revised table export

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: 25.12.3
+version: 25.12.6
 doi: 10.5281/zenodo.14527429
 identifiers:
 - type: url
@@ -1116,6 +1116,93 @@ references:
     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'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: FreesearchR
 Title: Easy data analysis for clinicians
-Version: 25.12.3
+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")),
@@ -69,7 +69,9 @@ Imports:
     NHANES,
     shiny.i18n,
     stRoke,
-    data.table
+    data.table,
+    viridis,
+    smd
 Suggests: 
     styler,
     devtools,
@@ -129,6 +131,7 @@ Collate:
     'report.R'
     'separate_string.R'
     'syntax_highlight.R'
+    'table-download-module.R'
     'theme.R'
     'translate.R'
     'ui_elements.R'

NAMESPACE

@@ -10,6 +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)
@@ -88,7 +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)

NEWS.md

@@ -1,3 +1,19 @@
+# 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.

R/app_version.R

@@ -1 +1 @@
-app_version <- function()'25.12.3'
+app_version <- function()'25.12.6'

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

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

R/hosted_version.R

@@ -1 +1 @@
-hosted_version <- function()'v25.12.3-251211'
+hosted_version <- function()'v25.12.6-251212'

R/missings-module.R

@@ -19,7 +19,7 @@ data_missings_ui <- function(id, ...) {
           bslib::accordion_panel(
             value = "acc_pan_mis",
             title = "Settings",
-            icon = bsicons::bs_icon("x-circle"),
+            icon = bsicons::bs_icon("gear"),
             shiny::uiOutput(ns("missings_method")),
             shiny::uiOutput(ns("missings_var")),
             shiny::helpText(i18n$t("Evaluate missingness by either comparing missing values across variables (optionally grouped by af categorical or dichotomous variable) or compare variables grouped by the missing status (missing or not) of an outcome variable. If there is a significant difference i the missingness, this may cause a bias in you data and should be considered carefully interpreting the data and analyses as data may not be missing at random.")),
@@ -31,6 +31,16 @@ data_missings_ui <- function(id, ...) {
               icon = shiny::icon("calculator"),
               disabled = FALSE
             )
+          ),
+          do.call(
+            bslib::accordion_panel,
+            c(
+              list(
+                title = "Download",
+                icon = bsicons::bs_icon("file-earmark-arrow-down")
+              ),
+              table_download_ui(id = ns("tbl_dwn"), title = NULL)
+            )
           )
         )
       ),
@@ -75,15 +85,15 @@ data_missings_server <- function(id,
           shiny::req(data())
           vectorSelectInput(
             inputId = ns("missings_method"),
-            label = i18n$t("Select missings analysis to apply"),
+            label = i18n$t("Analysis method for missingness overview"),
             choices = setNames(
               c(
                 "predictors",
                 "outcome"
               ),
               c(
-                i18n$t("Variables"),
-                i18n$t("By outcome")
+                i18n$t("Overview of missings across variables"),
+                i18n$t("Overview of difference in variables by missing status in outcome")
               )
             )
           )
@@ -96,15 +106,19 @@ data_missings_server <- function(id,
           shiny::req(input$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 {
+            label <- i18n$t("Select outcome variable for overview")
             df <- datar()[apply(datar(), 2, anyNA)]
+            col_subset <- names(df)
           }
           columnSelectInput(
             inputId = ns("missings_var"),
-            label = i18n$t("Select variable to stratify analysis"),
+            label = label,
             data = df,
-            col_subset = c("none", names(df)),
+            col_subset = col_subset,
             none_label = i18n$t("No variable")
           )
         })
@@ -129,10 +143,10 @@ data_missings_server <- function(id,
           tryCatch(
             {
               shiny::withProgress(message = i18n$t("Calculating. Hold tight for a moment.."), {
-              out <- do.call(
-                compare_missings,
-                modifyList(parameters, list(data = df_tbl))
-              )
+                out <- do.call(
+                  compare_missings,
+                  modifyList(parameters, list(data = df_tbl))
+                )
               })
             },
             error = function(err) {
@@ -144,7 +158,11 @@ data_missings_server <- function(id,
             # if (is.null(variabler()) || variabler() == "" || !variabler() %in% names(data()) || variabler() == "none") {
             # tbl <- rv$data()
             if (anyNA(datar())) {
-              title <- i18n$t("No variable chosen for analysis")
+              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")
             }
@@ -196,6 +214,13 @@ data_missings_server <- function(id,
         }
       )
 
