chore: updated docs and render

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 +85,38 @@ 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)
+    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".
@@ -123,19 +143,31 @@ 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"
@@ -148,21 +180,26 @@ 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()
 
@@ -182,8 +219,7 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
         curve_type = "sigmoid"
       ) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(sec)),
                                    size = 2,
-        width = 1 / 3.4
+                                   width = 1 / 3.4)
-      )
   } else {
     p <- p +
       ggalluvial::geom_alluvium(
@@ -197,8 +233,7 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
         curve_type = "sigmoid"
       ) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(pri)),
                                    size = 2,
-        width = 1 / 3.4
+                                   width = 1 / 3.4)
-      )
   }
 
   ## Will fail to use stat="stratum" if library is not loaded.
@@ -208,13 +243,10 @@ 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() +

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.
@@ -21,9 +20,9 @@ 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 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:
 
@@ -35,15 +34,15 @@ 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 |
-|-------------------------|-----------------------------------------------------------------------------|-----------|
+|--------------|--------------------------------------------|--------------|
 | `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_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` |
+| `CHECK_APP_VERSION` | Always print version check results. Checks app version against latest release on GitHub. | `FALSE` |
 
 ### Run from R (or RStudio)
 
@@ -59,7 +58,7 @@ If you're working with data in R, **FreesearchR** is a quick and easy tool for e
     library(FreesearchR)
     # Load sample data (e.g., mtcars) to make it available in the app
     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.

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) |

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")
 }