moving notes on visuals

.Rbuildignore

@@ -12,3 +12,4 @@
 ^docs$
 ^pkgdown$
 ^dev$
+^data-raw$

DESCRIPTION

@@ -15,9 +15,9 @@ Imports:
     dplyr,
     glue,
     gtsummary,
-    haven,
     here,
     quarto,
+    haven,
     readODS,
     readr,
     shiny,
@@ -29,17 +29,14 @@ Imports:
     parameters,
     DT,
     performance,
-    ggiraph,
     qqplotr,
     see,
     patchwork,
     easystats,
     DHARMa,
     IDEAFilter,
-    sparkline,
     datamods,
     toastui,
-    webshot,
     lubridate,
     bsicons,
     thematic,
@@ -48,18 +45,11 @@ Imports:
     classInt,
     htmltools,
     rlang,
-    data.table,
     apexcharter,
     esquisse,
-    janitor,
     flextable,
     gt,
-    kableExtra,
     rankinPlot,
-    sjPlot,
-    gvlma,
-    psych,
-    jtools,
     Hmisc,
     ggstats,
     rempsyc,
@@ -74,6 +64,7 @@ Suggests:
     styler,
     devtools,
     rhub,
+    webshot,
     usethis,
     roxygen2,
     pak,
@@ -87,3 +78,6 @@ URL: https://github.com/agdamsbo/FreesearchR, https://agdamsbo.github.io/Freesea
 BugReports: https://github.com/agdamsbo/FreesearchR/issues
 VignetteBuilder: knitr
 Config/testthat/edition: 3
+Depends: 
+    R (>= 3.5)
+LazyData: true

R/app_version.R

@@ -1 +1 @@
-app_version <- function()'Version: 25.4.3.250422'
+app_version <- function()'v25.4.3.250423'

R/data_plots.R

@@ -695,7 +695,7 @@ line_break <- function(data, lineLength = 20, force = FALSE) {
 #' @export
 #'
 wrap_plot_list <- function(data, tag_levels = NULL) {
-  if (ggplot2::is.ggplot(data[[1]])) {
+  if (ggplot2::is_ggplot(data[[1]])) {
     if (length(data) > 1) {
       out <- data |>
         (\(.x){
@@ -732,7 +732,7 @@ wrap_plot_list <- function(data, tag_levels = NULL) {
 align_axes <- function(...) {
   # https://stackoverflow.com/questions/62818776/get-axis-limits-from-ggplot-object
   # https://github.com/thomasp85/patchwork/blob/main/R/plot_multipage.R#L150
-  if (ggplot2::is.ggplot(..1)) {
+  if (ggplot2::is_ggplot(..1)) {
     ## Assumes list of ggplots
     p <- list(...)
   } else if (is.list(..1)) {

R/helpers.R

@@ -87,7 +87,7 @@ read_input <- function(file, consider.na = c("NA", '""', "")) {
   if (ext == "csv") {
     df <- readr::read_csv(file = file, na = consider.na)
   } else if (ext %in% c("xls", "xlsx")) {
-    df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na)
+    df <- readxl::read_excel(file = file, na.strings = consider.na)
   } else if (ext == "dta") {
     df <- haven::read_dta(file = file)
   } else if (ext == "ods") {
@@ -428,7 +428,7 @@ sort_by <- function(x, y, na.rm = FALSE, ...) {
 
 
 get_ggplot_label <- function(data, label) {
-  assertthat::assert_that(ggplot2::is.ggplot(data))
+  assertthat::assert_that(ggplot2::is_ggplot(data))
   data$labels[[label]]
 }
 

R/import-file-ext.R

@@ -298,7 +298,8 @@ import_file_server <- function(id,
     )
 
     observeEvent(input$see_data, {
-      tryCatch({
+      tryCatch(
+        {
           datamods:::show_data(default_parsing(temporary_rv$data), title = datamods:::i18n("Imported data"), type = show_data_in)
         },
         # warning = function(warn) {
@@ -312,7 +313,8 @@ import_file_server <- function(id,
 
     output$table <- toastui::renderDatagrid2({
       req(temporary_rv$data)
-      tryCatch({
+      tryCatch(
+        {
           toastui::datagrid(
             data = setNames(head(temporary_rv$data, 5), make.names(names(temporary_rv$data), unique = TRUE)),
             theme = "striped",
@@ -418,13 +420,22 @@ import_xls <- function(file, sheet, skip, na.strings) {
 
       sheet |>
         purrr::map(\(.x){
-          openxlsx2::read_xlsx(
+          readxl::read_excel(
-            file = file,
+            path = file,
             sheet = .x,
-            skip_empty_rows = TRUE,
+            na = na.strings,
-            start_row = skip - 1,
+            skip = skip,
-            na.strings = na.strings
+            .name_repair = "unique_quiet",
+            trim_ws = TRUE
           )
+
+          # openxlsx2::read_xlsx(
+          #   file = file,
+          #   sheet = .x,
+          #   skip_empty_rows = TRUE,
+          #   start_row = skip - 1,
+          #   na.strings = na.strings
+          # )
         }) |>
         purrr::reduce(dplyr::full_join)
     },

R/plot_box.R

@@ -46,7 +46,7 @@ plot_box_single <- function(data, pri, sec=NULL, seed = 2103) {
 
   if (is.null(sec)) {
     sec <- "All"
-    data[[y]] <- sec
+    data[[sec]] <- sec
   }
 
   discrete <- !data_type(data[[sec]]) %in% "continuous"

R/plot_sankey.R

@@ -22,7 +22,7 @@ sankey_ready <- function(data, pri, sec, numbers = "count", ...) {
   data[c(pri, sec)] <- data[c(pri, sec)] |>
     dplyr::mutate(dplyr::across(!dplyr::where(is.factor), forcats::as_factor))
 