+
+      table_download_server(
+        id = "tbl_dwn",
+        data = shiny::reactive(rv$table),
+        file_name = "missings_table"
+      )
+
       return(shiny::reactive(rv$table))
     }
   )
@@ -210,7 +235,8 @@ missing_demo_app <- function() {
         title = i18n$t("Missings"),
         icon = bsicons::bs_icon("x-circle")
       ),
-      data_missings_ui(id = "data")
+      data_missings_ui(id = "data"),
+      gt::gt_output("table_p")
     )
   )
   server <- function(input, output, session) {
@@ -218,7 +244,15 @@ missing_demo_app <- function() {
     data_demo[sample(1:32, 10), "cyl"] <- NA
     data_demo[sample(1:32, 8), "vs"] <- NA
 
-    data_missings_server(id = "data", data = data_demo)
+    rv <- shiny::reactiveValues(
+      table = NULL
+    )
+
+    rv$table <- data_missings_server(id = "data", data = data_demo)
+
+    output$table_p <- gt::render_gt({
+      rv$table
+    })
 
     # visual_summary_server(id = "visual", data = data_demo)
 

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()

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()

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"),

R/validation.R

@@ -335,7 +335,7 @@ validation_lib <- function(name = NULL) {
     "mcar" = function(x, y) {
       ### Placeholder for missingness validation
       list(
-        string = i18n$t("There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nnonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."),
+        string = i18n$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,

SESSION.md

@@ -11,11 +11,11 @@
 |collate     |en_US.UTF-8                                    |
 |ctype       |en_US.UTF-8                                    |
 |tz          |Europe/Copenhagen                              |
-|date        |2025-12-11                                     |
+|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 |25.12.3.251211                                 |
+|FreesearchR |25.12.6.251212                                 |
                                                                                 
                                                                                 
 --------------------------------------------------------------------------------
@@ -26,6 +26,8 @@
 |apexcharter       |0.4.4         |2024-09-06 |CRAN (R 4.4.1) |
 |askpass           |1.2.1         |2024-10-04 |CRAN (R 4.4.1) |
 |assertthat        |0.2.1         |2019-03-21 |CRAN (R 4.4.1) |
+|attachment        |0.4.5         |2025-03-14 |CRAN (R 4.4.1) |
+|attempt           |0.3.1         |2020-05-03 |CRAN (R 4.4.1) |
 |backports         |1.5.0         |2024-05-23 |CRAN (R 4.4.1) |
 |base64enc         |0.1-3         |2015-07-28 |CRAN (R 4.4.1) |
 |bayestestR        |0.17.0        |2025-08-29 |CRAN (R 4.4.1) |
@@ -44,6 +46,7 @@
 |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) |
+|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) |
@@ -53,6 +56,7 @@
 |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        |1.3.0         |2025-10-11 |CRAN (R 4.4.1) |
@@ -61,6 +65,8 @@
 |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            |0.6.39        |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                |0.34.0        |2025-09-02 |CRAN (R 4.4.1) |
@@ -83,7 +89,7 @@
 |foreach           |1.5.2         |2022-02-02 |CRAN (R 4.4.0) |
 |foreign           |0.8-90        |2025-03-31 |CRAN (R 4.4.1) |
 |Formula           |1.2-5         |2023-02-24 |CRAN (R 4.4.1) |
-|FreesearchR       |25.12.3       |NA         |NA             |
+|FreesearchR       |25.12.6       |NA         |NA             |
 |fs                |1.6.6         |2025-04-12 |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) |
@@ -111,6 +117,7 @@
 |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) |
@@ -120,12 +127,15 @@
 |lifecycle         |1.0.4         |2023-11-07 |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) |
+|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            |1.7-4         |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) |
 |minqa             |1.2.8         |2024-08-17 |CRAN (R 4.4.1) |
 |mvtnorm           |1.3-3         |2025-01-10 |CRAN (R 4.4.1) |
@@ -138,9 +148,11 @@
 |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) |
+|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            |1.11.1        |2025-09-17 |CRAN (R 4.4.1) |
@@ -155,6 +167,7 @@
 |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             |1.2.0         |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           |0.0.7         |2025-09-05 |CRAN (R 4.4.1) |
 |quarto            |1.5.1         |2025-09-04 |CRAN (R 4.4.1) |
@@ -165,6 +178,7 @@
 |R6                |2.6.1         |2025-02-15 |CRAN (R 4.4.1) |
 |ragg              |1.5.0         |2025-09-02 |CRAN (R 4.4.1) |
 |rankinPlot        |1.1.0         |2023-01-30 |CRAN (R 4.4.0) |
+|rappdirs          |0.3.3         |2021-01-31 |CRAN (R 4.4.1) |
 |rbibutils         |2.4           |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) |
@@ -197,11 +211,12 @@
 |sessioninfo       |1.2.3         |2025-02-05 |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) |
-|sourcetools       |0.1.7-1       |2023-02-01 |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           |1.6.0         |2025-11-04 |CRAN (R 4.4.1) |
 |stRoke            |25.9.2        |2025-09-30 |CRAN (R 4.4.1) |
@@ -219,9 +234,11 @@
 |twosamples        |2.0.1         |2023-06-23 |CRAN (R 4.4.1) |
 |tzdb              |0.5.0         |2025-03-15 |CRAN (R 4.4.1) |
 |usethis           |3.2.1         |2025-09-06 |CRAN (R 4.4.1) |
-|utf8              |1.2.6         |2025-06-08 |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) |
+|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) |
@@ -229,4 +246,5 @@
 |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              |2.3.11        |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) |

