2025-09-12 18:09:39 +02:00
12 changed files with 51 additions and 143 deletions
--- a/.Rbuildignore
+++ b/.Rbuildignore
@ -14,6 +14,6 @@
 ^data-raw$
 ^CITATION\.cff$
 ^app_hosted$
-^app*$
+^app$
 ^page$
 ^demo$
--- a/.gitignore
+++ b/.gitignore
@ -10,8 +10,7 @@ inst/shiny-examples/casting/functions.R
 functions.R
 docs
 inst/doc
-app_dev
-app_stable
+app_hosted
 app
 page
 demo
--- a/CITATION.cff
+++ b/CITATION.cff
@ -9,11 +9,8 @@ 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: 25.5.2
+version: 25.5.1
 doi: 10.5281/zenodo.14527429
-identifiers:
- type: url
-  value: https://app.FreesearchR.org/
 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
  visualise data and export key metrics and regression analysis results in a publication
@ -977,19 +974,6 @@ references:
    email: alboukadel.kassambara@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.ggcorrplot
- type: software
-  title: shinyjs
-  abstract: 'shinyjs: Easily Improve the User Experience of Your Shiny Apps in Seconds'
-  notes: Imports
-  url: https://deanattali.com/shinyjs/
-  repository: https://CRAN.R-project.org/package=shinyjs
-  authors:
-  - family-names: Attali
-    given-names: Dean
-    email: daattali@gmail.com
-    orcid: https://orcid.org/0000-0002-5645-3493
-  year: '2025'
-  doi: 10.32614/CRAN.package.shinyjs
 - type: software
  title: styler
  abstract: 'styler: Non-Invasive Pretty Printing of R Code'
--- a/7
+++ b/7
@ -1,6 +1,6 @@
 Package: FreesearchR
 Title: A free and open-source browser based data analysis tool for researchers with publication ready output
-Version: 25.5.2
+Version: 25.5.1
 Authors@R: c(
    person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-7559-1154")),
@ -62,8 +62,7 @@ Imports:
    eulerr,
    ggforce,
    RcppArmadillo,
-    ggcorrplot,
-    shinyjs
+    ggcorrplot
 Suggests: 
    styler,
    devtools,
@ -79,7 +78,7 @@ Suggests:
    shinytest,
    covr,
    cffr
-URL: https://github.com/agdamsbo/FreesearchR, https://agdamsbo.github.io/FreesearchR/, https://app.FreesearchR.org/
+URL: https://github.com/agdamsbo/FreesearchR, https://agdamsbo.github.io/FreesearchR/
 BugReports: https://github.com/agdamsbo/FreesearchR/issues
 VignetteBuilder: knitr
 Config/testthat/edition: 3
--- a/NEWS.md
+++ b/NEWS.md
@ -1,11 +1,3 @@
-# FreesearchR 25.5.2
-
- *FIX*: correct export of plots. The solution in the last version broke more than it solved.
-
- *NEW*: added simple loading animation.
-
-A privately hosted version is now live on app.freesearchr.org. For now, it is hosted on Hetzner with Yunohost.
-
 # FreesearchR 25.5.1

 - *FIX*: correct export of single variable plot.
--- a/R/app_version.R
+++ b/R/app_version.R
@ -1 +1 @@
-app_version <- function()'25.5.2'
+app_version <- function()'25.5.1'
--- a/R/data_plots.R
+++ b/R/data_plots.R
@ -395,9 +395,7 @@ data_visuals_server <- function(id,
        content = function(file) {
          if (inherits(rv$plot,"patchwork")){
            plot <- rv$plot
-          } else if (inherits(rv$plot,"ggplot")){
-            plot <- rv$plot
-          }else {
+          } else {
            plot <- rv$plot[[1]]

          }
@ -423,6 +421,7 @@ data_visuals_server <- function(id,
  )
 }

+
 #' Select all from vector but
 #'
 #' @param data vector
--- a/R/hosted_version.R
+++ b/R/hosted_version.R
@ -1 +1 @@
-hosted_version <- function()'v25.5.2-250508'
+hosted_version <- function()'v25.5.1-250507'
--- a/R/sysdata.rda
+++ b/R/sysdata.rda
--- a/SESSION.md
+++ b/SESSION.md
@ -11,11 +11,11 @@
 |collate     |en_US.UTF-8                                |
 |ctype       |en_US.UTF-8                                |
 |tz          |Europe/Copenhagen                          |
-|date        |2025-05-08                                 |
+|date        |2025-05-05                                 |
 |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 |25.5.2.250508                              |
+|FreesearchR |25.5.1.250505                              |
                                                                                