-  out <- dplyr::count(data, !!dplyr::sym(pri), !!dplyr::sym(sec))
+  out <- dplyr::count(data, !!dplyr::sym(pri), !!dplyr::sym(sec), .drop = FALSE)
 
   out <- out |>
     dplyr::group_by(!!dplyr::sym(pri)) |>
@@ -73,9 +73,17 @@ str_remove_last <- function(data, pattern = "\n") {
 #' @examples
 #' ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)))
 #' ds |> plot_sankey("first", "last")
-#' ds |> plot_sankey("first", "last", color.group = "y")
+#' ds |> plot_sankey("first", "last", color.group = "sec")
-#' ds |> plot_sankey("first", "last", z = "g", color.group = "y")
+#' ds |> plot_sankey("first", "last", ter = "g", color.group = "sec")
-plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "x", colors = NULL) {
+#' mtcars |>
+#'   default_parsing() |>
+#'   plot_sankey("cyl", "gear", "am", color.group = "pri")
+#' ## In this case, the last plot as the secondary variable in wrong order
+#' ## Dont know why...
+#' mtcars |>
+#'   default_parsing() |>
+#'   plot_sankey("cyl", "gear", "vs", color.group = "pri")
+plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors = NULL) {
   if (!is.null(ter)) {
     ds <- split(data, data[ter])
   } else {
@@ -83,16 +91,12 @@ plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "x", colors =
   }
 
   out <- lapply(ds, \(.ds){
-    plot_sankey_single(.ds, x = pri, y = sec, color.group = color.group, colors = colors)
+    plot_sankey_single(.ds, pri = pri, sec = sec, color.group = color.group, colors = colors)
   })
 
   patchwork::wrap_plots(out)
 }
 
-default_theme <- function() {
-  theme_void()
-}
-
 #' Beautiful sankey plot
 #'
 #' @param color.group set group to colour by. "x" or "y".
@@ -106,15 +110,26 @@ default_theme <- function() {
 #' @examples
 #' ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)))
 #' ds |> plot_sankey_single("first", "last")
-#' ds |> plot_sankey_single("first", "last", color.group = "y")
+#' ds |> plot_sankey_single("first", "last", color.group = "sec")
 #' data.frame(
 #'   g = sample(LETTERS[1:2], 100, TRUE),
 #'   first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)),
 #'   last = sample(c(TRUE, FALSE, FALSE), 100, TRUE)
 #' ) |>
 #'   plot_sankey_single("first", "last", color.group = "pri")
+#' mtcars |>
+#'   default_parsing() |>
+#'   str()
+#' plot_sankey_single("cyl", "vs", color.group = "pri")
 plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), colors = NULL, ...) {
   color.group <- match.arg(color.group)
+
+  data_orig <- data
+  data[c(pri, sec)] <- data[c(pri, sec)] |>
+    dplyr::mutate(dplyr::across(dplyr::where(is.factor), forcats::fct_drop))
+
+  # browser()
+
   data <- data |> sankey_ready(pri = pri, sec = sec, ...)
 
   library(ggalluvial)
@@ -124,11 +139,17 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
 
   if (is.null(colors)) {
     if (color.group == "sec") {
-      main.colors <- viridisLite::viridis(n = length(levels(data[[sec]])))
+      main.colors <- viridisLite::viridis(n = length(levels(data_orig[[sec]])))
+      ## Only keep colors for included levels
+      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))
     } else {
-      main.colors <- viridisLite::viridis(n = length(levels(data[[pri]])))
+      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))
     }
@@ -146,7 +167,11 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
   if (color.group == "sec") {
     p <- p +
       ggalluvial::geom_alluvium(
-        ggplot2::aes(fill = !!dplyr::sym(sec), color = !!dplyr::sym(sec)),
+        ggplot2::aes(
+          fill = !!dplyr::sym(sec) # ,
+          ## Including will print strings when levels are empty
+          # color = !!dplyr::sym(sec)
+        ),
         width = 1 / 16,
         alpha = .8,
         knot.pos = 0.4,
@@ -158,7 +183,10 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
   } else {
     p <- p +
       ggalluvial::geom_alluvium(
-        ggplot2::aes(fill = !!dplyr::sym(pri), color = !!dplyr::sym(pri)),
+        ggplot2::aes(
+          fill = !!dplyr::sym(pri) # ,
+          # color = !!dplyr::sym(pri)
+        ),
         width = 1 / 16,
         alpha = .8,
         knot.pos = 0.4,
@@ -182,7 +210,7 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
       labels = group_labels
     ) +
     ggplot2::scale_fill_manual(values = colors[-1], na.value = colors[1]) +
-    ggplot2::scale_color_manual(values = main.colors) +
+    # ggplot2::scale_color_manual(values = main.colors) +
     ggplot2::theme_void() +
     ggplot2::theme(
       legend.position = "none",

README.md

@@ -1,4 +1,4 @@
-# FreesearchR
+# FreesearchR <img style="float: right;" src="logo-text-white-250.png">
 
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
@@ -48,3 +48,5 @@ Like any other project, this project was never possible without the great work o
 -   [gtsummary](https://www.danieldsjoberg.com/gtsummary/): superb and flexible way to create publication-ready analytical and summary tables.
 
 -   [dreamRs](https://github.com/dreamRs): maintainers of a broad selection of great extensions and tools for [Shiny](https://shiny.posit.co/).
+
+This project was all written by a human and not by any AI-based tools.

