feat: sankey plotting supports logicals and missing values

DESCRIPTION

@@ -141,5 +141,6 @@ Collate:
     'update-variables-ext.R'
     'utils-labels.R'
     'validation.R'
+    'version_check.R'
     'visual_summary.R'
     'wide2long.R'

NEWS.md

@@ -1,6 +1,8 @@
 # FreesearchR 26.3.4
 
+*NEW* Added app version check against latest release on GitHub. Only runs if internet connection present. No other polling.
 
+*NEW* Added a "Missing" level to the sankey plot function and adjusted the label font size.
 
 # FreesearchR 26.3.3
 

R/hosted_version.R

@@ -1 +1 @@
-hosted_version <- function()'v26.3.4-260312'
+hosted_version <- function()'v26.3.4-260323'

R/launch_FreesearchR.R

@@ -8,6 +8,8 @@
 #' @param data_limit_default default data set observations limit
 #' @param data_limit_upper data set observations upper limit
 #' @param data_limit_lower data set observations lower limit
+#' @param check_app_version always attempt to check app version against latest
+#' release on GitHub. Default is FALSE
 #' @param ... passed on to `shiny::runApp()`
 #'
 #' @returns shiny app
@@ -22,12 +24,14 @@ launch_FreesearchR <- function(include_globalenv = TRUE,
                                data_limit_default = 1000,
                                data_limit_upper = 100000,
                                data_limit_lower = 1,
+                               check_app_version = FALSE,
                                ...) {
   Sys.setenv(
     INCLUDE_GLOBALENV = include_globalenv,
     DATA_LIMIT_DEFAULT = data_limit_default,
     DATA_LIMIT_UPPER = data_limit_upper,
-    DATA_LIMIT_LOWER = data_limit_lower
+    DATA_LIMIT_LOWER = data_limit_lower,
+    CHECK_APP_VERSION = check_app_version
   )
 
   appDir <- system.file("apps", "FreesearchR", package = "FreesearchR")

R/plot_sankey.R

@@ -33,15 +33,17 @@ sankey_ready <- function(data, pri, sec, numbers = "count", ...) {
     dplyr::ungroup()
 
   if (numbers == "count") {
-    out <- out |> dplyr::mutate(
+    out <- out |> dplyr::mutate(lx = factor(paste0(
-      lx = factor(paste0(!!dplyr::sym(pri), "\n(n=", gx.sum, ")")),
+      !!dplyr::sym(pri), "\n(n=", gx.sum, ")"
-      ly = factor(paste0(!!dplyr::sym(sec), "\n(n=", gy.sum, ")"))
+    )), ly = factor(paste0(
-    )
+      !!dplyr::sym(sec), "\n(n=", gy.sum, ")"
+    )))
   } else if (numbers == "percentage") {
-    out <- out |> dplyr::mutate(
+    out <- out |> dplyr::mutate(lx = factor(paste0(
-      lx = factor(paste0(!!dplyr::sym(pri), "\n(", round((gx.sum / sum(n)) * 100, 1), "%)")),
+      !!dplyr::sym(pri), "\n(", round((gx.sum / sum(n)) * 100, 1), "%)"
-      ly = factor(paste0(!!dplyr::sym(sec), "\n(", round((gy.sum / sum(n)) * 100, 1), "%)"))
+    )), ly = factor(paste0(
-    )
+      !!dplyr::sym(sec), "\n(", round((gy.sum / sum(n)) * 100, 1), "%)"
+    )))
   }
 
   if (is.factor(data[[pri]])) {
@@ -83,20 +85,39 @@ str_remove_last <- function(data, pattern = "\n") {
 #' mtcars |>
 #'   default_parsing() |>
 #'   plot_sankey("cyl", "gear", "vs", color.group = "pri")
-plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors = NULL,missing.level="Missing") {
+#'
+#'   # stRoke::trial |> plot_sankey("mrs_1", "mrs_6")
+#'   # stRoke::trial |> plot_sankey("active", "male")
+plot_sankey <- function(data,
+                        pri,
+                        sec,
+                        ter = NULL,
+                        color.group = "pri",
+                        colors = NULL,
+                        missing.level = "Missing") {
   if (!is.null(ter)) {
     ds <- split(data, data[ter])
   } else {
     ds <- list(data)
   }
 
-  out <- lapply(ds, \(.ds){
+
-    plot_sankey_single(.ds, pri = pri, sec = sec, color.group = color.group, colors = colors,missing.level=missing.level)
+  out <- lapply(ds, \(.ds) {
+    plot_sankey_single(
+      .ds,
+      pri = pri,
+      sec = sec,
+      color.group = color.group,
+      colors = colors,
+      missing.level = missing.level
+    )
   })
 
   patchwork::wrap_plots(out)
 }
 
+
+
 #' Beautiful sankey plot
 #'
 #' @param color.group set group to colour by. "x" or "y".
@@ -123,41 +144,66 @@ plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors
 #' stRoke::trial |>
 #'   default_parsing() |>
 #'   plot_sankey_single("diabetes", "hypertension")
-plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), colors = NULL,missing.level="Missing", ...) {
+plot_sankey_single <- function(data,
+                               pri,
+                               sec,
+                               color.group = c("pri", "sec"),
+                               colors = NULL,
+                               missing.level = "Missing",
+                               ...) {
   color.group <- match.arg(color.group)
 
-  # browser()
   data_orig <- data
-  data[c(pri, sec)] <- data[c(pri, sec)] |>
+
-    dplyr::mutate(
+  data[c(pri, sec)] <- with_labels(data,{
-      # dplyr::across(dplyr::where(is.logical), as.factor),
+    data[c(pri, sec)] |>
-      dplyr::across(dplyr::where(is.factor), forcats::fct_drop)#,
+      dplyr::mutate(
-      # dplyr::across(dplyr::where(is.factor), \(.x){forcats::fct_na_value_to_level(.x,missing.level)})
+        dplyr::across(dplyr::where(is.logical), as.factor),
-    )
+        dplyr::across(dplyr::where(is.factor), forcats::fct_drop),
+        dplyr::across(dplyr::where(is.factor), \(.x) {
+          if (anyNA(.x)) forcats::fct_na_value_to_level(.x, missing.level) else .x
+        })
+      )
+  })
 
 
-  data <- data |> sankey_ready(pri = pri, sec = sec, ...)
+  ## Aggregate data
+  data_aggr <- data |> sankey_ready(pri = pri, sec = sec, ...)
 
   na.color <- "#2986cc"
   box.color <- "#1E4B66"
 
   if (is.null(colors)) {
     if (color.group == "sec") {
+      if (anyNA(data_orig[[sec]])){
       main.colors <- viridisLite::viridis(n = length(levels(data_orig[[sec]])))
+      } else {
+        main.colors <- viridisLite::viridis(n = length(levels(data[[sec]])))
+      }
       ## Only keep colors for included levels
-      main.colors <- main.colors[match(levels(data[[sec]]), levels(data_orig[[sec]]))]
+        main.colors <- main.colors[match(levels(data[[sec]]), levels(data[[sec]]))]
 
       secondary.colors <- rep(na.color, length(levels(data[[pri]])))
-      label.colors <- Reduce(c, lapply(list(secondary.colors, rev(main.colors)), contrast_text))
+      label.colors <- Reduce(c, lapply(list(
+        secondary.colors, rev(main.colors)
+      ), contrast_text))
     } else {
-      main.colors <- viridisLite::viridis(n = length(levels(data_orig[[pri]])))
+      if (anyNA(data_orig[[sec]])){
+        main.colors <- viridisLite::viridis(n = length(levels(data_orig[[pri]])))
+      } else {
+        main.colors <- viridisLite::viridis(n = length(levels(data[[pri]])))
+      }
+      # main.colors <- viridisLite::viridis(n = length(levels(data[[pri]])))
       ## Only keep colors for included levels
-      main.colors <- main.colors[match(levels(data[[pri]]), levels(data_orig[[pri]]))]
+      main.colors <- main.colors[match(levels(data[[pri]]), levels(data[[pri]]))]
 
       secondary.colors <- rep(na.color, length(levels(data[[sec]])))
-      label.colors <- Reduce(c, lapply(list(rev(main.colors), secondary.colors), contrast_text))
+      label.colors <- Reduce(c, lapply(list(
+        rev(main.colors), secondary.colors
+      ), contrast_text))
     }
     colors <- c(na.color, main.colors, secondary.colors)
+    colors[is.na(colors)] <- "grey80"
   } else {
     label.colors <- contrast_text(colors)
   }
@@ -166,7 +212,9 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
     sapply(line_break) |>
     unname()
 
-  p <- ggplot2::ggplot(data, ggplot2::aes(y = n, axis1 = lx, axis2 = ly))
+  # browser()
+
+  p <- ggplot2::ggplot(data_aggr, ggplot2::aes(y = n, axis1 = lx, axis2 = ly))
 
   if (color.group == "sec") {
     p <- p +
@@ -181,9 +229,8 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
         knot.pos = 0.4,
         curve_type = "sigmoid"
       ) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(sec)),
-        size = 2,
+                                   size = 2,
-        width = 1 / 3.4
+                                   width = 1 / 3.4)
-      )
   } else {
     p <- p +
       ggalluvial::geom_alluvium(
@@ -196,9 +243,8 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
         knot.pos = 0.4,
         curve_type = "sigmoid"
       ) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(pri)),
-        size = 2,
+                                   size = 2,
-        width = 1 / 3.4
+                                   width = 1 / 3.4)
-      )
   }
 
   ## Will fail to use stat="stratum" if library is not loaded.
@@ -208,13 +254,10 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
       stat = "stratum",
       ggplot2::aes(label = after_stat(stratum)),
       colour = label.colors,
-      size = 8,
+      size = 6,
       lineheight = 1
     ) +
-    ggplot2::scale_x_continuous(
+    ggplot2::scale_x_continuous(breaks = 1:2, labels = group_labels) +
-      breaks = 1:2,
-      labels = group_labels
-    ) +
     ggplot2::scale_fill_manual(values = colors[-1], na.value = colors[1]) +
     # ggplot2::scale_color_manual(values = main.colors) +
     ggplot2::theme_void() +

R/ui_elements.R

@@ -25,6 +25,7 @@ ui_elements <- function(selection) {
         ## Default just output "NULL"
         ## This could probably be achieved more legantly, but this works.
         dev_banner(),
+        version_banner,
         landing_page_ui(i18n = i18n),
         # shiny::column(width = 2),
         # shiny::column(

R/validation.R

@@ -65,33 +65,6 @@ validation_server <- function(id,
 
       data_r <- if (shiny::is.reactive(data)) data else shiny::reactive(data)
 
