CITATION.cff

@@ -9,7 +9,7 @@ type: software
 license: AGPL-3.0-or-later
 title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers
   with publication ready output'
-version: 25.5.1
+version: 25.4.5
 doi: 10.5281/zenodo.14527429
 abstract: Easily evaluate and analysis clinical health data in your browser on a server
   or on your own device. Import data from multiple sources, summarise, modify and

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: FreesearchR
 Title: A free and open-source browser based data analysis tool for researchers with publication ready output
-Version: 25.5.1
+Version: 25.4.5
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154")),

NEWS.md

@@ -1,13 +1,3 @@
-# FreesearchR 25.5.1
-
-- *FIX*: correct export of single variable plot.
-
-- *NEW*: Include app version in report for reference.
-
-- *NEW*: Show progress on connecting to a REDCap database.
-
-- *FIX*: Data import code export.
-
 # FreesearchR 25.4.5
 
 - *BUG*: Regression results and code not returned correctly

R/app_version.R

@@ -1 +1 @@
-app_version <- function()'25.5.1'
+app_version <- function()'v25.4.5.250430'

R/data_plots.R

@@ -45,23 +45,15 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
           title = "Download",
           icon = bsicons::bs_icon("download"),
           shinyWidgets::noUiSliderInput(
-            inputId = ns("height_slide"),
+            inputId = ns("height"),
             label = "Plot height (mm)",
             min = 50,
             max = 300,
             value = 100,
             step = 1,
             format = shinyWidgets::wNumbFormat(decimals = 0),
-            color = datamods:::get_primary_color(),
+            color = datamods:::get_primary_color()
-            inline = TRUE
           ),
-          # shiny::numericInput(
-          #   inputId = ns("height_numeric"),
-          #   label = "Plot height (mm)",
-          #   min = 50,
-          #   max = 300,
-          #   value = 100
-          # ),
           shinyWidgets::noUiSliderInput(
             inputId = ns("width"),
             label = "Plot width (mm)",
@@ -380,32 +372,17 @@ data_visuals_server <- function(id,
         }
       })
 
-      # shiny::observeEvent(input$height_numeric, {
-      #   shinyWidgets::updateNoUiSliderInput(session, ns("height_slide"), value = input$height_numeric)
-      # }, ignoreInit = TRUE)
-      # shiny::observeEvent(input$height_slide, {
-      #   shiny::updateNumericInput(session, ns("height_numeric"), value = input$height_slide)
-      # }, ignoreInit = TRUE)
-
-
       output$download_plot <- shiny::downloadHandler(
         filename = shiny::reactive({
           paste0("plot.", input$plot_type)
         }),
         content = function(file) {
-          if (inherits(rv$plot,"patchwork")){
-            plot <- rv$plot
-          } else {
-            plot <- rv$plot[[1]]
-
-          }
-          # browser()
           shiny::withProgress(message = "Drawing the plot. Hold on for a moment..", {
             ggplot2::ggsave(
               filename = file,
-              plot = plot,
+              plot = rv$plot,
               width = input$width,
-              height = input$height_slide,
+              height = input$height,
               dpi = 300,
               units = "mm", scale = 2
             )
@@ -540,8 +517,8 @@ supported_plots <- function() {
       fun = "plot_euler",
       descr = "Euler diagram",
       note = "Generate area-proportional Euler diagrams to display set relationships",
-      primary.type = c("dichotomous", "categorical"),
+      primary.type = "dichotomous",
-      secondary.type = c("dichotomous", "categorical"),
+      secondary.type = "dichotomous",
       secondary.multi = TRUE,
       secondary.max = 4,
       tertiary.type = c("dichotomous", "categorical"),

R/helpers.R

@@ -65,7 +65,7 @@ write_rmd <- function(data, ...) {
   ## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041
   ## Outputs to the same as the .qmd file
   rmarkdown::render(
-    params = list(data.file = "web_data.rds",version=app_version()),
+    params = list(data.file = "web_data.rds"),
     # execute_params = list(data.file = temp),
     ...
   )

R/hosted_version.R

@@ -1 +0,0 @@
-hosted_version <- function()'v25.5.1-250505'