SESSION.md

@@ -0,0 +1,166 @@
+--------------------------------------------------------------------------------
+-------------------------------- R environment ---------------------------------
+--------------------------------------------------------------------------------
+|setting     |value                                      |
+|:-----------|:------------------------------------------|
+|version     |R version 4.4.1 (2024-06-14)               |
+|os          |macOS 15.3.1                               |
+|system      |aarch64, darwin20                          |
+|ui          |RStudio                                    |
+|language    |(EN)                                       |
+|collate     |en_US.UTF-8                                |
+|ctype       |en_US.UTF-8                                |
+|tz          |Europe/Copenhagen                          |
+|date        |2025-04-23                                 |
+|rstudio     |2024.12.1+563 Kousa Dogwood (desktop)      |
+|pandoc      |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
+|quarto      |1.6.40 @ /usr/local/bin/quarto             |
+|FreesearchR |25.4.3.250423                              |
+                                                                                
+                                                                                
+--------------------------------------------------------------------------------
+----------------------------------- packages -----------------------------------
+--------------------------------------------------------------------------------
+|package       |loadedversion |date       |source         |
+|:-------------|:-------------|:----------|:--------------|
+|apexcharter   |0.4.4         |2024-09-06 |CRAN (R 4.4.1) |
+|askpass       |1.2.1         |2024-10-04 |CRAN (R 4.4.1) |
+|assertthat    |0.2.1         |2019-03-21 |CRAN (R 4.4.1) |
+|backports     |1.5.0         |2024-05-23 |CRAN (R 4.4.1) |
+|bayestestR    |0.15.2        |2025-02-07 |CRAN (R 4.4.1) |
+|bit           |4.6.0         |2025-03-06 |CRAN (R 4.4.1) |
+|bit64         |4.6.0-1       |2025-01-16 |CRAN (R 4.4.1) |
+|boot          |1.3-31        |2024-08-28 |CRAN (R 4.4.1) |
+|broom         |1.0.8         |2025-03-28 |CRAN (R 4.4.1) |
+|broom.helpers |1.20.0        |2025-03-06 |CRAN (R 4.4.1) |
+|bsicons       |0.1.2         |2023-11-04 |CRAN (R 4.4.0) |
+|bslib         |0.9.0         |2025-01-30 |CRAN (R 4.4.1) |
+|cachem        |1.1.0         |2024-05-16 |CRAN (R 4.4.1) |
+|cellranger    |1.1.0         |2016-07-27 |CRAN (R 4.4.0) |
+|class         |7.3-23        |2025-01-01 |CRAN (R 4.4.1) |
+|classInt      |0.4-11        |2025-01-08 |CRAN (R 4.4.1) |
+|cli           |3.6.4         |2025-02-13 |CRAN (R 4.4.1) |
+|colorspace    |2.1-1         |2024-07-26 |CRAN (R 4.4.1) |
+|commonmark    |1.9.5         |2025-03-17 |CRAN (R 4.4.1) |
+|correlation   |0.8.7         |2025-03-03 |CRAN (R 4.4.1) |
+|crayon        |1.5.3         |2024-06-20 |CRAN (R 4.4.1) |
+|credentials   |2.0.2         |2024-10-04 |CRAN (R 4.4.1) |
+|crosstalk     |1.2.1         |2023-11-23 |CRAN (R 4.4.0) |
+|data.table    |1.17.0        |2025-02-22 |CRAN (R 4.4.1) |
+|datamods      |1.5.3         |2024-10-02 |CRAN (R 4.4.1) |
+|datawizard    |1.0.2         |2025-03-24 |CRAN (R 4.4.1) |
+|desc          |1.4.3         |2023-12-10 |CRAN (R 4.4.1) |
+|devtools      |2.4.5         |2022-10-11 |CRAN (R 4.4.0) |
+|DHARMa        |0.4.7         |2024-10-18 |CRAN (R 4.4.1) |
+|digest        |0.6.37        |2024-08-19 |CRAN (R 4.4.1) |
+|dplyr         |1.1.4         |2023-11-17 |CRAN (R 4.4.0) |
+|DT            |0.33          |2024-04-04 |CRAN (R 4.4.0) |
+|e1071         |1.7-16        |2024-09-16 |CRAN (R 4.4.1) |
+|easystats     |0.7.4         |2025-02-06 |CRAN (R 4.4.1) |
+|effectsize    |1.0.0         |2024-12-10 |CRAN (R 4.4.1) |
+|ellipsis      |0.3.2         |2021-04-29 |CRAN (R 4.4.1) |
+|esquisse      |2.1.0         |2025-02-21 |CRAN (R 4.4.1) |
+|evaluate      |1.0.3         |2025-01-10 |CRAN (R 4.4.1) |
+|farver        |2.1.2         |2024-05-13 |CRAN (R 4.4.1) |
+|fastmap       |1.2.0         |2024-05-15 |CRAN (R 4.4.1) |
+|fontawesome   |0.5.3         |2024-11-16 |CRAN (R 4.4.1) |
+|forcats       |1.0.0         |2023-01-29 |CRAN (R 4.4.0) |
+|FreesearchR   |25.4.3        |NA         |NA             |
+|fs            |1.6.6         |2025-04-12 |CRAN (R 4.4.1) |
+|generics      |0.1.3         |2022-07-05 |CRAN (R 4.4.1) |
+|gert          |2.1.5         |2025-03-25 |CRAN (R 4.4.1) |
+|ggplot2       |3.5.2         |2025-04-09 |CRAN (R 4.4.1) |
+|glue          |1.8.0         |2024-09-30 |CRAN (R 4.4.1) |
+|gt            |1.0.0         |2025-04-05 |CRAN (R 4.4.1) |
+|gtable        |0.3.6         |2024-10-25 |CRAN (R 4.4.1) |
+|gtsummary     |2.2.0         |2025-04-14 |CRAN (R 4.4.1) |
+|haven         |2.5.4         |2023-11-30 |CRAN (R 4.4.0) |
+|here          |1.0.1         |2020-12-13 |CRAN (R 4.4.1) |
+|hms           |1.1.3         |2023-03-21 |CRAN (R 4.4.0) |
+|htmltools     |0.5.8.1       |2024-04-04 |CRAN (R 4.4.1) |
+|htmlwidgets   |1.6.4         |2023-12-06 |CRAN (R 4.4.0) |