-      # observeEvent(data_r(), {
-      #   to_validate <- data()
-      #   valid_dims <- check_data(to_validate, n_row = n_row, n_col = n_col)
-      #
-      #   if (all(c(valid_dims$nrows, valid_dims$ncols))) {
-      #     valid_status <- "OK"
-      #   } else {
-      #     valid_status <- "Failed"
-      #   }
-      #
-      #   valid_results <- lapply(
-      #     X = c("nrows", "ncols"),
-      #     FUN = function(x) {
-      #       if (is.null(valid_dims[[x]]))
-      #         return(NULL)
-      #       label <- switch(
-      #         x,
-      #         "nrows" = n_row_label,
-      #         "ncols" = n_col_label
-      #       )
-      #       list(
-      #         status = ifelse(valid_dims[[x]], "OK", "Failed"),
-      #         label = paste0("<b>", label, "</b>")
-      #       )
-      #     }
-      #   )
-
       shiny::observeEvent(
         data_r(),
         {

R/version_check.R

@@ -0,0 +1,325 @@
+# version_check.R
+#
+# Runs a one-time version check at app startup and returns a ready-made
+# shinyWidgets::alert() UI element that can be placed directly in the UI
+# definition -- no server(), no renderUI(), no uiOutput() required.
+#
+# Because the check runs outside server(), it executes once when the app
+# process starts, so the banner is present immediately on first render with
+# no loading delay.
+#
+# Version detection uses two strategies, tried in order:
+#   1. utils::packageVersion() -- works when the package is installed locally.
+#   2. app_version argument    -- explicit fallback for environments where the
+#      package is not installed (e.g. shinyapps.io). Pass the result of your
+#      app_version() function here.
+#
+# Quick start:
+#
+#   # global.R (or top of app.R, before ui / server)
+#   source("version_check.R")
+#   version_banner <- check_app_version(
+#     github_user = "your-github-username",
+#     github_repo = "your-repo-name",
+#     app_version = app_version()   # fallback for shinyapps.io
+#   )
+#
+#   # ui.R -- drop the result anywhere in the UI tree
+#   fluidPage(
+#     version_banner,
+#     ...
+#   )
+#
+#   # Verbose / debug mode -- always show the banner:
+#   version_banner <- check_app_version(
+#     github_user = "your-github-username",
+#     github_repo = "your-repo-name",
+#     app_version = app_version(),
+#     verbose     = TRUE
+#   )
+
+
+# -- Internal helpers ----------------------------------------------------------
+
+#' Check internet connectivity
+#'
+#' @return Logical; TRUE if an internet connection is available.
+.has_internet <- function() {
+  tryCatch({
+    con <- url("https://api.github.com", open = "r")
+    close(con)
+    TRUE
+  }, error = function(e) FALSE)
+}
+
+
+#' Fetch the latest release version from a GitHub repository
+#'
+#' @param github_user GitHub username or organisation.
+#' @param github_repo Repository name.
+#'
+#' @return A character string with the version tag (e.g. "1.2.0"), or NULL on
+#'   failure.
+.get_latest_github_version <- function(github_user, github_repo) {
+  api_url <- sprintf(
+    "https://api.github.com/repos/%s/%s/releases/latest",
+    github_user,
+    github_repo
+  )
+
+  tryCatch({
+    response  <- readLines(url(api_url), warn = FALSE)
+    json_text <- paste(response, collapse = "")
+
+    tag <- regmatches(
+      json_text,
+      regexpr('"tag_name"\\s*:\\s*"([^"]+)"', json_text)
+    )
+
+    if (length(tag) == 0 || nchar(tag) == 0) return(NULL)
+
+    # Strip a leading "v" if present (e.g. "v1.2.0" -> "1.2.0")
+    sub('^"tag_name"\\s*:\\s*"v?([^"]+)"$', "\\1", tag)
+  }, error = function(e) NULL)
+}
+
+
+#' Resolve the current app version
+#'
+#' Tries two strategies in order:
+#' \enumerate{
+#'   \item \code{utils::packageVersion(package_name)} -- works when the package
+#'     is installed locally (development, local \code{runApp()}).
+#'   \item \code{app_version} argument -- an explicit version string supplied by
+#'     the caller, e.g. from an \code{app_version()} function bundled with the
+#'     app. Used on shinyapps.io where the package is not installed.
+#' }
+#'
+#' @param package_name Name of the package / repository.
+#' @param app_version  Optional fallback version string.
+#'
+#' @return A character string with the version (e.g. "1.1.0"), or NULL if
+#'   neither strategy succeeds.
+.resolve_app_version <- function(package_name, app_version = NULL) {
+
+  # Strategy 1: installed package
+  v <- tryCatch(
+    as.character(utils::packageVersion(package_name)),
+    error = function(e) NULL
+  )
+  if (!is.null(v)) {
+    message("[version_check] Version source: installed package")
+    return(v)
+  }
+
+  # Strategy 2: explicit fallback supplied by the caller
+  if (!is.null(app_version)) {
+    message("[version_check] Version source: app_version() fallback")
+    return(as.character(app_version))
+  }
+
+  NULL
+}
+
+
+#' Build a shinyWidgets::alert() UI element for the version banner
+#'
+#' @param current          Current installed version string.
+#' @param latest           Latest GitHub release version string, or NULL when
+#'   the check could not complete (e.g. no internet).
+#' @param update_available Logical; whether latest > current.
+#' @param github_user      GitHub username / organisation.
+#' @param github_repo      Repository name.
+#'
+#' @return A \code{shinyWidgets::alert()} UI element.
+.build_version_alert <- function(current,
+                                 latest,
+                                 update_available,
+                                 github_user,
+                                 github_repo) {
+
+  repo_url <- sprintf(
+    "https://github.com/%s/%s/releases/latest",
+    github_user,
+    github_repo
+  )
+
+  if (is.null(latest)) {
+    # Version check could not complete (no internet or API failure)
+    return(
+      shinyWidgets::alert(
+        tags$b("Version check failed. "),
+        sprintf(
+          "Running version %s. Could not reach GitHub to check for updates.",
+          current
+        ),
+        status      = "warning",
+        dismissible = TRUE
+      )
+    )
+  }
+
+  if (update_available) {
+    shinyWidgets::alert(
+      tags$b("Update available! "),
+      sprintf(
+        "You are running version %s. Version %s is available on GitHub.",
+        current, latest
+      ),
+      " ",
+      tags$a(href = repo_url, target = "_blank", "View release"),
+      status      = "warning",
+      dismissible = TRUE
+    )
+  } else {
+    # Up to date -- only shown in verbose mode
+    shinyWidgets::alert(
+      tags$b("Up to date. "),
+      sprintf(
+        "You are running version %s, which matches the latest release (%s).",
+        current, latest
+      ),
+      status      = "success",
+      dismissible = TRUE
+    )
+  }
+}
+
+
+# -- Public API ----------------------------------------------------------------
+
+#' Run a startup version check and return a banner UI element
+#'
+#' Call this \strong{outside} \code{server()} -- typically in
+#' \code{global.R} or at the top of \code{app.R} -- and embed the returned
+#' value directly in your UI definition. Because the check runs at startup
+#' the banner is present on first render with no loading delay, and no
+#' \code{uiOutput()} / \code{renderUI()} wiring is needed.
+#'
+#' \strong{Normal mode} (\code{verbose = FALSE}): returns a banner only when
+#' a newer version is available or when the check fails. Returns \code{NULL}
+#' when the app is up to date (Shiny silently ignores \code{NULL} in the UI).
+#'
+#' \strong{Verbose / debug mode} (\code{verbose = TRUE}): always returns a
+#' banner -- including a success banner when up to date -- so you can confirm
+#' the check ran and inspect both version strings during development.
+#'
+#' @param github_user  GitHub username or organisation that owns the repository.
+#' @param github_repo  Repository name. Also used as the package name for
+#'   \code{utils::packageVersion()}.
+#' @param app_version  Optional fallback version string for environments where
+#'   the package is not installed (e.g. shinyapps.io). Pass the result of your
+#'   \code{app_version()} function here. Ignored when \code{packageVersion()}
+#'   succeeds.
+#' @param verbose      Logical; if \code{TRUE} a banner is always returned.
+#'   Defaults to \code{FALSE}.
+#'
+#' @return A \code{shinyWidgets::alert()} UI element, or \code{NULL} when there
+#'   is nothing to show (up to date in non-verbose mode).
+#'
+#' @examples
+#' \dontrun{
+#' # global.R or top of app.R
+#' source("version_check.R")
+#' version_banner <- check_app_version(
+#'   github_user = "my-org",
+#'   github_repo = "my-shiny-app",
+#'   app_version = app_version()   # fallback for shinyapps.io
+#' )
+#'
+#' # ui.R
+#' fluidPage(
+#'   version_banner,
+#'   # ... rest of UI
+#' )
+#'
+#' # Verbose mode for development
+#' version_banner <- check_app_version(
+#'   github_user = "my-org",
+#'   github_repo = "my-shiny-app",
+#'   app_version = app_version(),
+#'   verbose     = TRUE
+#' )
+#' }
+check_app_version <- function(github_user,
+                              github_repo,
+                              app_version = NULL,
+                              verbose     = FALSE) {
+
+  # -- 1. Resolve current version ----------------------------------------------
+  local_version <- .resolve_app_version(github_repo, app_version)
+  if (is.null(local_version)) {
+    message(sprintf(
+      "[version_check] Could not determine version for '%s' (package not installed and no app_version() fallback supplied).",
+      github_repo
+    ))
+    return(NULL)
+  }
+
+  message(sprintf("[version_check] Current version: %s", local_version))
+
+  # -- 2. Internet check -------------------------------------------------------
+  if (!.has_internet()) {
+    message("[version_check] No internet connection detected -- skipping.")
+
+    if (verbose) {
+      return(.build_version_alert(
+        current          = local_version,
+        latest           = NULL,
+        update_available = FALSE,
+        github_user      = github_user,
+        github_repo      = github_repo
+      ))
+    }
+
+    return(NULL)
+  }
+
+  # -- 3. Fetch latest GitHub release ------------------------------------------
+  latest_version <- .get_latest_github_version(github_user, github_repo)
+  if (is.null(latest_version)) {
+    message("[version_check] Could not retrieve latest version from GitHub.")
+
+    if (verbose) {
+      return(.build_version_alert(
+        current          = local_version,
+        latest           = NULL,
+        update_available = FALSE,
+        github_user      = github_user,
+        github_repo      = github_repo
+      ))
+    }
+
+    return(NULL)
+  }
+
+  message(sprintf("[version_check] Latest GitHub release: %s", latest_version))
+
+  # -- 4. Compare versions -----------------------------------------------------
+  update_available <- numeric_version(latest_version) > numeric_version(local_version)
+
+  if (update_available) {
+    message(sprintf(
+      "[version_check] Update available: %s -> %s",
+      local_version, latest_version
+    ))
+  } else {
+    message(sprintf("[version_check] App is up to date (%s).", local_version))
+  }
+
+  # -- 5. Return banner --------------------------------------------------------
+  # An update was found       -> always return a warning banner
+  # Up to date + verbose      -> return a success banner
+  # Up to date + not verbose  -> return NULL (Shiny ignores NULL in the UI)
+  if (update_available || verbose) {
+    .build_version_alert(
+      current          = local_version,
+      latest           = latest_version,
+      update_available = update_available,
+      github_user      = github_user,
+      github_repo      = github_repo
+    )
+  } else {
+    NULL
+  }
+}