R/plot_euler.R

@@ -109,12 +109,6 @@ plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
 #' ) |> plot_euler_single()
 #' mtcars[c("vs", "am")] |> plot_euler_single()
 plot_euler_single <- function(data) {
-  # if (any("categorical" %in% data_type(data))){
-  #   shape <- "ellipse"
-  # } else {
-  #   shape <- "circle"
-  # }
-
   data |>
     ggeulerr(shape = "circle") +
     ggplot2::theme_void() +

R/redcap_read_shiny_module.R

@@ -112,7 +112,7 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
           tags$p(phosphoricons::ph("info", weight = "bold"), "Please specify data to download, then press 'Import'.")
         ),
         dismissible = TRUE
-      ) # ,
+      )#,
       ## TODO: Use busy indicator like on download to have button activate/deactivate
       # bslib::input_task_button(
       #   id = ns("data_import"),
@@ -200,9 +200,7 @@ m_redcap_readServer <- function(id) {
             )
 
             # browser()
-            shiny::withProgress({
+            imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters), silent = TRUE)
-              imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters), silent = TRUE)
-            },message = paste("Connecting to",data_rv$uri))
 
             ## TODO: Simplify error messages
             if (inherits(imported, "try-error") || NROW(imported) < 1 || ifelse(is.list(imported), !isTRUE(imported$success), FALSE)) {
@@ -229,10 +227,8 @@ m_redcap_readServer <- function(id) {
                 include_data_alert(
                   see_data_text = "Click to see data dictionary",
                   dataIdName = "see_data",
-                  extra = tags$p(
+                  extra = tags$p(tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
-                    tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
+                                 glue::glue("The {data_rv$info$project_title} project is loaded.")),
-                    glue::glue("The {data_rv$info$project_title} project is loaded.")
-                  ),
                   btn_show_data = TRUE
                 )
               )

SESSION.md

@@ -11,11 +11,11 @@
 |collate     |en_US.UTF-8                                |
 |ctype       |en_US.UTF-8                                |
 |tz          |Europe/Copenhagen                          |
-|date        |2025-05-05                                 |
+|date        |2025-04-30                                 |
 |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 |25.5.1.250505                              |
+|FreesearchR |25.4.5.250430                              |
                                                                                 