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")'

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"
@@ -299,3 +294,18 @@
 "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"

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."
@@ -299,3 +294,18 @@
 "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"

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."
@@ -299,3 +294,18 @@
 "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"

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"
@@ -299,3 +294,18 @@
 "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"

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.';
+//       });
+

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.';
+//       });
+

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.';
+//       });
+

inst/translations/translation_da.csv

@@ -150,7 +150,6 @@
 "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"
 "There is a total of {p_miss} % missing observations.","Der er i alt {p_miss} % manglende observationer."
 "Median:","Median:"
@@ -244,7 +243,6 @@
 "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:"
@@ -296,11 +294,18 @@
 "Words","Words"
 "Shorten to first letters","Shorten to first letters"
 "Shorten to first words","Shorten to first words"
-"Select missings analysis to apply","Select missings analysis to apply"
-"Variables","Variables"
-"By outcome","By outcome"
 "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.."
-"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nnonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nnonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"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"

inst/translations/translation_de.csv

@@ -103,7 +103,6 @@
 "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"
 "Grouped by {get_label(data,ter)}","Grouped by {get_label(data,ter)}"
 "Import data from REDCap","Import data from REDCap"
@@ -264,7 +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."
@@ -296,11 +294,18 @@
 "Words","Words"
 "Shorten to first letters","Shorten to first letters"
 "Shorten to first words","Shorten to first words"
-"Select missings analysis to apply","Select missings analysis to apply"
-"Variables","Variables"
-"By outcome","By outcome"
 "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.."
-"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nnonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nnonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"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"

inst/translations/translation_sv.csv

@@ -103,7 +103,6 @@
 "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"
 "Grouped by {get_label(data,ter)}","Grouped by {get_label(data,ter)}"
 "Import data from REDCap","Import data from REDCap"
@@ -264,7 +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."
@@ -296,11 +294,18 @@
 "Words","Words"
 "Shorten to first letters","Shorten to first letters"
 "Shorten to first words","Shorten to first words"
-"Select missings analysis to apply","Select missings analysis to apply"
-"Variables","Variables"
-"By outcome","By outcome"
 "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.."
-"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nnonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nnonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"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"

inst/translations/translation_sw.csv

@@ -150,7 +150,6 @@
 "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"
 "There is a total of {p_miss} % missing observations.","There is a total of {p_miss} % missing observations."
 "Median:","Median:"
@@ -244,7 +243,6 @@
 "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:"
@@ -296,11 +294,18 @@
 "Words","Words"
 "Shorten to first letters","Shorten to first letters"
 "Shorten to first words","Shorten to first words"
-"Select missings analysis to apply","Select missings analysis to apply"
-"Variables","Variables"
-"By outcome","By outcome"
 "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.."
-"There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nnonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}.","There is a significant difference in data missingness in {n_nonmcar} {ifelse(n_nnonmcar==1,'variable','variables')} grouped by the selected outcome/grouping variable {outcome}."
+"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"

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"))