+|httpuv        |1.6.16        |2025-04-16 |CRAN (R 4.4.1) |
+|IDEAFilter    |0.2.0         |2024-04-15 |CRAN (R 4.4.0) |
+|insight       |1.2.0         |2025-04-22 |CRAN (R 4.4.1) |
+|jquerylib     |0.1.4         |2021-04-26 |CRAN (R 4.4.0) |
+|jsonlite      |2.0.0         |2025-03-27 |CRAN (R 4.4.1) |
+|KernSmooth    |2.23-26       |2025-01-01 |CRAN (R 4.4.1) |
+|knitr         |1.50          |2025-03-16 |CRAN (R 4.4.1) |
+|later         |1.4.2         |2025-04-08 |CRAN (R 4.4.1) |
+|lattice       |0.22-7        |2025-04-02 |CRAN (R 4.4.1) |
+|lifecycle     |1.0.4         |2023-11-07 |CRAN (R 4.4.1) |
+|lme4          |1.1-37        |2025-03-26 |CRAN (R 4.4.1) |
+|magrittr      |2.0.3         |2022-03-30 |CRAN (R 4.4.1) |
+|MASS          |7.3-65        |2025-02-28 |CRAN (R 4.4.1) |
+|Matrix        |1.7-3         |2025-03-11 |CRAN (R 4.4.1) |
+|memoise       |2.0.1         |2021-11-26 |CRAN (R 4.4.0) |
+|mime          |0.13          |2025-03-17 |CRAN (R 4.4.1) |
+|miniUI        |0.1.2         |2025-04-17 |CRAN (R 4.4.1) |
+|minqa         |1.2.8         |2024-08-17 |CRAN (R 4.4.1) |
+|modelbased    |0.10.0        |2025-03-10 |CRAN (R 4.4.1) |
+|munsell       |0.5.1         |2024-04-01 |CRAN (R 4.4.1) |
+|nlme          |3.1-168       |2025-03-31 |CRAN (R 4.4.1) |
+|nloptr        |2.2.1         |2025-03-17 |CRAN (R 4.4.1) |
+|openssl       |2.3.2         |2025-02-03 |CRAN (R 4.4.1) |
+|openxlsx2     |1.14          |2025-03-20 |CRAN (R 4.4.1) |
+|parameters    |0.24.2        |2025-03-04 |CRAN (R 4.4.1) |
+|patchwork     |1.3.0         |2024-09-16 |CRAN (R 4.4.1) |
+|performance   |0.13.0        |2025-01-15 |CRAN (R 4.4.1) |
+|phosphoricons |0.2.1         |2024-04-08 |CRAN (R 4.4.0) |
+|pillar        |1.10.2        |2025-04-05 |CRAN (R 4.4.1) |
+|pkgbuild      |1.4.7         |2025-03-24 |CRAN (R 4.4.1) |
+|pkgconfig     |2.0.3         |2019-09-22 |CRAN (R 4.4.1) |
+|pkgload       |1.4.0         |2024-06-28 |CRAN (R 4.4.0) |
+|processx      |3.8.6         |2025-02-21 |CRAN (R 4.4.1) |
+|profvis       |0.4.0         |2024-09-20 |CRAN (R 4.4.1) |
+|promises      |1.3.2         |2024-11-28 |CRAN (R 4.4.1) |
+|proxy         |0.4-27        |2022-06-09 |CRAN (R 4.4.1) |
+|ps            |1.9.1         |2025-04-12 |CRAN (R 4.4.1) |
+|purrr         |1.0.4         |2025-02-05 |CRAN (R 4.4.1) |
+|quarto        |1.4.4         |2024-07-20 |CRAN (R 4.4.0) |
+|R6            |2.6.1         |2025-02-15 |CRAN (R 4.4.1) |
+|rbibutils     |2.3           |2024-10-04 |CRAN (R 4.4.1) |
+|RColorBrewer  |1.1-3         |2022-04-03 |CRAN (R 4.4.1) |
+|Rcpp          |1.0.14        |2025-01-12 |CRAN (R 4.4.1) |
+|Rdpack        |2.6.4         |2025-04-09 |CRAN (R 4.4.1) |
+|reactable     |0.4.4         |2023-03-12 |CRAN (R 4.4.0) |
+|readODS       |2.3.2         |2025-01-13 |CRAN (R 4.4.1) |
+|readr         |2.1.5         |2024-01-10 |CRAN (R 4.4.0) |
+|readxl        |1.4.5         |2025-03-07 |CRAN (R 4.4.1) |
+|reformulas    |0.4.0         |2024-11-03 |CRAN (R 4.4.1) |
+|remotes       |2.5.0         |2024-03-17 |CRAN (R 4.4.1) |
+|renv          |1.1.4         |2025-03-20 |CRAN (R 4.4.1) |
+|report        |0.6.1         |2025-02-07 |CRAN (R 4.4.1) |
+|rio           |1.2.3         |2024-09-25 |CRAN (R 4.4.1) |
+|rlang         |1.1.6         |2025-04-11 |CRAN (R 4.4.1) |
+|rmarkdown     |2.29          |2024-11-04 |CRAN (R 4.4.1) |
+|rprojroot     |2.0.4         |2023-11-05 |CRAN (R 4.4.1) |
+|rsconnect     |1.3.4         |2025-01-22 |CRAN (R 4.4.1) |
+|rstudioapi    |0.17.1        |2024-10-22 |CRAN (R 4.4.1) |
+|sass          |0.4.10        |2025-04-11 |CRAN (R 4.4.1) |
+|scales        |1.3.0         |2023-11-28 |CRAN (R 4.4.0) |
+|see           |0.11.0        |2025-03-11 |CRAN (R 4.4.1) |
+|sessioninfo   |1.2.3         |2025-02-05 |CRAN (R 4.4.1) |
+|shiny         |1.10.0        |2024-12-14 |CRAN (R 4.4.1) |
+|shinybusy     |0.3.3         |2024-03-09 |CRAN (R 4.4.0) |
+|shinyTime     |1.0.3         |2022-08-19 |CRAN (R 4.4.0) |
+|shinyWidgets  |0.9.0         |2025-02-21 |CRAN (R 4.4.1) |
+|stringi       |1.8.7         |2025-03-27 |CRAN (R 4.4.1) |
+|sys           |3.4.3         |2024-10-04 |CRAN (R 4.4.1) |
+|tibble        |3.2.1         |2023-03-20 |CRAN (R 4.4.0) |
+|tidyr         |1.3.1         |2024-01-24 |CRAN (R 4.4.1) |
+|tidyselect    |1.2.1         |2024-03-11 |CRAN (R 4.4.0) |
+|toastui       |0.4.0         |2025-04-03 |CRAN (R 4.4.1) |
+|tzdb          |0.5.0         |2025-03-15 |CRAN (R 4.4.1) |
+|urlchecker    |1.0.1         |2021-11-30 |CRAN (R 4.4.1) |
+|usethis       |3.1.0         |2024-11-26 |CRAN (R 4.4.1) |
+|vctrs         |0.6.5         |2023-12-01 |CRAN (R 4.4.0) |
+|vroom         |1.6.5         |2023-12-05 |CRAN (R 4.4.0) |
+|whisker       |0.4.1         |2022-12-05 |CRAN (R 4.4.1) |
+|withr         |3.0.2         |2024-10-28 |CRAN (R 4.4.1) |
+|writexl       |1.5.4         |2025-04-15 |CRAN (R 4.4.1) |
+|xfun          |0.52          |2025-04-02 |CRAN (R 4.4.1) |
+|xml2          |1.3.8         |2025-03-14 |CRAN (R 4.4.1) |
+|xtable        |1.8-4         |2019-04-21 |CRAN (R 4.4.1) |
+|yaml          |2.3.10        |2024-07-26 |CRAN (R 4.4.1) |
+|zip           |2.3.2         |2025-02-01 |CRAN (R 4.4.1) |