                                                                                 
 --------------------------------------------------------------------------------
@@ -24,8 +24,10 @@
 |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) |
+|base64enc     |0.1-3         |2015-07-28 |CRAN (R 4.4.1) |
 |bayestestR    |0.15.3        |2025-04-28 |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) |
@@ -35,14 +37,21 @@
 |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) |
+|cards         |0.6.0         |2025-04-11 |CRAN (R 4.4.1) |
 |cellranger    |1.1.0         |2016-07-27 |CRAN (R 4.4.0) |
+|cffr          |1.2.0         |2025-01-25 |CRAN (R 4.4.1) |
+|checkmate     |2.3.2         |2024-07-29 |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           |3.6.5         |2025-04-23 |CRAN (R 4.4.1) |
+|cluster       |2.1.8.1       |2025-03-12 |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) |
+|curl          |6.2.2         |2025-03-24 |CRAN (R 4.4.1) |
 |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) |
@@ -61,32 +70,47 @@
 |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) |
+|foreign       |0.8-90        |2025-03-31 |CRAN (R 4.4.1) |
+|Formula       |1.2-5         |2023-02-24 |CRAN (R 4.4.1) |
 |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) |
+|ggcorrplot    |0.1.4.1       |2023-09-05 |CRAN (R 4.4.0) |
 |ggplot2       |3.5.2         |2025-04-09 |CRAN (R 4.4.1) |
+|ggstats       |0.9.0         |2025-03-10 |CRAN (R 4.4.1) |
+|gh            |1.4.1         |2024-03-28 |CRAN (R 4.4.0) |
+|gitcreds      |0.1.2         |2022-09-08 |CRAN (R 4.4.1) |
 |glue          |1.8.0         |2024-09-30 |CRAN (R 4.4.1) |
+|gridExtra     |2.3           |2017-09-09 |CRAN (R 4.4.1) |
 |gt            |1.0.0         |2025-04-05 |CRAN (R 4.4.1) |
 |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) |
+|Hmisc         |5.2-3         |2025-03-16 |CRAN (R 4.4.1) |
 |hms           |1.1.3         |2023-03-21 |CRAN (R 4.4.0) |
+|htmlTable     |2.4.3         |2024-07-21 |CRAN (R 4.4.0) |
 |htmltools     |0.5.8.1       |2024-04-04 |CRAN (R 4.4.1) |
 |htmlwidgets   |1.6.4         |2023-12-06 |CRAN (R 4.4.0) |
 |httpuv        |1.6.16        |2025-04-16 |CRAN (R 4.4.1) |
+|httr2         |1.1.2         |2025-03-26 |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) |
+|jsonvalidate  |1.5.0         |2025-02-07 |CRAN (R 4.4.1) |
 |KernSmooth    |2.23-26       |2025-01-01 |CRAN (R 4.4.1) |
 |keyring       |1.3.2         |2023-12-11 |CRAN (R 4.4.0) |
 |knitr         |1.50          |2025-03-16 |CRAN (R 4.4.1) |
 |labeling      |0.4.3         |2023-08-29 |CRAN (R 4.4.1) |
+|labelled      |2.14.0        |2025-01-08 |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) |
+|litedown      |0.7           |2025-04-08 |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) |
+|markdown      |2.0           |2025-03-23 |CRAN (R 4.4.1) |
 |MASS          |7.3-65        |2025-02-28 |CRAN (R 4.4.1) |
 |Matrix        |1.7-3         |2025-03-11 |CRAN (R 4.4.1) |
 |memoise       |2.0.1         |2021-11-26 |CRAN (R 4.4.0) |
@@ -96,6 +120,8 @@
 |modelbased    |0.10.0        |2025-03-10 |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) |
+|nnet          |7.3-20        |2025-01-01 |CRAN (R 4.4.1) |
+|openssl       |2.3.2         |2025-02-03 |CRAN (R 4.4.1) |
 |openxlsx2     |1.15          |2025-04-25 |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) |
@@ -105,6 +131,7 @@
 |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) |
+|plyr          |1.8.9         |2023-10-02 |CRAN (R 4.4.1) |
 |processx      |3.8.6         |2025-02-21 |CRAN (R 4.4.1) |
 |profvis       |0.4.0         |2024-09-20 |CRAN (R 4.4.1) |
 |promises      |1.3.2         |2024-11-28 |CRAN (R 4.4.1) |
@@ -112,9 +139,13 @@
 |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) |
+|R.cache       |0.16.0        |2022-07-21 |CRAN (R 4.4.0) |
+|R.methodsS3   |1.8.2         |2022-06-13 |CRAN (R 4.4.1) |
+|R.oo          |1.27.0        |2024-11-01 |CRAN (R 4.4.1) |
+|R.utils       |2.13.0        |2025-02-24 |CRAN (R 4.4.1) |
 |R6            |2.6.1         |2025-02-15 |CRAN (R 4.4.1) |
 |ragg          |1.4.0         |2025-04-10 |CRAN (R 4.4.1) |
-|rankinPlot    |1.1.0         |2023-01-30 |CRAN (R 4.4.0) |
+|rappdirs      |0.3.3         |2021-01-31 |CRAN (R 4.4.1) |
 |rbibutils     |2.3           |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) |
@@ -127,12 +158,13 @@
 |REDCapR       |1.4.0         |2025-01-11 |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) |
-|rempsyc       |0.1.9         |2025-02-01 |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) |
+|reshape2      |1.4.4         |2020-04-09 |CRAN (R 4.4.0) |
 |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) |
+|rpart         |4.1.24        |2025-01-07 |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) |
@@ -145,6 +177,9 @@
 |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) |
+|stringr       |1.5.1         |2023-11-14 |CRAN (R 4.4.0) |
+|styler        |1.10.3        |2024-04-07 |CRAN (R 4.4.0) |
+|sys           |3.4.3         |2024-10-04 |CRAN (R 4.4.1) |
 |systemfonts   |1.2.2         |2025-04-04 |CRAN (R 4.4.1) |
 |textshaping   |1.0.0         |2025-01-20 |CRAN (R 4.4.1) |
 |tibble        |3.2.1         |2023-03-20 |CRAN (R 4.4.0) |
@@ -154,8 +189,8 @@
 |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) |
+|V8            |6.0.3         |2025-03-26 |CRAN (R 4.4.1) |
 |vctrs         |0.6.5         |2023-12-01 |CRAN (R 4.4.0) |
-|viridisLite   |0.4.2         |2023-05-02 |CRAN (R 4.4.1) |
 |vroom         |1.6.5         |2023-12-05 |CRAN (R 4.4.0) |
 |withr         |3.0.2         |2024-10-28 |CRAN (R 4.4.1) |
 |writexl       |1.5.4         |2025-04-15 |CRAN (R 4.4.1) |