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")

renv.lock

@@ -2556,6 +2556,39 @@
       "Maintainer": "Folashade Daniel <fdaniel@microsoft.com>",
       "Repository": "CRAN"
     },
+    "doconv": {
+      "Package": "doconv",
+      "Version": "0.3.3",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Document Conversion to 'PDF' or 'PNG'",
+      "Authors@R": "c( person(\"David\", \"Gohel\", role = c(\"aut\", \"cre\"), email = \"david.gohel@ardata.fr\"), person(given = \"ArData\", role = \"cph\"), person(\"David\", \"Hajage\", role = \"ctb\", comment = \"initial powershell code\") )",
+      "Description": "It provides the ability to generate images from documents of different types. Three main features are provided: functions for generating document thumbnails, functions for performing visual tests of documents and a function for updating fields and table of contents of a 'Microsoft Word' or 'RTF' document. In order to work, 'LibreOffice' must be installed on the machine and or 'Microsoft Word'. If the latter is available, it can be used to produce PDF documents or images identical to the originals; otherwise, 'LibreOffice' is used and the rendering can be sometimes different from the original documents.",
+      "License": "MIT + file LICENSE",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "Imports": [
+        "magick",
+        "pdftools",
+        "locatexec",
+        "processx",
+        "tools"
+      ],
+      "Depends": [
+        "R (>= 4.0.0)"
+      ],
+      "Suggests": [
+        "tinytest",
+        "testthat",
+        "webshot2"
+      ],
+      "BugReports": "https://github.com/ardata-fr/doconv/issues",
+      "SystemRequirements": "LibreOffice, Microsoft Word",
+      "NeedsCompilation": "no",
+      "Author": "David Gohel [aut, cre], ArData [cph], David Hajage [ctb] (initial powershell code)",
+      "Maintainer": "David Gohel <david.gohel@ardata.fr>",
+      "Repository": "CRAN"
+    },
     "downlit": {
       "Package": "downlit",
       "Version": "0.4.5",
@@ -5307,6 +5340,26 @@
       "Maintainer": "Achim Zeileis <Achim.Zeileis@R-project.org>",
       "Repository": "CRAN"
     },
+    "locatexec": {
+      "Package": "locatexec",
+      "Version": "0.1.1",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Detection and Localization of Executable Files",
+      "Authors@R": "c( person(\"David\", \"Gohel\", role = c(\"aut\", \"cre\"), email = \"david.gohel@ardata.fr\"), person(given = \"ArData\", role = \"cph\") )",
+      "Description": "A set of functions to locate some programs  available on the user machine. The package provides functions to locate  'Node.js', 'npm', 'LibreOffice', 'Microsoft Word', 'Microsoft PowerPoint',  'Microsoft Excel', 'Python', 'pip', 'Mozilla Firefox' and 'Google Chrome'. User can test the availability of a program with eventually a version  and call it with function system2() or system(). This allows the use of  a single function to retrieve the path to a program regardless of the  operating system and its configuration.",
+      "License": "MIT + file LICENSE",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.1.1",
+      "Imports": [
+        "utils"
+      ],
+      "BugReports": "https://github.com/ardata-fr/locatexec/issues",
+      "NeedsCompilation": "no",
+      "Author": "David Gohel [aut, cre], ArData [cph]",
+      "Maintainer": "David Gohel <david.gohel@ardata.fr>",
+      "Repository": "CRAN"
+    },
     "lubridate": {
       "Package": "lubridate",
       "Version": "1.9.4",
@@ -5353,6 +5406,54 @@
       "Author": "Vitalie Spinu [aut, cre], Garrett Grolemund [aut], Hadley Wickham [aut], Davis Vaughan [ctb], Ian Lyttle [ctb], Imanuel Costigan [ctb], Jason Law [ctb], Doug Mitarotonda [ctb], Joseph Larmarange [ctb], Jonathan Boiser [ctb], Chel Hee Lee [ctb]",
       "Repository": "CRAN"
     },
+    "magick": {
+      "Package": "magick",
+      "Version": "2.9.0",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Advanced Graphics and Image-Processing in R",
+      "Authors@R": "person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\"))",
+      "Description": "Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. Also includes a graphics device for creating drawing onto images using pixel coordinates.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://docs.ropensci.org/magick/ https://ropensci.r-universe.dev/magick",