_pkgdown.yml

@@ -8,13 +8,14 @@ template:
     base_font: {google: "Montserrat"}
     heading_font: {google: "Public Sans"}
     # code_font: {google: "Open Sans"}
+  # Adding the switch destroys the theme colors
   light-switch: false
 
 navbar:
   bg: primary
   structure:
     left:  [intro, reference, articles, roadmap, q_a, news]
-    right: [search, github, lightswitch]
+    right: [search, github]
   components:
     roadmap:
       text: Roadmap

data-raw/session.R

@@ -0,0 +1,19 @@
+## code to prepare `session` dataset goes here
+
+session <- devtools::session_info()
+
+platform <- c(session$platform,
+      "FreesearchR"=paste(gsub("Version: ","",readLines(here::here('DESCRIPTION'))[3]),format(Sys.time(),format = '%y%m%d'),sep='.'))
+
+platform <- data.frame(option=names(platform),value=Reduce(c,platform))
+
+libs <- as.data.frame(session$packages)[names(session$packages) %in% c("package","loadedversion","date","source")]
+
+rownames(libs) <- NULL
+
+session_data <- list(
+  platform=platform,
+  libs=libs
+)
+
+usethis::use_data(session_data,internal = TRUE, overwrite = TRUE)

inst/apps/FreesearchR/app.R

@@ -10,7 +10,7 @@
 #### Current file: /Users/au301842/FreesearchR/R//app_version.R 
 ########
 
-app_version <- function()'Version: 25.4.3.250422'
+app_version <- function()'v25.4.3.250423'
 
 
 ########
@@ -1801,7 +1801,7 @@ line_break <- function(data, lineLength = 20, force = FALSE) {
 #' @export
 #'
 wrap_plot_list <- function(data, tag_levels = NULL) {
-  if (ggplot2::is.ggplot(data[[1]])) {
+  if (ggplot2::is_ggplot(data[[1]])) {
     if (length(data) > 1) {
       out <- data |>
         (\(.x){
@@ -1838,7 +1838,7 @@ wrap_plot_list <- function(data, tag_levels = NULL) {
 align_axes <- function(...) {
   # https://stackoverflow.com/questions/62818776/get-axis-limits-from-ggplot-object
   # https://github.com/thomasp85/patchwork/blob/main/R/plot_multipage.R#L150
-  if (ggplot2::is.ggplot(..1)) {
+  if (ggplot2::is_ggplot(..1)) {
     ## Assumes list of ggplots
     p <- list(...)
   } else if (is.list(..1)) {
@@ -2497,7 +2497,7 @@ read_input <- function(file, consider.na = c("NA", '""', "")) {
   if (ext == "csv") {
     df <- readr::read_csv(file = file, na = consider.na)
   } else if (ext %in% c("xls", "xlsx")) {
-    df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na)
+    df <- readxl::read_excel(file = file, na.strings = consider.na)
   } else if (ext == "dta") {
     df <- haven::read_dta(file = file)
   } else if (ext == "ods") {
@@ -2838,7 +2838,7 @@ sort_by <- function(x, y, na.rm = FALSE, ...) {
 
 
 get_ggplot_label <- function(data, label) {
-  assertthat::assert_that(ggplot2::is.ggplot(data))
+  assertthat::assert_that(ggplot2::is_ggplot(data))
   data$labels[[label]]
 }
 
@@ -3368,7 +3368,8 @@ import_file_server <- function(id,
     )
 
     observeEvent(input$see_data, {
-      tryCatch({
+      tryCatch(
+        {
           datamods:::show_data(default_parsing(temporary_rv$data), title = datamods:::i18n("Imported data"), type = show_data_in)
         },
         # warning = function(warn) {
@@ -3382,7 +3383,8 @@ import_file_server <- function(id,
 
     output$table <- toastui::renderDatagrid2({
       req(temporary_rv$data)
-      tryCatch({
+      tryCatch(
+        {
           toastui::datagrid(
             data = setNames(head(temporary_rv$data, 5), make.names(names(temporary_rv$data), unique = TRUE)),
             theme = "striped",
@@ -3488,13 +3490,22 @@ import_xls <- function(file, sheet, skip, na.strings) {
 