inst/apps/FreesearchR/app.R

@@ -10,7 +10,7 @@
 #### Current file: /Users/au301842/FreesearchR/R//app_version.R 
 ########
 
-app_version <- function()'25.5.1'
+app_version <- function()'v25.4.4.250430'
 
 
 ########
@@ -1619,23 +1619,15 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
           title = "Download",
           icon = bsicons::bs_icon("download"),
           shinyWidgets::noUiSliderInput(
-            inputId = ns("height_slide"),
+            inputId = ns("height"),
             label = "Plot height (mm)",
             min = 50,
             max = 300,
             value = 100,
             step = 1,
             format = shinyWidgets::wNumbFormat(decimals = 0),
-            color = datamods:::get_primary_color(),
+            color = datamods:::get_primary_color()
-            inline = TRUE
           ),
-          # shiny::numericInput(
-          #   inputId = ns("height_numeric"),
-          #   label = "Plot height (mm)",
-          #   min = 50,
-          #   max = 300,
-          #   value = 100
-          # ),
           shinyWidgets::noUiSliderInput(
             inputId = ns("width"),
             label = "Plot width (mm)",
@@ -1954,32 +1946,17 @@ data_visuals_server <- function(id,
         }
       })
 
-      # shiny::observeEvent(input$height_numeric, {
-      #   shinyWidgets::updateNoUiSliderInput(session, ns("height_slide"), value = input$height_numeric)
-      # }, ignoreInit = TRUE)
-      # shiny::observeEvent(input$height_slide, {
-      #   shiny::updateNumericInput(session, ns("height_numeric"), value = input$height_slide)
-      # }, ignoreInit = TRUE)
-
-
       output$download_plot <- shiny::downloadHandler(
         filename = shiny::reactive({
           paste0("plot.", input$plot_type)
         }),
         content = function(file) {
-          if (inherits(rv$plot,"patchwork")){
-            plot <- rv$plot
-          } else {
-            plot <- rv$plot[[1]]
-
-          }
-          # browser()
           shiny::withProgress(message = "Drawing the plot. Hold on for a moment..", {
             ggplot2::ggsave(
               filename = file,
-              plot = plot,
+              plot = rv$plot,
               width = input$width,
-              height = input$height_slide,
+              height = input$height,
               dpi = 300,
               units = "mm", scale = 2
             )
@@ -2114,8 +2091,8 @@ supported_plots <- function() {
       fun = "plot_euler",
       descr = "Euler diagram",
       note = "Generate area-proportional Euler diagrams to display set relationships",
-      primary.type = c("dichotomous", "categorical"),
+      primary.type = "dichotomous",
-      secondary.type = c("dichotomous", "categorical"),
+      secondary.type = "dichotomous",
       secondary.multi = TRUE,
       secondary.max = 4,
       tertiary.type = c("dichotomous", "categorical"),
@@ -3361,7 +3338,7 @@ write_rmd <- function(data, ...) {
   ## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041
   ## Outputs to the same as the .qmd file
   rmarkdown::render(
-    params = list(data.file = "web_data.rds",version=app_version()),
+    params = list(data.file = "web_data.rds"),
     # execute_params = list(data.file = temp),
     ...
   )
@@ -3950,13 +3927,6 @@ is_identical_to_previous <- function(data, no.name = TRUE) {
 }
 