README.md

@@ -1,10 +1,9 @@
-# FreesearchR <a href="https://agdamsbo.github.io/FreesearchR/"><img src="man/figures/logo.png" align="right" height="70" alt="FreesearchR website" /></a>
+# FreesearchR <a href="https://agdamsbo.github.io/FreesearchR/"><img src="man/figures/logo.png" alt="FreesearchR website" align="right" height="70"/></a>
 
 <!-- badges: start -->
-[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14527429.svg)](https://doi.org/10.5281/zenodo.14527429) 
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14527429.svg)](https://doi.org/10.5281/zenodo.14527429) [![rhub](https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml/badge.svg)](https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml) [![FreesearchR](https://img.shields.io/badge/Shiny-shinyapps.io-blue?style=flat&labelColor=white&logo=RStudio&logoColor=blue)](https://agdamsbo.shinyapps.io/FreesearchR/)
-[![rhub](https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml/badge.svg)](https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml)
+
-[![FreesearchR](https://img.shields.io/badge/Shiny-shinyapps.io-blue?style=flat&labelColor=white&logo=RStudio&logoColor=blue)](https://agdamsbo.shinyapps.io/FreesearchR/)
 <!-- badges: end -->
 
 The [***FreesearchR***](https://app.freesearchr.org) is a simple, clinical health data exploration and analysis tool to democratise clinical research by assisting any researcher to easily evaluate and analyse data and export publication ready results.
@@ -19,11 +18,11 @@ All feedback is welcome and can be shared as a GitHub issue. Any suggestions on
 
 This app has the following simple goals:
 
-1.   help the health clinician getting an overview of data in quality improvement projects and clinical research
+1.  help the health clinician getting an overview of data in quality improvement projects and clinical research
 
-1.   help learners get a good start analysing data and coding in *R*
+2.  help learners get a good start analysing data and coding in *R*
 
-1.   ease quick data overview and basic visualisations for any clinical researcher
+3.  ease quick data overview and basic visualisations for any clinical researcher
 
 Here’s a polished and restructured version of your README section for clarity, conciseness, and user-friendliness:
 
@@ -35,32 +34,32 @@ The **FreesearchR** app can be run locally on your machine, ensuring no data is
 
 The app can be configured either by passing a named list to `run_app()` or by setting environment variables in a **Docker Compose** file. The following variables control data access and display behavior. If no values are provided, the app will use the defaults listed below.
 
-
 **Configuration Variables**
 
-| Variable                | Description                                                                 | Default   |
+| Variable | Description | Default |
-|-------------------------|-----------------------------------------------------------------------------|-----------|
+|--------------|--------------------------------------------|--------------|
-| `INCLUDE_GLOBALENV`     | Load datasets already present in the global R environment into the app    | `FALSE`   |
+| `INCLUDE_GLOBALENV` | Load datasets already present in the global R environment into the app | `FALSE` |
-| `DATA_LIMIT_DEFAULT`    | Default number of observations for previewing or working with a dataset            | `10,000`  |
+| `DATA_LIMIT_DEFAULT` | Default number of observations for previewing or working with a dataset | `10,000` |
-| `DATA_LIMIT_UPPER`      | Maximum number of observations a user can set for the upper limit. If set to 0, no uppper limit is applied.                    | `100,000` |
+| `DATA_LIMIT_UPPER` | Maximum number of observations a user can set for the upper limit. If set to 0, no uppper limit is applied. | `100,000` |
-| `DATA_LIMIT_LOWER`      | Minimum number of observations a user can set for the lower limit                    | `1`       |
+| `DATA_LIMIT_LOWER` | Minimum number of observations a user can set for the lower limit | `1` |
+| `CHECK_APP_VERSION` | Always print version check results. Checks app version against latest release on GitHub. | `FALSE` |
 
 ### Run from R (or RStudio)
 
 If you're working with data in R, **FreesearchR** is a quick and easy tool for exploratory analysis.
 
-1. **Requirement:** Ensure you have [R](https://www.r-project.org/) installed, and optionally an editor like [RStudio](https://posit.co/download/rstudio-desktop/).
+1.  **Requirement:** Ensure you have [R](https://www.r-project.org/) installed, and optionally an editor like [RStudio](https://posit.co/download/rstudio-desktop/).
 
-2. Open the **R console** and run the following code to install the `{FreesearchR}` package and launch the app:
+2.  Open the **R console** and run the following code to install the `{FreesearchR}` package and launch the app:
 
-   ```r
+    ``` r
-   if (!require("devtools")) install.packages("devtools")
+    if (!require("devtools")) install.packages("devtools")
-   devtools::install_github("agdamsbo/FreesearchR")
+    devtools::install_github("agdamsbo/FreesearchR")
-   library(FreesearchR)
+    library(FreesearchR)
-   # Load sample data (e.g., mtcars) to make it available in the app
+    # Load sample data (e.g., mtcars) to make it available in the app
-   data(mtcars)
+    data(mtcars)
-   launch_FreesearchR(INCLUDE_GLOBALENV=TRUE)
+    launch_FreesearchR(INCLUDE_GLOBALENV=TRUE,CHECK_APP_VERSION=TRUE)
-   ```
+    ```
 
 All the variables specified above can also be passed to the app on launch from R. Set DATA_LIMIT_UPPER=0 to remove upper data limit. This limit is set to protect the online app version from choking and crashing on large data sets.
 
@@ -70,7 +69,7 @@ For advanced users, you can deploy **FreesearchR** using Docker. A data folder c
 
 To mount a local data folder, add a `volumes` entry to your `docker-compose.yml` file:
 