       sheet |>
         purrr::map(\(.x){
-          openxlsx2::read_xlsx(
+          readxl::read_excel(
-            file = file,
+            path = file,
             sheet = .x,
-            skip_empty_rows = TRUE,
+            na = na.strings,
-            start_row = skip - 1,
+            skip = skip,
-            na.strings = na.strings
+            .name_repair = "unique_quiet",
+            trim_ws = TRUE
           )
+
+          # openxlsx2::read_xlsx(
+          #   file = file,
+          #   sheet = .x,
+          #   skip_empty_rows = TRUE,
+          #   start_row = skip - 1,
+          #   na.strings = na.strings
+          # )
         }) |>
         purrr::reduce(dplyr::full_join)
     },
@@ -3738,13 +3749,14 @@ plot_box <- function(data, pri, sec, ter = NULL) {
 #' @export
 #'
 #' @examples
+#' mtcars |> plot_box_single("mpg")
 #' mtcars |> plot_box_single("mpg","cyl")
 plot_box_single <- function(data, pri, sec=NULL, seed = 2103) {
   set.seed(seed)
 
   if (is.null(sec)) {
     sec <- "All"
-    data[[y]] <- sec
+    data[[sec]] <- sec
   }
 
   discrete <- !data_type(data[[sec]]) %in% "continuous"
@@ -4075,7 +4087,7 @@ sankey_ready <- function(data, pri, sec, numbers = "count", ...) {
   data[c(pri, sec)] <- data[c(pri, sec)] |>
     dplyr::mutate(dplyr::across(!dplyr::where(is.factor), forcats::as_factor))
 
-  out <- dplyr::count(data, !!dplyr::sym(pri), !!dplyr::sym(sec))
+  out <- dplyr::count(data, !!dplyr::sym(pri), !!dplyr::sym(sec), .drop = FALSE)
 
   out <- out |>
     dplyr::group_by(!!dplyr::sym(pri)) |>
@@ -4126,9 +4138,17 @@ str_remove_last <- function(data, pattern = "\n") {
 #' @examples
 #' ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)))
 #' ds |> plot_sankey("first", "last")
-#' ds |> plot_sankey("first", "last", color.group = "y")
+#' ds |> plot_sankey("first", "last", color.group = "sec")
-#' ds |> plot_sankey("first", "last", z = "g", color.group = "y")
+#' ds |> plot_sankey("first", "last", ter = "g", color.group = "sec")
-plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "x", colors = NULL) {
+#' mtcars |>
+#'   default_parsing() |>
+#'   plot_sankey("cyl", "gear", "am", color.group = "pri")
+#' ## In this case, the last plot as the secondary variable in wrong order
+#' ## Dont know why...
+#' mtcars |>
+#'   default_parsing() |>
+#'   plot_sankey("cyl", "gear", "vs", color.group = "pri")
+plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors = NULL) {
   if (!is.null(ter)) {
     ds <- split(data, data[ter])
   } else {
@@ -4136,16 +4156,12 @@ plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "x", colors =
   }
 
   out <- lapply(ds, \(.ds){
-    plot_sankey_single(.ds, x = pri, y = sec, color.group = color.group, colors = colors)
+    plot_sankey_single(.ds, pri = pri, sec = sec, color.group = color.group, colors = colors)
   })
 
   patchwork::wrap_plots(out)
 }
 
-default_theme <- function() {
-  theme_void()
-}
-
 #' Beautiful sankey plot
 #'
 #' @param color.group set group to colour by. "x" or "y".
@@ -4159,15 +4175,26 @@ default_theme <- function() {
 #' @examples
 #' ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)))
 #' ds |> plot_sankey_single("first", "last")
-#' ds |> plot_sankey_single("first", "last", color.group = "y")
+#' ds |> plot_sankey_single("first", "last", color.group = "sec")
 #' data.frame(
 #'   g = sample(LETTERS[1:2], 100, TRUE),
 #'   first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)),
 #'   last = sample(c(TRUE, FALSE, FALSE), 100, TRUE)
 #' ) |>
 #'   plot_sankey_single("first", "last", color.group = "pri")
+#' mtcars |>
+#'   default_parsing() |>
+#'   str()
+#' plot_sankey_single("cyl", "vs", color.group = "pri")
 plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), colors = NULL, ...) {
   color.group <- match.arg(color.group)
+
+  data_orig <- data
+  data[c(pri, sec)] <- data[c(pri, sec)] |>
+    dplyr::mutate(dplyr::across(dplyr::where(is.factor), forcats::fct_drop))
+
+  # browser()
+
   data <- data |> sankey_ready(pri = pri, sec = sec, ...)
 
   library(ggalluvial)
@@ -4177,11 +4204,17 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
 