+      "BugReports": "https://github.com/ropensci/magick/issues",
+      "SystemRequirements": "ImageMagick++: ImageMagick-c++-devel (rpm) or libmagick++-dev (deb)",
+      "VignetteBuilder": "knitr",
+      "Depends": [
+        "R (>= 4.1.0)"
+      ],
+      "Imports": [
+        "Rcpp (>= 0.12.12)",
+        "magrittr",
+        "curl"
+      ],
+      "LinkingTo": [
+        "Rcpp"
+      ],
+      "Suggests": [
+        "av",
+        "spelling",
+        "jsonlite",
+        "methods",
+        "knitr",
+        "rmarkdown",
+        "rsvg",
+        "webp",
+        "pdftools",
+        "ggplot2",
+        "gapminder",
+        "IRdisplay",
+        "tesseract",
+        "gifski"
+      ],
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "Language": "en-US",
+      "NeedsCompilation": "yes",
+      "Author": "Jeroen Ooms [aut, cre] (ORCID: <https://orcid.org/0000-0002-4035-0289>)",
+      "Maintainer": "Jeroen Ooms <jeroenooms@gmail.com>",
+      "Repository": "CRAN"
+    },
     "magrittr": {
       "Package": "magrittr",
       "Version": "2.0.4",
@@ -6221,6 +6322,38 @@
       "NeedsCompilation": "yes",
       "Repository": "CRAN"
     },
+    "pdftools": {
+      "Package": "pdftools",
+      "Version": "3.6.0",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Text Extraction, Rendering and Converting of PDF Documents",
+      "Authors@R": "person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\"))",
+      "Description": "Utilities based on 'libpoppler' <https://poppler.freedesktop.org> for extracting text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further  processing in R.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://ropensci.r-universe.dev/pdftools, https://docs.ropensci.org/pdftools/",
+      "BugReports": "https://github.com/ropensci/pdftools/issues",
+      "SystemRequirements": "Poppler C++ API: libpoppler-cpp-dev (deb) or poppler-cpp-devel (rpm), and poppler-data (rpm/deb) package.",
+      "Encoding": "UTF-8",
+      "Imports": [
+        "Rcpp (>= 0.12.12)",
+        "qpdf"
+      ],
+      "LinkingTo": [
+        "Rcpp"
+      ],
+      "Suggests": [
+        "png",
+        "webp",
+        "tesseract",
+        "testthat"
+      ],
+      "RoxygenNote": "7.3.2",
+      "NeedsCompilation": "yes",
+      "Author": "Jeroen Ooms [aut, cre] (ORCID: <https://orcid.org/0000-0002-4035-0289>)",
+      "Maintainer": "Jeroen Ooms <jeroenooms@gmail.com>",
+      "Repository": "CRAN"
+    },
     "performance": {
       "Package": "performance",
       "Version": "0.15.3",
@@ -6936,6 +7069,36 @@
       "Author": "Matteo Fasiolo [aut, cre], Ben Griffiths [aut], Simon N. Wood [ctb], Margaux Zaffran [ctb], Yannig Goude [ctb], Raphael Nedellec [ctb]",
       "Repository": "CRAN"
     },
+    "qpdf": {
+      "Package": "qpdf",
+      "Version": "1.4.1",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Split, Combine and Compress PDF Files",
+      "Authors@R": "c(person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"),  email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Ben\", \"Raymond\", role = \"ctb\"), person(\"Jay Berkenbilt\", role = \"cph\", comment = \"Author of libqpdf\"))",
+      "Description": "Content-preserving transformations transformations of PDF files such  as split, combine, and compress. This package interfaces directly to the 'qpdf'  C++ library <https://qpdf.sourceforge.io/> and does not require any command  line utilities. Note that 'qpdf' does not read actual content from PDF files:  to extract text and data you need the 'pdftools' package.",
+      "License": "Apache License 2.0",
+      "URL": "https://docs.ropensci.org/qpdf/ https://ropensci.r-universe.dev/qpdf",
+      "BugReports": "https://github.com/ropensci/qpdf/issues",
+      "Encoding": "UTF-8",
+      "Imports": [
+        "Rcpp",
+        "askpass",
+        "curl"
+      ],
+      "LinkingTo": [
+        "Rcpp"
+      ],
+      "RoxygenNote": "7.2.1",
+      "Suggests": [
+        "testthat"
+      ],
+      "SystemRequirements": "libjpeg",
+      "NeedsCompilation": "yes",
+      "Author": "Jeroen Ooms [aut, cre] (ORCID: <https://orcid.org/0000-0002-4035-0289>), Ben Raymond [ctb], Jay Berkenbilt [cph] (Author of libqpdf)",