-```yaml
+``` yaml
 services:
   shiny:
     image: ghcr.io/agdamsbo/freesearchr:latest
@@ -86,9 +85,9 @@ services:
     restart: on-failure
 ```
 
-- The `:ro` flag mounts the folder as **read-only**, preventing the app from modifying your original data files.
+-   The `:ro` flag mounts the folder as **read-only**, preventing the app from modifying your original data files.
 
-- If no volume is mounted, the app will start without any preloaded datasets.
+-   If no volume is mounted, the app will start without any preloaded datasets.
 
 ## Code of Conduct
 

SESSION.md

@@ -11,11 +11,11 @@
 |collate     |en_US.UTF-8                                |
 |ctype       |en_US.UTF-8                                |
 |tz          |Europe/Copenhagen                          |
-|date        |2026-03-12                                 |
+|date        |2026-03-23                                 |
 |rstudio     |2026.01.1+403 Apple Blossom (desktop)      |
 |pandoc      |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
 |quarto      |1.7.30 @ /usr/local/bin/quarto             |
-|FreesearchR |26.3.4.260312                              |
+|FreesearchR |26.3.4.260323                              |
                                                                                 
                                                                                 
 --------------------------------------------------------------------------------
@@ -33,6 +33,7 @@
 |bit64             |4.6.0-1       |2025-01-16 |CRAN (R 4.5.0) |
 |bitops            |1.0-9         |2024-10-03 |CRAN (R 4.5.0) |
 |boot              |1.3-32        |2025-08-29 |CRAN (R 4.5.0) |
+|brio              |1.1.5         |2024-04-24 |CRAN (R 4.5.0) |
 |broom             |1.0.12        |2026-01-27 |CRAN (R 4.5.2) |
 |broom.helpers     |1.22.0        |2025-09-17 |CRAN (R 4.5.0) |
 |bsicons           |0.1.2         |2023-11-04 |CRAN (R 4.5.0) |
@@ -43,6 +44,7 @@
 |cardx             |0.3.2         |2026-02-05 |CRAN (R 4.5.2) |
 |caTools           |1.18.3        |2024-09-04 |CRAN (R 4.5.0) |
 |cellranger        |1.1.0         |2016-07-27 |CRAN (R 4.5.0) |
+|cffr              |1.2.1         |2026-01-12 |CRAN (R 4.5.2) |
 |checkmate         |2.3.4         |2026-02-03 |CRAN (R 4.5.2) |
 |class             |7.3-23        |2025-01-01 |CRAN (R 4.5.0) |
 |classInt          |0.4-11        |2025-01-08 |CRAN (R 4.5.0) |
@@ -52,6 +54,7 @@
 |colorspace        |2.1-2         |2025-09-22 |CRAN (R 4.5.0) |
 |commonmark        |2.0.0         |2025-07-07 |CRAN (R 4.5.0) |
 |crayon            |1.5.3         |2024-06-20 |CRAN (R 4.5.0) |
+|curl              |7.0.0         |2025-08-19 |CRAN (R 4.5.0) |
 |data.table        |1.18.2.1      |2026-01-27 |CRAN (R 4.5.2) |
 |datamods          |1.5.3         |2024-10-02 |CRAN (R 4.5.0) |
 |datawizard        |1.3.0         |2025-10-11 |CRAN (R 4.5.0) |
@@ -66,7 +69,7 @@
 |e1071             |1.7-17        |2025-12-18 |CRAN (R 4.5.2) |
 |easystats         |0.7.5         |2025-07-11 |CRAN (R 4.5.0) |
 |ellipsis          |0.3.2         |2021-04-29 |CRAN (R 4.5.0) |
-|emmeans           |2.0.2         |2026-03-05 |CRAN (R 4.5.2) |
+|emmeans           |2.0.1         |2025-12-16 |CRAN (R 4.5.2) |
 |esquisse          |2.1.0         |2025-02-21 |CRAN (R 4.5.0) |
 |estimability      |1.5.1         |2024-05-12 |CRAN (R 4.5.0) |
 |eulerr            |7.0.4         |2025-09-24 |CRAN (R 4.5.0) |
@@ -74,6 +77,7 @@
 |farver            |2.1.2         |2024-05-13 |CRAN (R 4.5.0) |
 |fastmap           |1.2.0         |2024-05-15 |CRAN (R 4.5.0) |
 |flextable         |0.9.11        |2026-02-13 |CRAN (R 4.5.2) |
+|fontawesome       |0.5.3         |2024-11-16 |CRAN (R 4.5.0) |
 |fontBitstreamVera |0.1.1         |2017-02-01 |CRAN (R 4.5.0) |
 |fontLiberation    |0.1.0         |2016-10-15 |CRAN (R 4.5.0) |
 |fontquiver        |0.2.1         |2017-02-01 |CRAN (R 4.5.0) |
@@ -109,9 +113,11 @@
 |iterators         |1.0.14        |2022-02-05 |CRAN (R 4.5.0) |
 |jquerylib         |0.1.4         |2021-04-26 |CRAN (R 4.5.0) |
 |jsonlite          |2.0.0         |2025-03-27 |CRAN (R 4.5.0) |
+|jsonvalidate      |1.5.0         |2025-02-07 |CRAN (R 4.5.0) |
 |KernSmooth        |2.23-26       |2025-01-01 |CRAN (R 4.5.0) |
 |keyring           |1.4.1         |2025-06-15 |CRAN (R 4.5.0) |
 |knitr             |1.51          |2025-12-20 |CRAN (R 4.5.2) |
+|labeling          |0.4.3         |2023-08-29 |CRAN (R 4.5.0) |
 |later             |1.4.8         |2026-03-05 |CRAN (R 4.5.2) |
 |lattice           |0.22-7        |2025-04-02 |CRAN (R 4.5.2) |
 |lifecycle         |1.0.5         |2026-01-08 |CRAN (R 4.5.2) |
@@ -123,7 +129,7 @@
 |memoise           |2.0.1         |2021-11-26 |CRAN (R 4.5.0) |
 |mime              |0.13          |2025-03-17 |CRAN (R 4.5.0) |
 |minqa             |1.2.8         |2024-08-17 |CRAN (R 4.5.0) |
-|mvtnorm           |1.3-5         |2026-03-11 |CRAN (R 4.5.2) |
+|mvtnorm           |1.3-2         |2024-11-04 |CRAN (R 4.5.2) |
 |NHANES            |2.1.0         |2015-07-02 |CRAN (R 4.5.0) |
 |nlme              |3.1-168       |2025-03-31 |CRAN (R 4.5.0) |
 |nloptr            |2.2.1         |2025-03-17 |CRAN (R 4.5.0) |
@@ -156,6 +162,7 @@
 |R6                |2.6.1         |2025-02-15 |CRAN (R 4.5.0) |
 |ragg              |1.5.1         |2026-03-06 |CRAN (R 4.5.2) |
 |rankinPlot        |1.1.0         |2023-01-30 |CRAN (R 4.5.0) |
+|rappdirs          |0.3.4         |2026-01-17 |CRAN (R 4.5.2) |
 |rbibutils         |2.4.1         |2026-01-21 |CRAN (R 4.5.2) |
 |RColorBrewer      |1.1-3         |2022-04-03 |CRAN (R 4.5.0) |
 |Rcpp              |1.1.1         |2026-01-10 |CRAN (R 4.5.2) |
@@ -197,6 +204,7 @@
 |stringr           |1.6.0         |2025-11-04 |CRAN (R 4.5.0) |
 |stRoke            |25.9.2        |2025-09-30 |CRAN (R 4.5.0) |
 |systemfonts       |1.3.2         |2026-03-05 |CRAN (R 4.5.2) |
+|testthat          |3.3.2         |2026-01-11 |CRAN (R 4.5.2) |
 |textshaping       |1.0.5         |2026-03-06 |CRAN (R 4.5.2) |
 |thematic          |0.1.8         |2025-09-29 |CRAN (R 4.5.0) |
 |tibble            |3.3.1         |2026-01-11 |CRAN (R 4.5.2) |
@@ -208,7 +216,9 @@
 |twosamples        |2.0.1         |2023-06-23 |CRAN (R 4.5.0) |
 |tzdb              |0.5.0         |2025-03-15 |CRAN (R 4.5.0) |
 |usethis           |3.2.1         |2025-09-06 |CRAN (R 4.5.0) |
+|utf8              |1.2.6         |2025-06-08 |CRAN (R 4.5.0) |
 |uuid              |1.2-2         |2026-01-23 |CRAN (R 4.5.2) |
+|V8                |8.0.1         |2025-10-10 |CRAN (R 4.5.0) |
 |vctrs             |0.7.1         |2026-01-23 |CRAN (R 4.5.2) |
 |viridis           |0.6.5         |2024-01-29 |CRAN (R 4.5.0) |
 |viridisLite       |0.4.3         |2026-02-04 |CRAN (R 4.5.2) |

app_docker/app.R

@@ -1,7 +1,7 @@
 
 
 ########
-#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmpZZ6Yua/file58174f49b1bf.R 
+#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmprPVhaz/file70562aff8e9e.R 
 ########
 
 i18n_path <- here::here("translations")
@@ -4514,7 +4514,7 @@ data_types <- function() {
 #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R 
 ########
 
-hosted_version <- function()'v26.3.4-260312'
+hosted_version <- function()'v26.3.4-260323'
 
 
 ########
@@ -5964,6 +5964,8 @@ landing_page_ui <- function(i18n) {
 #' @param data_limit_default default data set observations limit
 #' @param data_limit_upper data set observations upper limit
 #' @param data_limit_lower data set observations lower limit
+#' @param check_app_version always attempt to check app version against latest
+#' release on GitHub. Default is FALSE
 #' @param ... passed on to `shiny::runApp()`
 #'
 #' @returns shiny app
@@ -5978,12 +5980,14 @@ launch_FreesearchR <- function(include_globalenv = TRUE,
                                data_limit_default = 1000,
                                data_limit_upper = 100000,
                                data_limit_lower = 1,
+                               check_app_version = FALSE,
                                ...) {
   Sys.setenv(
     INCLUDE_GLOBALENV = include_globalenv,
     DATA_LIMIT_DEFAULT = data_limit_default,
     DATA_LIMIT_UPPER = data_limit_upper,
-    DATA_LIMIT_LOWER = data_limit_lower
+    DATA_LIMIT_LOWER = data_limit_lower,
+    CHECK_APP_VERSION = check_app_version
   )
 
   appDir <- system.file("apps", "FreesearchR", package = "FreesearchR")
@@ -7054,15 +7058,17 @@ sankey_ready <- function(data, pri, sec, numbers = "count", ...) {
     dplyr::ungroup()
 
   if (numbers == "count") {
-    out <- out |> dplyr::mutate(
+    out <- out |> dplyr::mutate(lx = factor(paste0(
-      lx = factor(paste0(!!dplyr::sym(pri), "\n(n=", gx.sum, ")")),
+      !!dplyr::sym(pri), "\n(n=", gx.sum, ")"
-      ly = factor(paste0(!!dplyr::sym(sec), "\n(n=", gy.sum, ")"))
+    )), ly = factor(paste0(
-    )
+      !!dplyr::sym(sec), "\n(n=", gy.sum, ")"
+    )))
   } else if (numbers == "percentage") {
-    out <- out |> dplyr::mutate(
+    out <- out |> dplyr::mutate(lx = factor(paste0(
-      lx = factor(paste0(!!dplyr::sym(pri), "\n(", round((gx.sum / sum(n)) * 100, 1), "%)")),
+      !!dplyr::sym(pri), "\n(", round((gx.sum / sum(n)) * 100, 1), "%)"
-      ly = factor(paste0(!!dplyr::sym(sec), "\n(", round((gy.sum / sum(n)) * 100, 1), "%)"))
+    )), ly = factor(paste0(
-    )
+      !!dplyr::sym(sec), "\n(", round((gy.sum / sum(n)) * 100, 1), "%)"
+    )))
   }
 
   if (is.factor(data[[pri]])) {
@@ -7104,20 +7110,38 @@ str_remove_last <- function(data, pattern = "\n") {
 #' mtcars |>
 #'   default_parsing() |>
 #'   plot_sankey("cyl", "gear", "vs", color.group = "pri")
-plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors = NULL,missing.level="Missing") {
+#'
+#'   # stRoke::trial |> plot_sankey("mrs_1", "mrs_6")
+plot_sankey <- function(data,
+                        pri,
+                        sec,
+                        ter = NULL,
+                        color.group = "pri",
+                        colors = NULL,
+                        missing.level = "Missing") {
   if (!is.null(ter)) {
     ds <- split(data, data[ter])
   } else {
     ds <- list(data)
   }
 
-  out <- lapply(ds, \(.ds){
+
-    plot_sankey_single(.ds, pri = pri, sec = sec, color.group = color.group, colors = colors,missing.level=missing.level)
+  out <- lapply(ds, \(.ds) {
+    plot_sankey_single(
+      .ds,
+      pri = pri,
+      sec = sec,
+      color.group = color.group,
+      colors = colors,
+      missing.level = missing.level
+    )
   })
 
   patchwork::wrap_plots(out)
 }
 
+
+
 #' Beautiful sankey plot
 #'
 #' @param color.group set group to colour by. "x" or "y".
@@ -7144,19 +7168,31 @@ plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors
 #' stRoke::trial |>
 #'   default_parsing() |>
 #'   plot_sankey_single("diabetes", "hypertension")
-plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), colors = NULL,missing.level="Missing", ...) {
+plot_sankey_single <- function(data,
+                               pri,
+                               sec,
+                               color.group = c("pri", "sec"),