   if (is.null(colors)) {
     if (color.group == "sec") {
-      main.colors <- viridisLite::viridis(n = length(levels(data[[sec]])))
+      main.colors <- viridisLite::viridis(n = length(levels(data_orig[[sec]])))
+      ## Only keep colors for included levels
+      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))
     } else {
-      main.colors <- viridisLite::viridis(n = length(levels(data[[pri]])))
+      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))
     }
@@ -4199,7 +4232,11 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
   if (color.group == "sec") {
     p <- p +
       ggalluvial::geom_alluvium(
-        ggplot2::aes(fill = !!dplyr::sym(sec), color = !!dplyr::sym(sec)),
+        ggplot2::aes(
+          fill = !!dplyr::sym(sec) # ,
+          ## Including will print strings when levels are empty
+          # color = !!dplyr::sym(sec)
+        ),
         width = 1 / 16,
         alpha = .8,
         knot.pos = 0.4,
@@ -4211,7 +4248,10 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
   } else {
     p <- p +
       ggalluvial::geom_alluvium(
-        ggplot2::aes(fill = !!dplyr::sym(pri), color = !!dplyr::sym(pri)),
+        ggplot2::aes(
+          fill = !!dplyr::sym(pri) # ,
+          # color = !!dplyr::sym(pri)
+        ),
         width = 1 / 16,
         alpha = .8,
         knot.pos = 0.4,
@@ -4235,7 +4275,7 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
       labels = group_labels
     ) +
     ggplot2::scale_fill_manual(values = colors[-1], na.value = colors[1]) +
-    ggplot2::scale_color_manual(values = main.colors) +
+    # ggplot2::scale_color_manual(values = main.colors) +
     ggplot2::theme_void() +
     ggplot2::theme(
       legend.position = "none",
@@ -8399,7 +8439,7 @@ ui_elements <- list(
               shiny::uiOutput(outputId = "column_filter"),
               shiny::helpText("Variable ", tags$a(
                 "data type",
-                href = "https://agdamsbo.github.io/FreesearchR/articles/FreesearchR.html",
+                href = "https://agdamsbo.github.io/FreesearchR/articles/data-types.html",
                 target = "_blank",
                 rel = "noopener noreferrer"
               ), " filtering."),
@@ -8596,15 +8636,13 @@ ui_elements <- list(
         data_visuals_ui("visuals"),
         shiny::tagList(
           bslib::nav_spacer(),
-          bslib::nav_panel(
+          bslib::nav_item(
-            title = "Notes",
+            # shiny::img(shiny::icon("book")),
-            shiny::fluidRow(
+            shiny::tags$a(
-              shiny::column(width = 2),
+              href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
-              shiny::column(
+              "Notes (external)",
-                width = 8,
+              target = "_blank",
-                shiny::markdown(readLines("www/notes_visuals.md")),
+              rel = "noopener noreferrer"
-                shiny::column(width = 2)
-              )
             )
           )
         )
@@ -8774,11 +8812,11 @@ ui <- bslib::page_fixed(
       style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
       shiny::p(
         style = "margin: 1",
-        "Data is only stored for analyses and deleted immediately afterwards."
+        "Data is only stored for analyses and deleted when the app is closed."
       ),
       shiny::p(
         style = "margin: 1; color: #888;",
-        "AG Damsbo | v", app_version(), " | ", shiny::tags$a("AGPLv3 license", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer")
+        shiny::tags$a("AG Damsbo", href = "https://andreas.gdamsbo.dk/", target = "_blank", rel = "noopener noreferrer")," | ", app_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer")
       ),
     )
   )

inst/apps/FreesearchR/ui.R

@@ -359,15 +359,13 @@ ui_elements <- list(
         data_visuals_ui("visuals"),
         shiny::tagList(
           bslib::nav_spacer(),
-          bslib::nav_panel(
+          bslib::nav_item(
-            title = "Notes",
+            # shiny::img(shiny::icon("book")),
-            shiny::fluidRow(
+            shiny::tags$a(
-              shiny::column(width = 2),
+              href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
-              shiny::column(
+              "Notes (external)",
-                width = 8,
+              target = "_blank",
-                shiny::markdown(readLines("www/notes_visuals.md")),
+              rel = "noopener noreferrer"
-                shiny::column(width = 2)
-              )
             )
           )
         )
@@ -537,11 +535,11 @@ ui <- bslib::page_fixed(
       style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
       shiny::p(
         style = "margin: 1",
-        "Data is only stored for analyses and deleted immediately afterwards."
+        "Data is only stored for analyses and deleted when the app is closed."
       ),
       shiny::p(
         style = "margin: 1; color: #888;",
-        "AG Damsbo | v", app_version(), " | ", shiny::tags$a("AGPLv3 license", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer")
+        shiny::tags$a("AG Damsbo", href = "https://andreas.gdamsbo.dk/", target = "_blank", rel = "noopener noreferrer")," | ", app_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer")
       ),
     )
   )

inst/apps/FreesearchR/www/intro.md

@@ -1,4 +1,4 @@
-# Welcome
+# Welcome <img style="float: right;" src="logo-text-white-250.png">
 
 This is the ***FreesearchR*** data analysis tool. We intend the ***FreesearchR*** to be a powerful and free tool for easy data evaluation and analysis at the hands of the clinician. If you need more advanced tools for regression models or plotting, you'll probably be better off using *R* or similar directly on your own machine.
 
@@ -6,7 +6,7 @@ By intention, this tool has been designed to be simple to use with a minimum of
 
 There are some simple steps to go through (see corresponding tabs in the top):
 
-1.  Import data (a spreadsheet/file on your machine, direct export from a REDCap server, or a local file provided with a package) to get started.
+1.  Import data to get started. This can be a spreadsheet/file on your machine, direct export from a REDCap server, sample data or data from a your local environment if run locally.
 
 1.  Data inspection and  modification (change variable classes, create new variables (categorical from numeric or time data, or completely new variables from the data)
 
@@ -20,10 +20,14 @@ There are some simple steps to go through (see corresponding tabs in the top):
     
     -   Plot regression analysis coefficients
 
-    -   Evaluation of model assumptions
+    -   Evaluate model assumptions
 
-1.  Export the the analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/) as well as the data with preserved metadata.
+1.  Export results
 
-The full [project documentation is here](https://agdamsbo.github.io/FreesearchR/) for documenting the project, functions, road map and more. If you're interested in the source code, then [everything is open and you are free to read, copy, modify and improve](https://github.com/agdamsbo/FreesearchR), and please let us know if you want to contribute!
+    -   Descriptive and regression analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/)
     
-Contributions can be reporting issues, suggesting new functionality, improving code or any other feedback. [It all goes here](https://github.com/agdamsbo/FreesearchR/issues).
+    -   Modified data with preserved metadata
+    
+    -   Code to recreate all steps locally
+
+The full [project documentation is here](https://agdamsbo.github.io/FreesearchR/) and all code used is [freely available to read, copy, modify and improve](https://github.com/agdamsbo/FreesearchR) under an [open source license](https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md)! Contributions are welcome and much appreciated and can be reporting issues, suggesting new functionality, improving code or any other feedback [here](https://github.com/agdamsbo/FreesearchR/issues).

inst/apps/FreesearchR/www/notes_visuals.md

@@ -1,11 +0,0 @@
-# Basic visualisations
-
-The goal of ***FreesearchR*** is to keep things simple. Visuals can get very complicated. We provide a selection of plots, that helps visualise typical clinical and will be enough for most use cases, and for publishing to most journals.
-
-If you want to go further, have a look at these sites with suggestions and sample code for data plotting:
-
--   [*R* Charts](https://r-charts.com/): Extensive gallery with great plots
-
--   [*R* Graph gallery](https://r-graph-gallery.com/): Another gallery with great graphs
-
--   [graphics principles](https://graphicsprinciples.github.io/): Easy to follow recommendations for clear visuals. 

man/data-plots.Rd

@@ -32,7 +32,7 @@ plot_ridge(data, x, y, z = NULL, ...)
 
 sankey_ready(data, pri, sec, numbers = "count", ...)
 
