:00
Andreas Gammelgaard Damsbo	af523edc00	feat: the missingness module was overhauled to include two different analysis methods and a better, standalone module Some checks are pending pkgdown.yaml / pkgdown (push) Waiting to run Details	2025-12-11 09:34:40 +01:00
Andreas Gammelgaard Damsbo	fab5c6cf22	fix: modal ui hanging, rerender Some checks failed pkgdown.yaml / pkgdown (push) Has been cancelled Details	2025-12-03 22:01:28 +01:00
Andreas Gammelgaard Damsbo	f2c1c974e0	feat: new cut methods	2025-12-03 22:01:03 +01:00
Andreas Gammelgaard Damsbo	cc853b2ede	new version coming Some checks failed pkgdown.yaml / pkgdown (push) Has been cancelled Details	2025-12-02 14:02:00 +01:00
Andreas Gammelgaard Damsbo	8c7fafe51c	updated for new version	2025-12-02 13:59:05 +01:00
Andreas Gammelgaard Damsbo	987069dd90	feat: change to custom function for modifying factors	2025-12-02 13:58:37 +01:00
Andreas Gammelgaard Damsbo	d0d4e950d1	fix: better code export handling	2025-12-02 13:57:50 +01:00
Andreas Gammelgaard Damsbo	54dd332cd8	examples removed to enable rendering Some checks failed pkgdown.yaml / pkgdown (push) Has been cancelled Details	2025-11-19 14:07:00 +01:00
Andreas Gammelgaard Damsbo	c2fa49e914	examples updated	2025-11-19 11:22:47 +01:00
Andreas Gammelgaard Damsbo	67e425d510	getting started migrated as well	2025-11-19 10:56:16 +01:00
Andreas Gammelgaard Damsbo	fde5a22526	docs: vignettes migrated see NEWS	2025-11-19 10:37:12 +01:00
Andreas Gammelgaard Damsbo	735ef71425	Merge pull request #2 from Lindisfritjof/patch-1 Some checks failed pkgdown.yaml / pkgdown (push) Has been cancelled Details Update README.md	2025-11-11 20:21:41 +01:00
Øjvind Fritjof Arnfred	8e9901a64e	Update README.md Minor spelling correction	2025-11-11 13:52:01 +01:00