+      "Maintainer": "Jeroen Ooms <jeroenooms@gmail.com>",
+      "Repository": "CRAN"
+    },
     "qqconf": {
       "Package": "qqconf",
       "Version": "1.3.2",
@@ -8397,6 +8560,39 @@
       "Maintainer": "Dean Attali <daattali@gmail.com>",
       "Repository": "CRAN"
     },
+    "smd": {
+      "Package": "smd",
+      "Version": "0.8.0",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Compute Standardized Mean Differences",
+      "Authors@R": "c(person(\"Bradley\", \"Saul\", role = c(\"aut\", \"cre\"),  email = \"bradleysaul@fastmail.com\"), person(\"Alex\", \"Breskin\", role = c(\"ctb\"),  email = \"alexbreskin@gmail.com\"), person(\"Catie\", \"Wiener\", role = c(\"ctb\"),  email = \"cwiener@live.unc.edu\"), person(\"Matt\", \"Phelan\", role = c(\"ctb\"),  email = \"mpphelan1@gmail.com\"), person(\"Daniel\", \"Sjoberg\", role = c(\"ctb\"), email = \"danield.sjoberg@gmail.com\"), person(\"Nuvan\", \"Rathnayaka\", role = c(\"ctb\"), email = \"nuvanrath@proton.me\"), person(\"Malcolm\", \"Barrett\", role = c(\"ctb\"),  email = \"malcolmbarrett@gmail.com\") )",
+      "Description": "Computes standardized mean differences and confidence intervals for  multiple data types based on Yang, D., & Dalton, J. E. (2012)  <https://support.sas.com/resources/papers/proceedings12/335-2012.pdf>.",
+      "Imports": [
+        "MASS (>= 7.3-50)",
+        "methods (>= 3.5.1)"
+      ],
+      "Suggests": [
+        "testthat",
+        "stddiff",
+        "tableone",
+        "knitr",
+        "dplyr",
+        "purrr",
+        "markdown",
+        "rmarkdown"
+      ],
+      "License": "MIT + file LICENSE",
+      "URL": "https://bsaul.github.io/smd/",
+      "BugReports": "https://github.com/bsaul/smd/issues",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "VignetteBuilder": "knitr",
+      "Repository": "CRAN",
+      "NeedsCompilation": "no",
+      "Author": "Bradley Saul [aut, cre], Alex Breskin [ctb], Catie Wiener [ctb], Matt Phelan [ctb], Daniel Sjoberg [ctb], Nuvan Rathnayaka [ctb], Malcolm Barrett [ctb]",
+      "Maintainer": "Bradley Saul <bradleysaul@fastmail.com>"
+    },
     "sourcetools": {
       "Package": "sourcetools",
       "Version": "0.1.7-1",
@@ -9154,6 +9350,52 @@
       "Maintainer": "Davis Vaughan <davis@posit.co>",
       "Repository": "CRAN"
     },
+    "viridis": {
+      "Package": "viridis",
+      "Version": "0.6.5",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Colorblind-Friendly Color Maps for R",
+      "Date": "2024-01-28",
+      "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )",
+      "Maintainer": "Simon Garnier <garnier@njit.edu>",
+      "Description": "Color maps designed to improve graph readability for readers with  common forms of color blindness and/or color vision deficiency. The color  maps are also perceptually-uniform, both in regular form and also when  converted to black-and-white for printing. This package also contains  'ggplot2' bindings for discrete and continuous color and fill scales. A lean version of the package called 'viridisLite' that does not include the  'ggplot2' bindings can be found at  <https://cran.r-project.org/package=viridisLite>.",
+      "License": "MIT + file LICENSE",
+      "Encoding": "UTF-8",
+      "Depends": [
+        "R (>= 2.10)",
+        "viridisLite (>= 0.4.0)"
+      ],
+      "Imports": [
+        "ggplot2 (>= 1.0.1)",
+        "gridExtra"
+      ],
+      "Suggests": [
+        "hexbin (>= 1.27.0)",
+        "scales",
+        "MASS",
+        "knitr",
+        "dichromat",
+        "colorspace",
+        "httr",
+        "mapproj",
+        "vdiffr",
+        "svglite (>= 1.2.0)",
+        "testthat",
+        "covr",
+        "rmarkdown",
+        "maps",
+        "terra"
+      ],
+      "LazyData": "true",
+      "VignetteBuilder": "knitr",
+      "URL": "https://sjmgarnier.github.io/viridis/, https://github.com/sjmgarnier/viridis/",
+      "BugReports": "https://github.com/sjmgarnier/viridis/issues",
+      "RoxygenNote": "7.3.1",
+      "NeedsCompilation": "no",
+      "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]",
+      "Repository": "CRAN"
+    },
     "viridisLite": {
       "Package": "viridisLite",
       "Version": "0.4.2",