-plot_sankey(data, pri, sec, ter = NULL, color.group = "x", colors = NULL)
+plot_sankey(data, pri, sec, ter = NULL, color.group = "pri", colors = NULL)
 
 plot_scatter(data, pri, sec, ter = NULL)
 
@@ -103,6 +103,7 @@ mtcars |> plot_box(pri = "mpg", sec = "cyl", ter = "gear")
 mtcars |>
   default_parsing() |>
   plot_box(pri = "mpg", sec = "cyl", ter = "gear")
+mtcars |> plot_box_single("mpg")
 mtcars |> plot_box_single("mpg","cyl")
 mtcars |> plot_hbars(pri = "carb", sec = "cyl")
 mtcars |> plot_hbars(pri = "carb", sec = NULL)
@@ -121,8 +122,16 @@ data.frame(
   sankey_ready("first", "last")
 ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)))
 ds |> plot_sankey("first", "last")
-ds |> plot_sankey("first", "last", color.group = "y")
+ds |> plot_sankey("first", "last", color.group = "sec")
-ds |> plot_sankey("first", "last", z = "g", color.group = "y")
+ds |> plot_sankey("first", "last", ter = "g", color.group = "sec")
+mtcars |>
+  default_parsing() |>
+  plot_sankey("cyl", "gear", "am", color.group = "pri")
+## In this case, the last plot as the secondary variable in wrong order
+## Dont know why...
+mtcars |>
+  default_parsing() |>
+  plot_sankey("cyl", "gear", "vs", color.group = "pri")
 mtcars |> plot_scatter(pri = "mpg", sec = "wt")
 mtcars |> plot_violin(pri = "mpg", sec = "cyl", ter = "gear")
 }

man/plot_sankey_single.Rd

@@ -30,11 +30,15 @@ Beautiful sankey plot
 \examples{
 ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)))
 ds |> plot_sankey_single("first", "last")
-ds |> plot_sankey_single("first", "last", color.group = "y")
+ds |> plot_sankey_single("first", "last", color.group = "sec")
 data.frame(
   g = sample(LETTERS[1:2], 100, TRUE),
   first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)),
   last = sample(c(TRUE, FALSE, FALSE), 100, TRUE)
 ) |>
   plot_sankey_single("first", "last", color.group = "pri")
+mtcars |>
+  default_parsing() |>
+  str()
+plot_sankey_single("cyl", "vs", color.group = "pri")
 }

tests/testthat/test-data_plots.R

@@ -46,7 +46,7 @@ test_that("create_plot works", {
   p <- p_list[[1]] + ggplot2::labs(title = "Test plot")
 
   expect_equal(length(p_list), 2)
-  expect_true(ggplot2::is.ggplot(p))
+  expect_true(ggplot2::is_ggplot(p))
 
   # Includes helper functions
   #   wrap_plot_list
@@ -60,7 +60,7 @@ test_that("create_plot works", {
   )
 
   lapply(p_list, \(.x){
-    expect_true(ggplot2::is.ggplot(.x))
+    expect_true(ggplot2::is_ggplot(.x))
   })
 
   purrr::map2(p_list, list(11, 11), \(.x, .y){

vignettes/data-types.Rmd

@@ -12,6 +12,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
+options(rmarkdown.html_vignette.check_title = FALSE)
 ```
 
 ```{r setup}

vignettes/session.Rmd

@@ -0,0 +1,35 @@
+---
+title: "Session info"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{session}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+options(rmarkdown.html_vignette.check_title = FALSE)
+```
+
+```{r setup}
+library(FreesearchR)
+```
+
+This is the session info on the primary build machine. Inspect loaded packages and the latest build info.
+
+## Platform info
+
+```{r}
+FreesearchR:::session_data$platform |> knitr::kable()
+```
+
+
+## Libraries
+
+```{r}
+FreesearchR:::session_data$libs|> knitr::kable()
+```

vignettes/visuals.Rmd

@@ -0,0 +1,55 @@
+---
+title: "On visuals"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{visuals}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+options(rmarkdown.html_vignette.check_title = FALSE)
+```
+
+```{r setup}
+library(FreesearchR)
+```
+
+## Basic visualisations
+
+The goal of ***FreesearchR*** is to keep things simple. Visuals can get very complicated. We provide a selection of plots, that helps visualise typical clinical and will be enough for most use cases, and for publishing to most journals.
+
+If you want to go further, have a look at these sites with suggestions and sample code for data plotting:
+
+-   [*R* Charts](https://r-charts.com/): Extensive gallery with great plots
+
+-   [*R* Graph gallery](https://r-graph-gallery.com/): Another gallery with great graphs
+
+-   [graphics principles](https://graphicsprinciples.github.io/): Easy to follow recommendations for clear visuals. 
+
+
+### Available plots
+
+Below are the available plot types listed.
+
+```{r echo = FALSE, eval = TRUE}
+c("continuous", "dichotomous", "categorical") |> 
+  lapply(\(.x){
+    dplyr::bind_cols(
+      dplyr::tibble("Data type"=.x),
+      supported_plots() |> 
+      lapply(\(.y){
+        if (.x %in% .y$primary.type){
+          .y[c("descr","note")]|> dplyr::bind_cols()
+        }
+})|> 
+  dplyr::bind_rows() |> 
+  setNames(c("Plot type","Description")))
+  }) |> 
+  dplyr::bind_rows() |> 
+  knitr::kable()
+```