+                               colors = NULL,
+                               missing.level = "Missing",
+                               ...) {
   color.group <- match.arg(color.group)
 
+
+  # browser()
+  # if (is.na(ds[c(pri,sec)]))
+
   # browser()
   data_orig <- data
+
   data[c(pri, sec)] <- data[c(pri, sec)] |>
     dplyr::mutate(
-      # dplyr::across(dplyr::where(is.logical), as.factor),
+      dplyr::across(dplyr::where(is.logical), as.factor),
-      dplyr::across(dplyr::where(is.factor), forcats::fct_drop)#,
+      dplyr::across(dplyr::where(is.factor), forcats::fct_drop),
-      # dplyr::across(dplyr::where(is.factor), \(.x){forcats::fct_na_value_to_level(.x,missing.level)})
+      dplyr::across(dplyr::where(is.factor), \(.x) {
+        forcats::fct_na_value_to_level(.x, missing.level)
+      })
     )
 
-
   data <- data |> sankey_ready(pri = pri, sec = sec, ...)
 
   na.color <- "#2986cc"
@@ -7169,21 +7205,26 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
       main.colors <- main.colors[match(levels(data[[sec]]), levels(data_orig[[sec]]))]
 
       secondary.colors <- rep(na.color, length(levels(data[[pri]])))
-      label.colors <- Reduce(c, lapply(list(secondary.colors, rev(main.colors)), contrast_text))
+      label.colors <- Reduce(c, lapply(list(
+        secondary.colors, rev(main.colors)
+      ), contrast_text))
     } else {
       main.colors <- viridisLite::viridis(n = length(levels(data_orig[[pri]])))
       ## Only keep colors for included levels
       main.colors <- main.colors[match(levels(data[[pri]]), levels(data_orig[[pri]]))]
 
       secondary.colors <- rep(na.color, length(levels(data[[sec]])))
-      label.colors <- Reduce(c, lapply(list(rev(main.colors), secondary.colors), contrast_text))
+      label.colors <- Reduce(c, lapply(list(
+        rev(main.colors), secondary.colors
+      ), contrast_text))
     }
     colors <- c(na.color, main.colors, secondary.colors)
+    colors[is.na(colors)] <- "grey80"
   } else {
     label.colors <- contrast_text(colors)
   }
 
-  group_labels <- c(get_label(data, pri), get_label(data, sec)) |>
+  group_labels <- c(get_label(data_orig, pri), get_label(data_orig, sec)) |>
     sapply(line_break) |>
     unname()
 
@@ -7202,9 +7243,8 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
         knot.pos = 0.4,
         curve_type = "sigmoid"
       ) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(sec)),
-        size = 2,
+                                   size = 2,
-        width = 1 / 3.4
+                                   width = 1 / 3.4)
-      )
   } else {
     p <- p +
       ggalluvial::geom_alluvium(
@@ -7217,9 +7257,8 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
         knot.pos = 0.4,
         curve_type = "sigmoid"
       ) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(pri)),
-        size = 2,
+                                   size = 2,
-        width = 1 / 3.4
+                                   width = 1 / 3.4)
-      )
   }
 
   ## Will fail to use stat="stratum" if library is not loaded.
@@ -7229,13 +7268,10 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
       stat = "stratum",
       ggplot2::aes(label = after_stat(stratum)),
       colour = label.colors,
-      size = 8,
+      size = 6,
       lineheight = 1
     ) +
-    ggplot2::scale_x_continuous(
+    ggplot2::scale_x_continuous(breaks = 1:2, labels = group_labels) +
-      breaks = 1:2,
-      labels = group_labels
-    ) +
     ggplot2::scale_fill_manual(values = colors[-1], na.value = colors[1]) +
     # ggplot2::scale_color_manual(values = main.colors) +
     ggplot2::theme_void() +
@@ -10772,6 +10808,7 @@ ui_elements <- function(selection) {
         ## Default just output "NULL"
         ## This could probably be achieved more legantly, but this works.
         dev_banner(),
+        version_banner,
         landing_page_ui(i18n = i18n),
         # shiny::column(width = 2),
         # shiny::column(
@@ -12832,33 +12869,6 @@ validation_server <- function(id,
 
       data_r <- if (shiny::is.reactive(data)) data else shiny::reactive(data)
 
-      # observeEvent(data_r(), {
-      #   to_validate <- data()
-      #   valid_dims <- check_data(to_validate, n_row = n_row, n_col = n_col)
-      #
-      #   if (all(c(valid_dims$nrows, valid_dims$ncols))) {
-      #     valid_status <- "OK"
-      #   } else {
-      #     valid_status <- "Failed"
-      #   }
-      #
-      #   valid_results <- lapply(
-      #     X = c("nrows", "ncols"),
-      #     FUN = function(x) {
-      #       if (is.null(valid_dims[[x]]))
-      #         return(NULL)
-      #       label <- switch(
-      #         x,
-      #         "nrows" = n_row_label,
-      #         "ncols" = n_col_label
-      #       )
-      #       list(
-      #         status = ifelse(valid_dims[[x]], "OK", "Failed"),
-      #         label = paste0("<b>", label, "</b>")
-      #       )
-      #     }
-      #   )
-
       shiny::observeEvent(
         data_r(),
         {
@@ -13242,6 +13252,337 @@ make_validation_alerts <- function(data) {
 }
 
 
+########
+#### Current file: /Users/au301842/FreesearchR/R//version_check.R 
+########
+
+# version_check.R
+#
+# Runs a one-time version check at app startup and returns a ready-made
+# shinyWidgets::alert() UI element that can be placed directly in the UI
+# definition -- no server(), no renderUI(), no uiOutput() required.
+#
+# Because the check runs outside server(), it executes once when the app
+# process starts, so the banner is present immediately on first render with
+# no loading delay.
+#
+# Version detection uses two strategies, tried in order:
+#   1. utils::packageVersion() -- works when the package is installed locally.
+#   2. app_version argument    -- explicit fallback for environments where the
+#      package is not installed (e.g. shinyapps.io). Pass the result of your
+#      app_version() function here.
+#
+# Quick start:
+#
+#   # global.R (or top of app.R, before ui / server)
+#   source("version_check.R")
+#   version_banner <- check_app_version(
+#     github_user = "your-github-username",
+#     github_repo = "your-repo-name",
+#     app_version = app_version()   # fallback for shinyapps.io
+#   )
+#
+#   # ui.R -- drop the result anywhere in the UI tree
+#   fluidPage(
+#     version_banner,
+#     ...
+#   )
+#
+#   # Verbose / debug mode -- always show the banner:
+#   version_banner <- check_app_version(
+#     github_user = "your-github-username",
+#     github_repo = "your-repo-name",
+#     app_version = app_version(),
+#     verbose     = TRUE
+#   )
+
+
+# -- Internal helpers ----------------------------------------------------------
+
+#' Check internet connectivity
+#'
+#' @return Logical; TRUE if an internet connection is available.
+.has_internet <- function() {
+  tryCatch({
+    con <- url("https://api.github.com", open = "r")
+    close(con)
+    TRUE
+  }, error = function(e) FALSE)
+}
+
+
+#' Fetch the latest release version from a GitHub repository
+#'
+#' @param github_user GitHub username or organisation.
+#' @param github_repo Repository name.
+#'
+#' @return A character string with the version tag (e.g. "1.2.0"), or NULL on
+#'   failure.
+.get_latest_github_version <- function(github_user, github_repo) {
+  api_url <- sprintf(
+    "https://api.github.com/repos/%s/%s/releases/latest",
+    github_user,
+    github_repo
+  )
+
+  tryCatch({
+    response  <- readLines(url(api_url), warn = FALSE)
+    json_text <- paste(response, collapse = "")
+
+    tag <- regmatches(
+      json_text,
+      regexpr('"tag_name"\\s*:\\s*"([^"]+)"', json_text)
+    )
+
+    if (length(tag) == 0 || nchar(tag) == 0) return(NULL)
+
+    # Strip a leading "v" if present (e.g. "v1.2.0" -> "1.2.0")
+    sub('^"tag_name"\\s*:\\s*"v?([^"]+)"$', "\\1", tag)
+  }, error = function(e) NULL)
+}
+
+
+#' Resolve the current app version
+#'
+#' Tries two strategies in order:
+#' \enumerate{
+#'   \item \code{utils::packageVersion(package_name)} -- works when the package
+#'     is installed locally (development, local \code{runApp()}).
+#'   \item \code{app_version} argument -- an explicit version string supplied by
+#'     the caller, e.g. from an \code{app_version()} function bundled with the
+#'     app. Used on shinyapps.io where the package is not installed.
+#' }
+#'
+#' @param package_name Name of the package / repository.
+#' @param app_version  Optional fallback version string.
+#'
+#' @return A character string with the version (e.g. "1.1.0"), or NULL if
+#'   neither strategy succeeds.
+.resolve_app_version <- function(package_name, app_version = NULL) {
+
+  # Strategy 1: installed package
+  v <- tryCatch(
+    as.character(utils::packageVersion(package_name)),
+    error = function(e) NULL
+  )
+  if (!is.null(v)) {
+    message("[version_check] Version source: installed package")
+    return(v)
+  }
+
+  # Strategy 2: explicit fallback supplied by the caller
+  if (!is.null(app_version)) {
+    message("[version_check] Version source: app_version() fallback")
+    return(as.character(app_version))
+  }
+
+  NULL
+}
+
+
+#' Build a shinyWidgets::alert() UI element for the version banner
+#'
+#' @param current          Current installed version string.
+#' @param latest           Latest GitHub release version string, or NULL when
+#'   the check could not complete (e.g. no internet).
+#' @param update_available Logical; whether latest > current.
+#' @param github_user      GitHub username / organisation.
+#' @param github_repo      Repository name.
+#'
+#' @return A \code{shinyWidgets::alert()} UI element.
+.build_version_alert <- function(current,
+                                 latest,
+                                 update_available,
+                                 github_user,
+                                 github_repo) {
+
+  repo_url <- sprintf(
+    "https://github.com/%s/%s/releases/latest",
+    github_user,
+    github_repo
+  )
+
+  if (is.null(latest)) {
+    # Version check could not complete (no internet or API failure)
+    return(
+      shinyWidgets::alert(
+        tags$b("Version check failed. "),
+        sprintf(
+          "Running version %s. Could not reach GitHub to check for updates.",
+          current
+        ),
+        status      = "warning",
+        dismissible = TRUE
+      )
+    )
+  }
+
+  if (update_available) {
+    shinyWidgets::alert(
+      tags$b("Update available! "),
+      sprintf(
+        "You are running version %s. Version %s is available on GitHub.",
+        current, latest
+      ),
+      " ",
+      tags$a(href = repo_url, target = "_blank", "View release"),
+      status      = "warning",
+      dismissible = TRUE
+    )
+  } else {
+    # Up to date -- only shown in verbose mode
+    shinyWidgets::alert(
+      tags$b("Up to date. "),
+      sprintf(
+        "You are running version %s, which matches the latest release (%s).",
+        current, latest
+      ),
+      status      = "success",
+      dismissible = TRUE
+    )
+  }
+}
+
+
+# -- Public API ----------------------------------------------------------------