 
-########
-#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R 
-########
-
-hosted_version <- function()'v25.5.1-250505'
-
-
 ########
 #### Current file: /Users/au301842/FreesearchR/R//html_dependency_freesearchr.R 
 ########
@@ -4814,12 +4784,6 @@ plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
 #' ) |> plot_euler_single()
 #' mtcars[c("vs", "am")] |> plot_euler_single()
 plot_euler_single <- function(data) {
-  # if (any("categorical" %in% data_type(data))){
-  #   shape <- "ellipse"
-  # } else {
-  #   shape <- "circle"
-  # }
-
   data |>
     ggeulerr(shape = "circle") +
     ggplot2::theme_void() +
@@ -5477,7 +5441,7 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
           tags$p(phosphoricons::ph("info", weight = "bold"), "Please specify data to download, then press 'Import'.")
         ),
         dismissible = TRUE
-      ) # ,
+      )#,
       ## TODO: Use busy indicator like on download to have button activate/deactivate
       # bslib::input_task_button(
       #   id = ns("data_import"),
@@ -5565,9 +5529,7 @@ m_redcap_readServer <- function(id) {
             )
 
             # browser()
-            shiny::withProgress({
+            imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters), silent = TRUE)
-              imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters), silent = TRUE)
-            },message = paste("Connecting to",data_rv$uri))
 
             ## TODO: Simplify error messages
             if (inherits(imported, "try-error") || NROW(imported) < 1 || ifelse(is.list(imported), !isTRUE(imported$success), FALSE)) {
@@ -5594,10 +5556,8 @@ m_redcap_readServer <- function(id) {
                 include_data_alert(
                   see_data_text = "Click to see data dictionary",
                   dataIdName = "see_data",
-                  extra = tags$p(
+                  extra = tags$p(tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
-                    tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
+                                 glue::glue("The {data_rv$info$project_title} project is loaded.")),
-                    glue::glue("The {data_rv$info$project_title} project is loaded.")
-                  ),
                   btn_show_data = TRUE
                 )
               )
@@ -7561,8 +7521,7 @@ regression_server <- function(id,
 
       shiny::observeEvent(
         list(
-          data_r(),
+          data_r()
-          regression_vars()
         ),
         {
           rv$list$regression$tables <- NULL
@@ -9438,8 +9397,8 @@ ui_elements <- list(
               width = 9,
               shiny::tags$p(
                 shiny::markdown("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."),
-                shiny::markdown("There are more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."),
+                shiny::markdown("There are also more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."),
-                shiny::markdown("Please note that data modifications are applied before any filtering.")
+                shiny::markdown("Please note that data modifications are applied before any data or variable filtering is applied.")
               )
             )
           ),
@@ -9728,28 +9687,14 @@ ui_elements <- list(
     ),
   ##############################################################################
   #########
-  #########  Feedback link
+  #########  Documentation panel
-  #########
-  ##############################################################################
-  "feedback" = bslib::nav_item(
-    # shiny::img(shiny::icon("book")),
-    shiny::tags$a(
-      href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8",
-      "Feedback",shiny::icon("arrow-up-right-from-square"),
-      target = "_blank",
-      rel = "noopener noreferrer"
-    )
-  ),
-  ##############################################################################
-  #########
-  #########  Documentation link
   #########
   ##############################################################################
   "docs" = bslib::nav_item(
     # shiny::img(shiny::icon("book")),
     shiny::tags$a(
       href = "https://agdamsbo.github.io/FreesearchR/",
-      "Docs",shiny::icon("arrow-up-right-from-square"),
+      "Docs (external)",
       target = "_blank",
       rel = "noopener noreferrer"
     )
@@ -9791,7 +9736,6 @@ ui <- bslib::page_fixed(
     ui_elements$analyze,
     ui_elements$download,
     bslib::nav_spacer(),
-    ui_elements$feedback,
     ui_elements$docs,
     fillable = FALSE,
     footer = shiny::tags$footer(
@@ -9802,7 +9746,7 @@ ui <- bslib::page_fixed(
       ),
       shiny::p(
         style = "margin: 1; color: #888;",
-        shiny::tags$a("Docs", href = "https://agdamsbo.github.io/FreesearchR/", target = "_blank", rel = "noopener noreferrer")," | ", hosted_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"), " | ", shiny::tags$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer")
+        shiny::tags$a("Docs", href = "https://agdamsbo.github.io/FreesearchR/", 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"), " | ", shiny::tags$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer")
       ),
     )
   )
@@ -9829,7 +9773,9 @@ library(quarto)
 library(here)
 library(broom)
 library(broom.helpers)
+# library(REDCapCAST)
 library(easystats)
+# library(esquisse)
 library(patchwork)
 library(DHARMa)
 library(apexcharter)
@@ -9840,17 +9786,32 @@ library(shinyWidgets)
 library(DT)
 library(data.table)
 library(gtsummary)
+# library(FreesearchR)
+
+# source("functions.R")
 