+
+#' Run a startup version check and return a banner UI element
+#'
+#' Call this \strong{outside} \code{server()} -- typically in
+#' \code{global.R} or at the top of \code{app.R} -- and embed the returned
+#' value directly in your UI definition. Because the check runs at startup
+#' the banner is present on first render with no loading delay, and no
+#' \code{uiOutput()} / \code{renderUI()} wiring is needed.
+#'
+#' \strong{Normal mode} (\code{verbose = FALSE}): returns a banner only when
+#' a newer version is available or when the check fails. Returns \code{NULL}
+#' when the app is up to date (Shiny silently ignores \code{NULL} in the UI).
+#'
+#' \strong{Verbose / debug mode} (\code{verbose = TRUE}): always returns a
+#' banner -- including a success banner when up to date -- so you can confirm
+#' the check ran and inspect both version strings during development.
+#'
+#' @param github_user  GitHub username or organisation that owns the repository.
+#' @param github_repo  Repository name. Also used as the package name for
+#'   \code{utils::packageVersion()}.
+#' @param app_version  Optional fallback version string for environments where
+#'   the package is not installed (e.g. shinyapps.io). Pass the result of your
+#'   \code{app_version()} function here. Ignored when \code{packageVersion()}
+#'   succeeds.
+#' @param verbose      Logical; if \code{TRUE} a banner is always returned.
+#'   Defaults to \code{FALSE}.
+#'
+#' @return A \code{shinyWidgets::alert()} UI element, or \code{NULL} when there
+#'   is nothing to show (up to date in non-verbose mode).
+#'
+#' @examples
+#' \dontrun{
+#' # global.R or top of app.R
+#' source("version_check.R")
+#' version_banner <- check_app_version(
+#'   github_user = "my-org",
+#'   github_repo = "my-shiny-app",
+#'   app_version = app_version()   # fallback for shinyapps.io
+#' )
+#'
+#' # ui.R
+#' fluidPage(
+#'   version_banner,
+#'   # ... rest of UI
+#' )
+#'
+#' # Verbose mode for development
+#' version_banner <- check_app_version(
+#'   github_user = "my-org",
+#'   github_repo = "my-shiny-app",
+#'   app_version = app_version(),
+#'   verbose     = TRUE
+#' )
+#' }
+check_app_version <- function(github_user,
+                              github_repo,
+                              app_version = NULL,
+                              verbose     = FALSE) {
+
+  # -- 1. Resolve current version ----------------------------------------------
+  local_version <- .resolve_app_version(github_repo, app_version)
+  if (is.null(local_version)) {
+    message(sprintf(
+      "[version_check] Could not determine version for '%s' (package not installed and no app_version() fallback supplied).",
+      github_repo
+    ))
+    return(NULL)
+  }
+
+  message(sprintf("[version_check] Current version: %s", local_version))
+
+  # -- 2. Internet check -------------------------------------------------------
+  if (!.has_internet()) {
+    message("[version_check] No internet connection detected -- skipping.")
+
+    if (verbose) {
+      return(.build_version_alert(
+        current          = local_version,
+        latest           = NULL,
+        update_available = FALSE,
+        github_user      = github_user,
+        github_repo      = github_repo
+      ))
+    }
+
+    return(NULL)
+  }
+
+  # -- 3. Fetch latest GitHub release ------------------------------------------
+  latest_version <- .get_latest_github_version(github_user, github_repo)
+  if (is.null(latest_version)) {
+    message("[version_check] Could not retrieve latest version from GitHub.")
+
+    if (verbose) {
+      return(.build_version_alert(
+        current          = local_version,
+        latest           = NULL,
+        update_available = FALSE,
+        github_user      = github_user,
+        github_repo      = github_repo
+      ))
+    }
+
+    return(NULL)
+  }
+
+  message(sprintf("[version_check] Latest GitHub release: %s", latest_version))
+
+  # -- 4. Compare versions -----------------------------------------------------
+  update_available <- numeric_version(latest_version) > numeric_version(local_version)
+
+  if (update_available) {
+    message(sprintf(
+      "[version_check] Update available: %s -> %s",
+      local_version, latest_version
+    ))
+  } else {
+    message(sprintf("[version_check] App is up to date (%s).", local_version))
+  }
+
+  # -- 5. Return banner --------------------------------------------------------
+  # An update was found       -> always return a warning banner
+  # Up to date + verbose      -> return a success banner
+  # Up to date + not verbose  -> return NULL (Shiny ignores NULL in the UI)
+  if (update_available || verbose) {
+    .build_version_alert(
+      current          = local_version,
+      latest           = latest_version,
+      update_available = update_available,
+      github_user      = github_user,
+      github_repo      = github_repo
+    )
+  } else {
+    NULL
+  }
+}
+
+
 ########
 #### Current file: /Users/au301842/FreesearchR/R//visual_summary.R 
 ########
@@ -13714,6 +14055,7 @@ INCLUDE_GLOBALENV <- get_config("INCLUDE_GLOBALENV", default = FALSE)
 DATA_LIMIT_DEFAULT <- get_config("DATA_LIMIT_DEFAULT", default = 10000)
 DATA_LIMIT_UPPER <- get_config("DATA_LIMIT_UPPER", default = 100000)
 DATA_LIMIT_LOWER <- get_config("DATA_LIMIT_LOWER", default = 1)
+CHECK_APP_VERSION <- get_config("CHECK_APP_VERSION", default = FALSE)
 
 ## Loads folder passed to the docker container and mounted as below:
 ##
@@ -13726,6 +14068,10 @@ DATA_LIMIT_LOWER <- get_config("DATA_LIMIT_LOWER", default = 1)
 ##  All files in the ./data/ folder is attempted loaded
 load_folder()
 
+## App version check
+
+version_banner <- check_app_version("agdamsbo", "FreesearchR",app_version = app_version(),verbose=CHECK_APP_VERSION)
+
 
 ########
 #### Current file: /Users/au301842/FreesearchR/app/ui.R 

inst/apps/FreesearchR/app.R

@@ -1,7 +1,7 @@
 
 
 ########
-#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmpmhqokQ/file1a147dcf977e.R 
+#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmprPVhaz/file70565b30c8af.R 
 ########
 
 i18n_path <- system.file("translations", package = "FreesearchR")
@@ -64,7 +64,7 @@ i18n$set_translation_language("en")
 #### Current file: /Users/au301842/FreesearchR/R//app_version.R 
 ########
 
-app_version <- function()'26.3.3'
+app_version <- function()'26.3.4'
 
 
 ########
@@ -4514,7 +4514,7 @@ data_types <- function() {
 #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R 
 ########
 
-hosted_version <- function()'v26.3.3-260312'
+hosted_version <- function()'v26.3.4-260323'
 
 
 ########
@@ -5964,6 +5964,8 @@ landing_page_ui <- function(i18n) {
 #' @param data_limit_default default data set observations limit
 #' @param data_limit_upper data set observations upper limit
 #' @param data_limit_lower data set observations lower limit
+#' @param check_app_version always attempt to check app version against latest
+#' release on GitHub. Default is FALSE
 #' @param ... passed on to `shiny::runApp()`
 #'
 #' @returns shiny app
@@ -5978,12 +5980,14 @@ launch_FreesearchR <- function(include_globalenv = TRUE,
                                data_limit_default = 1000,
                                data_limit_upper = 100000,
                                data_limit_lower = 1,
+                               check_app_version = FALSE,
                                ...) {
   Sys.setenv(
     INCLUDE_GLOBALENV = include_globalenv,
     DATA_LIMIT_DEFAULT = data_limit_default,
     DATA_LIMIT_UPPER = data_limit_upper,
-    DATA_LIMIT_LOWER = data_limit_lower
+    DATA_LIMIT_LOWER = data_limit_lower,
+    CHECK_APP_VERSION = check_app_version
   )
 
   appDir <- system.file("apps", "FreesearchR", package = "FreesearchR")
@@ -7054,15 +7058,17 @@ sankey_ready <- function(data, pri, sec, numbers = "count", ...) {
     dplyr::ungroup()
 
   if (numbers == "count") {
-    out <- out |> dplyr::mutate(
+    out <- out |> dplyr::mutate(lx = factor(paste0(
-      lx = factor(paste0(!!dplyr::sym(pri), "\n(n=", gx.sum, ")")),
+      !!dplyr::sym(pri), "\n(n=", gx.sum, ")"
-      ly = factor(paste0(!!dplyr::sym(sec), "\n(n=", gy.sum, ")"))
+    )), ly = factor(paste0(
-    )
+      !!dplyr::sym(sec), "\n(n=", gy.sum, ")"
+    )))
   } else if (numbers == "percentage") {
-    out <- out |> dplyr::mutate(
+    out <- out |> dplyr::mutate(lx = factor(paste0(
-      lx = factor(paste0(!!dplyr::sym(pri), "\n(", round((gx.sum / sum(n)) * 100, 1), "%)")),
+      !!dplyr::sym(pri), "\n(", round((gx.sum / sum(n)) * 100, 1), "%)"
-      ly = factor(paste0(!!dplyr::sym(sec), "\n(", round((gy.sum / sum(n)) * 100, 1), "%)"))
+    )), ly = factor(paste0(
-    )
+      !!dplyr::sym(sec), "\n(", round((gy.sum / sum(n)) * 100, 1), "%)"
+    )))
   }
 
   if (is.factor(data[[pri]])) {
@@ -7104,20 +7110,38 @@ str_remove_last <- function(data, pattern = "\n") {
 #' mtcars |>
 #'   default_parsing() |>
 #'   plot_sankey("cyl", "gear", "vs", color.group = "pri")
-plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors = NULL,missing.level="Missing") {
+#'
+#'   # stRoke::trial |> plot_sankey("mrs_1", "mrs_6")
+plot_sankey <- function(data,
+                        pri,
+                        sec,
+                        ter = NULL,
+                        color.group = "pri",
+                        colors = NULL,
+                        missing.level = "Missing") {
   if (!is.null(ter)) {
     ds <- split(data, data[ter])
   } else {
     ds <- list(data)
   }
 
-  out <- lapply(ds, \(.ds){
+
-    plot_sankey_single(.ds, pri = pri, sec = sec, color.group = color.group, colors = colors,missing.level=missing.level)
+  out <- lapply(ds, \(.ds) {
+    plot_sankey_single(
+      .ds,
+      pri = pri,
+      sec = sec,
+      color.group = color.group,
+      colors = colors,
+      missing.level = missing.level
+    )
   })
 
   patchwork::wrap_plots(out)
 }
 
+
+
 #' Beautiful sankey plot
 #'
 #' @param color.group set group to colour by. "x" or "y".
@@ -7144,19 +7168,31 @@ plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors
 #' stRoke::trial |>
 #'   default_parsing() |>
 #'   plot_sankey_single("diabetes", "hypertension")
-plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), colors = NULL,missing.level="Missing", ...) {
+plot_sankey_single <- function(data,
+                               pri,
+                               sec,
+                               color.group = c("pri", "sec"),
+                               colors = NULL,
+                               missing.level = "Missing",
+                               ...) {
   color.group <- match.arg(color.group)
 
+
+  # browser()
+  # if (is.na(ds[c(pri,sec)]))
+
   # browser()
   data_orig <- data
+
   data[c(pri, sec)] <- data[c(pri, sec)] |>
     dplyr::mutate(
-      # dplyr::across(dplyr::where(is.logical), as.factor),
+      dplyr::across(dplyr::where(is.logical), as.factor),
-      dplyr::across(dplyr::where(is.factor), forcats::fct_drop)#,
+      dplyr::across(dplyr::where(is.factor), forcats::fct_drop),