 data(starwars)
 data(mtcars)
+mtcars_date <- mtcars |> append_column(as.Date(sample(1:365, nrow(mtcars))), "rand_dates")
+mtcars_date$date <- as.Date(sample(seq_len(365), nrow(mtcars)))
 data(trial)
 
 
+# light <- custom_theme()
+#
+# dark <- custom_theme(bg = "#000",fg="#fff")
+
+
 server <- function(input, output, session) {
   ## Listing files in www in session start to keep when ending and removing
   ## everything else.
   files.to.keep <- list.files("www/")
 
+  output$docs_file <- shiny::renderUI({
+    # shiny::includeHTML("www/docs.html")
+    shiny::HTML(readLines("www/docs.html"))
+  })
+
   ##############################################################################
   #########
   #########  Night mode (just very popular, not really needed)
@@ -10293,12 +10254,10 @@ server <- function(input, output, session) {
   # })
 
   output$code_import <- shiny::renderUI({
-    shiny::req(rv$code$import)
     prismCodeBlock(paste0("#Data import\n", rv$code$import))
   })
 
-  output$code_format <- shiny::renderUI({
+  output$code_import <- shiny::renderUI({
-    shiny::req(rv$code$format)
     prismCodeBlock(paste0("#Data import formatting\n", rv$code$format))
   })
 
@@ -10521,11 +10480,20 @@ server <- function(input, output, session) {
       paste0("report.", input$output_type)
     }),
     content = function(file, type = input$output_type) {
+      # browser()
+      # shiny::req(rv$list$regression)
       ## Notification is not progressing
       ## Presumably due to missing
+      # browser()
       # Simplified for .rmd output attempt
       format <- ifelse(type == "docx", "word_document", "odt_document")
 
+      # browser()
+      # if (shiny::is.reactive(rv$regression)){
+      #   rv$list$regression <- rv$regression()
+      # }
+
+      # rv$list$regression <- rv$regression()
       rv$list$regression <- rv$regression()
 
       shiny::withProgress(message = "Generating the report. Hold on for a moment..", {

inst/apps/FreesearchR/www/intro.md

@@ -30,4 +30,4 @@ Here is a brief summary of the functions:
     
     -   Code to recreate all steps locally
 
-The full [project documentation is here](https://agdamsbo.github.io/FreesearchR/) where you'll find detailed description of the app and link to the source code! If you want to [share feedback, please follow this link to a simple survey](https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8).
+The full [project documentation is here](https://agdamsbo.github.io/FreesearchR/) where you'll find detailed description of the app and link to the source code! If you want to [share feedback, please follow this link to a simple survey](https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8), or share on [GitHub](https://github.com/agdamsbo/FreesearchR/issues).

inst/apps/FreesearchR/www/report.rmd

@@ -6,7 +6,6 @@ author: FreesearchR data analysis tool
 toc: false
 params:
   data.file: NA
-  version: NA
 ---
 
 ```{r setup, echo = FALSE}
@@ -47,7 +46,7 @@ Research should be free and open with easy access for all. The FreesearchR tool
 
 ## Methods
 
-Analyses were conducted using the *FreesearchR* data analysis web-tool version `r params$version` based on *R* version 4.4.1.
+Analyses were conducted in the *FreesearchR* data analysis web-tool based on R version 4.4.1.
 
 ## Results