-      # dplyr::across(dplyr::where(is.factor), \(.x){forcats::fct_na_value_to_level(.x,missing.level)})
+      dplyr::across(dplyr::where(is.factor), \(.x) {
+        forcats::fct_na_value_to_level(.x, missing.level)
+      })
     )
 
-
   data <- data |> sankey_ready(pri = pri, sec = sec, ...)
 
   na.color <- "#2986cc"
@@ -7169,21 +7205,26 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
       main.colors <- main.colors[match(levels(data[[sec]]), levels(data_orig[[sec]]))]
 
       secondary.colors <- rep(na.color, length(levels(data[[pri]])))
-      label.colors <- Reduce(c, lapply(list(secondary.colors, rev(main.colors)), contrast_text))
+      label.colors <- Reduce(c, lapply(list(
+        secondary.colors, rev(main.colors)
+      ), contrast_text))
     } else {
       main.colors <- viridisLite::viridis(n = length(levels(data_orig[[pri]])))
       ## Only keep colors for included levels
       main.colors <- main.colors[match(levels(data[[pri]]), levels(data_orig[[pri]]))]
 
       secondary.colors <- rep(na.color, length(levels(data[[sec]])))
-      label.colors <- Reduce(c, lapply(list(rev(main.colors), secondary.colors), contrast_text))
+      label.colors <- Reduce(c, lapply(list(
+        rev(main.colors), secondary.colors
+      ), contrast_text))
     }
     colors <- c(na.color, main.colors, secondary.colors)
+    colors[is.na(colors)] <- "grey80"
   } else {
     label.colors <- contrast_text(colors)
   }
 
-  group_labels <- c(get_label(data, pri), get_label(data, sec)) |>
+  group_labels <- c(get_label(data_orig, pri), get_label(data_orig, sec)) |>
     sapply(line_break) |>
     unname()
 
@@ -7202,9 +7243,8 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
         knot.pos = 0.4,
         curve_type = "sigmoid"
       ) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(sec)),
-        size = 2,
+                                   size = 2,
-        width = 1 / 3.4
+                                   width = 1 / 3.4)
-      )
   } else {
     p <- p +
       ggalluvial::geom_alluvium(
@@ -7217,9 +7257,8 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
         knot.pos = 0.4,
         curve_type = "sigmoid"
       ) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(pri)),
-        size = 2,
+                                   size = 2,
-        width = 1 / 3.4
+                                   width = 1 / 3.4)
-      )
   }
 
   ## Will fail to use stat="stratum" if library is not loaded.
@@ -7229,13 +7268,10 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
       stat = "stratum",
       ggplot2::aes(label = after_stat(stratum)),
       colour = label.colors,
-      size = 8,
+      size = 6,
       lineheight = 1
     ) +
-    ggplot2::scale_x_continuous(
+    ggplot2::scale_x_continuous(breaks = 1:2, labels = group_labels) +
-      breaks = 1:2,
-      labels = group_labels
-    ) +
     ggplot2::scale_fill_manual(values = colors[-1], na.value = colors[1]) +
     # ggplot2::scale_color_manual(values = main.colors) +
     ggplot2::theme_void() +
@@ -10772,6 +10808,7 @@ ui_elements <- function(selection) {
         ## Default just output "NULL"
         ## This could probably be achieved more legantly, but this works.
         dev_banner(),
+        version_banner,
         landing_page_ui(i18n = i18n),
         # shiny::column(width = 2),
         # shiny::column(
@@ -12832,33 +12869,6 @@ validation_server <- function(id,
 
       data_r <- if (shiny::is.reactive(data)) data else shiny::reactive(data)
 
-      # observeEvent(data_r(), {
-      #   to_validate <- data()
-      #   valid_dims <- check_data(to_validate, n_row = n_row, n_col = n_col)
-      #
-      #   if (all(c(valid_dims$nrows, valid_dims$ncols))) {
-      #     valid_status <- "OK"
-      #   } else {
-      #     valid_status <- "Failed"
-      #   }
-      #
-      #   valid_results <- lapply(
-      #     X = c("nrows", "ncols"),
-      #     FUN = function(x) {
-      #       if (is.null(valid_dims[[x]]))
-      #         return(NULL)
-      #       label <- switch(
-      #         x,
-      #         "nrows" = n_row_label,
-      #         "ncols" = n_col_label
-      #       )
-      #       list(
-      #         status = ifelse(valid_dims[[x]], "OK", "Failed"),
-      #         label = paste0("<b>", label, "</b>")
-      #       )
-      #     }
-      #   )
-
       shiny::observeEvent(
         data_r(),
         {
@@ -13242,6 +13252,337 @@ make_validation_alerts <- function(data) {
 }
 
 
+########
+#### Current file: /Users/au301842/FreesearchR/R//version_check.R 
+########
+
+# version_check.R
+#
+# Runs a one-time version check at app startup and returns a ready-made
+# shinyWidgets::alert() UI element that can be placed directly in the UI
+# definition -- no server(), no renderUI(), no uiOutput() required.
+#
+# Because the check runs outside server(), it executes once when the app
+# process starts, so the banner is present immediately on first render with
+# no loading delay.
+#
+# Version detection uses two strategies, tried in order:
+#   1. utils::packageVersion() -- works when the package is installed locally.
+#   2. app_version argument    -- explicit fallback for environments where the
+#      package is not installed (e.g. shinyapps.io). Pass the result of your
+#      app_version() function here.
+#
+# Quick start:
+#
+#   # global.R (or top of app.R, before ui / server)
+#   source("version_check.R")
+#   version_banner <- check_app_version(
+#     github_user = "your-github-username",
+#     github_repo = "your-repo-name",
+#     app_version = app_version()   # fallback for shinyapps.io
+#   )
+#
+#   # ui.R -- drop the result anywhere in the UI tree
+#   fluidPage(
+#     version_banner,
+#     ...
+#   )
+#
+#   # Verbose / debug mode -- always show the banner:
+#   version_banner <- check_app_version(
+#     github_user = "your-github-username",
+#     github_repo = "your-repo-name",
+#     app_version = app_version(),
+#     verbose     = TRUE
+#   )
+
+
+# -- Internal helpers ----------------------------------------------------------
+
+#' Check internet connectivity
+#'
+#' @return Logical; TRUE if an internet connection is available.
+.has_internet <- function() {
+  tryCatch({
+    con <- url("https://api.github.com", open = "r")
+    close(con)
+    TRUE
+  }, error = function(e) FALSE)
+}
+
+
+#' Fetch the latest release version from a GitHub repository
+#'
+#' @param github_user GitHub username or organisation.
+#' @param github_repo Repository name.
+#'
+#' @return A character string with the version tag (e.g. "1.2.0"), or NULL on
+#'   failure.
+.get_latest_github_version <- function(github_user, github_repo) {
+  api_url <- sprintf(
+    "https://api.github.com/repos/%s/%s/releases/latest",
+    github_user,
+    github_repo
+  )
+
+  tryCatch({
+    response  <- readLines(url(api_url), warn = FALSE)
+    json_text <- paste(response, collapse = "")
+
+    tag <- regmatches(
+      json_text,
+      regexpr('"tag_name"\\s*:\\s*"([^"]+)"', json_text)
+    )
+
+    if (length(tag) == 0 || nchar(tag) == 0) return(NULL)
+
+    # Strip a leading "v" if present (e.g. "v1.2.0" -> "1.2.0")
+    sub('^"tag_name"\\s*:\\s*"v?([^"]+)"$', "\\1", tag)
+  }, error = function(e) NULL)
+}
+
+
+#' Resolve the current app version
+#'
+#' Tries two strategies in order:
+#' \enumerate{
+#'   \item \code{utils::packageVersion(package_name)} -- works when the package
+#'     is installed locally (development, local \code{runApp()}).
+#'   \item \code{app_version} argument -- an explicit version string supplied by
+#'     the caller, e.g. from an \code{app_version()} function bundled with the
+#'     app. Used on shinyapps.io where the package is not installed.
+#' }
+#'
+#' @param package_name Name of the package / repository.
+#' @param app_version  Optional fallback version string.
+#'
+#' @return A character string with the version (e.g. "1.1.0"), or NULL if
+#'   neither strategy succeeds.
+.resolve_app_version <- function(package_name, app_version = NULL) {
+
+  # Strategy 1: installed package
+  v <- tryCatch(
+    as.character(utils::packageVersion(package_name)),
+    error = function(e) NULL
+  )
+  if (!is.null(v)) {
+    message("[version_check] Version source: installed package")
+    return(v)
+  }
+
+  # Strategy 2: explicit fallback supplied by the caller
+  if (!is.null(app_version)) {
+    message("[version_check] Version source: app_version() fallback")
+    return(as.character(app_version))
+  }
+
+  NULL
+}
+
+
+#' Build a shinyWidgets::alert() UI element for the version banner
+#'
+#' @param current          Current installed version string.
+#' @param latest           Latest GitHub release version string, or NULL when
+#'   the check could not complete (e.g. no internet).
+#' @param update_available Logical; whether latest > current.
+#' @param github_user      GitHub username / organisation.
+#' @param github_repo      Repository name.
+#'
+#' @return A \code{shinyWidgets::alert()} UI element.
+.build_version_alert <- function(current,
+                                 latest,
+                                 update_available,
+                                 github_user,
+                                 github_repo) {
+
+  repo_url <- sprintf(
+    "https://github.com/%s/%s/releases/latest",
+    github_user,
+    github_repo
+  )
+
+  if (is.null(latest)) {
+    # Version check could not complete (no internet or API failure)
+    return(
+      shinyWidgets::alert(
+        tags$b("Version check failed. "),
+        sprintf(
+          "Running version %s. Could not reach GitHub to check for updates.",
+          current
+        ),
+        status      = "warning",
+        dismissible = TRUE
+      )
+    )
+  }
+
+  if (update_available) {
+    shinyWidgets::alert(
+      tags$b("Update available! "),
+      sprintf(
+        "You are running version %s. Version %s is available on GitHub.",
+        current, latest
+      ),
+      " ",
+      tags$a(href = repo_url, target = "_blank", "View release"),
+      status      = "warning",
+      dismissible = TRUE
+    )
+  } else {
+    # Up to date -- only shown in verbose mode
+    shinyWidgets::alert(
+      tags$b("Up to date. "),
+      sprintf(
+        "You are running version %s, which matches the latest release (%s).",
+        current, latest
+      ),
+      status      = "success",
+      dismissible = TRUE
+    )
+  }
+}
+
+
+# -- Public API ----------------------------------------------------------------
+
+#' Run a startup version check and return a banner UI element
+#'
+#' Call this \strong{outside} \code{server()} -- typically in
+#' \code{global.R} or at the top of \code{app.R} -- and embed the returned
+#' value directly in your UI definition. Because the check runs at startup
+#' the banner is present on first render with no loading delay, and no
+#' \code{uiOutput()} / \code{renderUI()} wiring is needed.
+#'
+#' \strong{Normal mode} (\code{verbose = FALSE}): returns a banner only when
+#' a newer version is available or when the check fails. Returns \code{NULL}
+#' when the app is up to date (Shiny silently ignores \code{NULL} in the UI).
+#'
+#' \strong{Verbose / debug mode} (\code{verbose = TRUE}): always returns a
+#' banner -- including a success banner when up to date -- so you can confirm
+#' the check ran and inspect both version strings during development.
+#'
+#' @param github_user  GitHub username or organisation that owns the repository.
+#' @param github_repo  Repository name. Also used as the package name for
+#'   \code{utils::packageVersion()}.
+#' @param app_version  Optional fallback version string for environments where
+#'   the package is not installed (e.g. shinyapps.io). Pass the result of your
+#'   \code{app_version()} function here. Ignored when \code{packageVersion()}
+#'   succeeds.
+#' @param verbose      Logical; if \code{TRUE} a banner is always returned.
+#'   Defaults to \code{FALSE}.
+#'
+#' @return A \code{shinyWidgets::alert()} UI element, or \code{NULL} when there
+#'   is nothing to show (up to date in non-verbose mode).
+#'
+#' @examples
+#' \dontrun{
+#' # global.R or top of app.R
+#' source("version_check.R")
+#' version_banner <- check_app_version(
+#'   github_user = "my-org",
+#'   github_repo = "my-shiny-app",
+#'   app_version = app_version()   # fallback for shinyapps.io
+#' )
+#'
+#' # ui.R
+#' fluidPage(
+#'   version_banner,
+#'   # ... rest of UI
+#' )
+#'
+#' # Verbose mode for development
+#' version_banner <- check_app_version(
+#'   github_user = "my-org",
+#'   github_repo = "my-shiny-app",
+#'   app_version = app_version(),
+#'   verbose     = TRUE
+#' )
+#' }
+check_app_version <- function(github_user,
+                              github_repo,
+                              app_version = NULL,
+                              verbose     = FALSE) {
+
+  # -- 1. Resolve current version ----------------------------------------------
+  local_version <- .resolve_app_version(github_repo, app_version)
+  if (is.null(local_version)) {
+    message(sprintf(
+      "[version_check] Could not determine version for '%s' (package not installed and no app_version() fallback supplied).",
+      github_repo
+    ))
+    return(NULL)
+  }
+
+  message(sprintf("[version_check] Current version: %s", local_version))
+
+  # -- 2. Internet check -------------------------------------------------------
+  if (!.has_internet()) {
+    message("[version_check] No internet connection detected -- skipping.")
+
+    if (verbose) {
+      return(.build_version_alert(
+        current          = local_version,
+        latest           = NULL,
+        update_available = FALSE,
+        github_user      = github_user,
+        github_repo      = github_repo
+      ))
+    }
+
+    return(NULL)
+  }
+
+  # -- 3. Fetch latest GitHub release ------------------------------------------
+  latest_version <- .get_latest_github_version(github_user, github_repo)
+  if (is.null(latest_version)) {
+    message("[version_check] Could not retrieve latest version from GitHub.")
+
+    if (verbose) {
+      return(.build_version_alert(
+        current          = local_version,
+        latest           = NULL,
+        update_available = FALSE,
+        github_user      = github_user,
+        github_repo      = github_repo
+      ))
+    }
+
+    return(NULL)
+  }
+
+  message(sprintf("[version_check] Latest GitHub release: %s", latest_version))
+
+  # -- 4. Compare versions -----------------------------------------------------
+  update_available <- numeric_version(latest_version) > numeric_version(local_version)
+
+  if (update_available) {
+    message(sprintf(
+      "[version_check] Update available: %s -> %s",
+      local_version, latest_version
+    ))
+  } else {
+    message(sprintf("[version_check] App is up to date (%s).", local_version))
+  }
+
+  # -- 5. Return banner --------------------------------------------------------
+  # An update was found       -> always return a warning banner
+  # Up to date + verbose      -> return a success banner
+  # Up to date + not verbose  -> return NULL (Shiny ignores NULL in the UI)
+  if (update_available || verbose) {
+    .build_version_alert(
+      current          = local_version,
+      latest           = latest_version,
+      update_available = update_available,
+      github_user      = github_user,
+      github_repo      = github_repo
+    )
+  } else {
+    NULL
+  }
+}
+
+
 ########
 #### Current file: /Users/au301842/FreesearchR/R//visual_summary.R 
 ########
@@ -13714,6 +14055,7 @@ INCLUDE_GLOBALENV <- get_config("INCLUDE_GLOBALENV", default = FALSE)
 DATA_LIMIT_DEFAULT <- get_config("DATA_LIMIT_DEFAULT", default = 10000)
 DATA_LIMIT_UPPER <- get_config("DATA_LIMIT_UPPER", default = 100000)
 DATA_LIMIT_LOWER <- get_config("DATA_LIMIT_LOWER", default = 1)
+CHECK_APP_VERSION <- get_config("CHECK_APP_VERSION", default = FALSE)
 
 ## Loads folder passed to the docker container and mounted as below:
 ##
@@ -13726,6 +14068,10 @@ DATA_LIMIT_LOWER <- get_config("DATA_LIMIT_LOWER", default = 1)
 ##  All files in the ./data/ folder is attempted loaded
 load_folder()
 
+## App version check
+
+version_banner <- check_app_version("agdamsbo", "FreesearchR",app_version = app_version(),verbose=CHECK_APP_VERSION)
+
 
 ########
 #### Current file: /Users/au301842/FreesearchR/app/ui.R 

man/check_app_version.Rd

@@ -0,0 +1,72 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/version_check.R
+\name{check_app_version}
+\alias{check_app_version}
+\title{Run a startup version check and return a banner UI element}
+\usage{
+check_app_version(
+  github_user,
+  github_repo,
+  app_version = NULL,
+  verbose = FALSE
+)
+}
+\arguments{
+\item{github_user}{GitHub username or organisation that owns the repository.}
+
+\item{github_repo}{Repository name. Also used as the package name for
+\code{utils::packageVersion()}.}
+
+\item{app_version}{Optional fallback version string for environments where
+the package is not installed (e.g. shinyapps.io). Pass the result of your
+\code{app_version()} function here. Ignored when \code{packageVersion()}
+succeeds.}
+
+\item{verbose}{Logical; if \code{TRUE} a banner is always returned.
+Defaults to \code{FALSE}.}
+}
+\value{
+A \code{shinyWidgets::alert()} UI element, or \code{NULL} when there
+is nothing to show (up to date in non-verbose mode).
+}
+\description{
+Call this \strong{outside} \code{server()} -- typically in
+\code{global.R} or at the top of \code{app.R} -- and embed the returned
+value directly in your UI definition. Because the check runs at startup
+the banner is present on first render with no loading delay, and no
+\code{uiOutput()} / \code{renderUI()} wiring is needed.
+}
+\details{
+\strong{Normal mode} (\code{verbose = FALSE}): returns a banner only when
+a newer version is available or when the check fails. Returns \code{NULL}
+when the app is up to date (Shiny silently ignores \code{NULL} in the UI).
+
+\strong{Verbose / debug mode} (\code{verbose = TRUE}): always returns a
+banner -- including a success banner when up to date -- so you can confirm
+the check ran and inspect both version strings during development.
+}
+\examples{
+\dontrun{
+# global.R or top of app.R
+source("version_check.R")
+version_banner <- check_app_version(
+  github_user = "my-org",
+  github_repo = "my-shiny-app",
+  app_version = app_version()   # fallback for shinyapps.io
+)
+
+# ui.R
+fluidPage(
+  version_banner,
+  # ... rest of UI
+)
+
+# Verbose mode for development
+version_banner <- check_app_version(
+  github_user = "my-org",
+  github_repo = "my-shiny-app",
+  app_version = app_version(),
+  verbose     = TRUE
+)
+}
+}

man/data-plots.Rd

@@ -170,6 +170,8 @@ mtcars |>
 mtcars |>
   default_parsing() |>
   plot_sankey("cyl", "gear", "vs", color.group = "pri")
+
+  # stRoke::trial |> plot_sankey("mrs_1", "mrs_6")
 mtcars |> plot_scatter(pri = "mpg", sec = "wt")
 mtcars |> plot_violin(pri = "mpg", sec = "cyl", ter = "gear")
 }

man/dot-build_version_alert.Rd

@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/version_check.R
+\name{.build_version_alert}
+\alias{.build_version_alert}
+\title{Build a shinyWidgets::alert() UI element for the version banner}
+\usage{
+.build_version_alert(
+  current,
+  latest,
+  update_available,
+  github_user,
+  github_repo
+)
+}
+\arguments{
+\item{current}{Current installed version string.}
+
+\item{latest}{Latest GitHub release version string, or NULL when
+the check could not complete (e.g. no internet).}
+
+\item{update_available}{Logical; whether latest > current.}
+
+\item{github_user}{GitHub username / organisation.}
+
+\item{github_repo}{Repository name.}
+}
+\value{
+A \code{shinyWidgets::alert()} UI element.
+}
+\description{
+Build a shinyWidgets::alert() UI element for the version banner
+}

man/dot-get_latest_github_version.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/version_check.R
+\name{.get_latest_github_version}
+\alias{.get_latest_github_version}
+\title{Fetch the latest release version from a GitHub repository}
+\usage{
+.get_latest_github_version(github_user, github_repo)
+}
+\arguments{
+\item{github_user}{GitHub username or organisation.}
+
+\item{github_repo}{Repository name.}
+}
+\value{
+A character string with the version tag (e.g. "1.2.0"), or NULL on
+failure.
+}
+\description{
+Fetch the latest release version from a GitHub repository
+}

man/dot-has_internet.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/version_check.R
+\name{.has_internet}
+\alias{.has_internet}
+\title{Check internet connectivity}
+\usage{
+.has_internet()
+}
+\value{
+Logical; TRUE if an internet connection is available.
+}
+\description{
+Check internet connectivity
+}

man/dot-resolve_app_version.Rd

@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/version_check.R
+\name{.resolve_app_version}
+\alias{.resolve_app_version}
+\title{Resolve the current app version}
+\usage{
+.resolve_app_version(package_name, app_version = NULL)
+}
+\arguments{
+\item{package_name}{Name of the package / repository.}
+
+\item{app_version}{Optional fallback version string.}
+}
+\value{
+A character string with the version (e.g. "1.1.0"), or NULL if
+neither strategy succeeds.
+}
+\description{
+Tries two strategies in order:
+\enumerate{
+\item \code{utils::packageVersion(package_name)} -- works when the package
+is installed locally (development, local \code{runApp()}).
+\item \code{app_version} argument -- an explicit version string supplied by
+the caller, e.g. from an \code{app_version()} function bundled with the
+app. Used on shinyapps.io where the package is not installed.
+}
+}

man/launch_FreesearchR.Rd

@@ -9,6 +9,7 @@ launch_FreesearchR(
   data_limit_default = 1000,
   data_limit_upper = 1e+05,
   data_limit_lower = 1,
+  check_app_version = FALSE,
   ...
 )
 }
@@ -22,6 +23,9 @@ when loading data}
 
 \item{data_limit_lower}{data set observations lower limit}
 
+\item{check_app_version}{always attempt to check app version against latest
+release on GitHub. Default is FALSE}
+
 \item{...}{passed on to \code{shiny::runApp()}}
 }
 \value{