                                                                                
 --------------------------------------------------------------------------------
@ -24,7 +24,6 @@
 |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    |0.15.3        |2025-04-28 |CRAN (R 4.4.1) |
@ -37,7 +36,6 @@
 |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) |
-|cffr          |1.2.0         |2025-01-25 |CRAN (R 4.4.1) |
 |class         |7.3-23        |2025-01-01 |CRAN (R 4.4.1) |
 |classInt      |0.4-11        |2025-01-08 |CRAN (R 4.4.1) |
 |cli           |3.6.5         |2025-04-23 |CRAN (R 4.4.1) |
@ -45,7 +43,6 @@
 |correlation   |0.8.7         |2025-03-03 |CRAN (R 4.4.1) |
 |crayon        |1.5.3         |2024-06-20 |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) |
@ -81,10 +78,10 @@
 |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) |
 |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) |
@ -99,9 +96,7 @@
 |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) |
-|openssl       |2.3.2         |2025-02-03 |CRAN (R 4.4.1) |
 |openxlsx2     |1.15          |2025-04-25 |CRAN (R 4.4.1) |
-|pak           |0.8.0.2       |2025-04-08 |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) |
@ -117,11 +112,9 @@
 |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) |
 |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) |
@ -134,6 +127,7 @@
 |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) |
 |rio           |1.2.3         |2024-09-25 |CRAN (R 4.4.1) |
@ -148,11 +142,11 @@
 |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) |
-|shinyjs       |2.1.0         |2021-12-23 |CRAN (R 4.4.0) |
 |shinyTime     |1.0.3         |2022-08-19 |CRAN (R 4.4.0) |
 |shinyWidgets  |0.9.0         |2025-02-21 |CRAN (R 4.4.1) |
 |stringi       |1.8.7         |2025-03-27 |CRAN (R 4.4.1) |
-|styler        |1.10.3        |2024-04-07 |CRAN (R 4.4.0) |
+|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) |
 |tidyr         |1.3.1         |2024-01-24 |CRAN (R 4.4.1) |
 |tidyselect    |1.2.1         |2024-03-11 |CRAN (R 4.4.0) |
@ -160,8 +154,8 @@
 |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) |
--- a/inst/apps/FreesearchR/app.R
+++ b/inst/apps/FreesearchR/app.R
@ -10,7 +10,7 @@
 #### Current file: /Users/au301842/FreesearchR/R//app_version.R 
 ########

-app_version <- function()'25.5.2'
+app_version <- function()'25.5.1'


 ########
@ -1969,9 +1969,7 @@ data_visuals_server <- function(id,
        content = function(file) {
          if (inherits(rv$plot,"patchwork")){
            plot <- rv$plot
-          } else if (inherits(rv$plot,"ggplot")){
-            plot <- rv$plot
-          }else {
+          } else {
            plot <- rv$plot[[1]]

          }
@ -1997,6 +1995,7 @@ data_visuals_server <- function(id,
  )
 }

+
 #' Select all from vector but
 #'
 #' @param data vector
@ -3955,7 +3954,7 @@ is_identical_to_previous <- function(data, no.name = TRUE) {
 #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R 
 ########

-hosted_version <- function()'v25.5.2-250508'
+hosted_version <- function()'v25.5.1-250507'


 ########
@ -9398,12 +9397,7 @@ ui_elements <- list(
          fluidRow(
            shiny::column(
              width = 9,
-              data_summary_ui(id = "data_summary"),
-              shiny::br(),
-              shiny::br(),
-              shiny::br(),
-              shiny::br(),
-              shiny::br()
+              data_summary_ui(id = "data_summary")
            ),
            shiny::column(
              width = 3,
@ -9741,7 +9735,7 @@ ui_elements <- list(
    # shiny::img(shiny::icon("book")),
    shiny::tags$a(
      href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8",
-      "Feedback", shiny::icon("arrow-up-right-from-square"),
+      "Feedback",shiny::icon("arrow-up-right-from-square"),
      target = "_blank",
      rel = "noopener noreferrer"
    )
@ -9755,7 +9749,7 @@ ui_elements <- list(
    # shiny::img(shiny::icon("book")),
    shiny::tags$a(
      href = "https://agdamsbo.github.io/FreesearchR/",
-      "Docs", shiny::icon("arrow-up-right-from-square"),
+      "Docs",shiny::icon("arrow-up-right-from-square"),
      target = "_blank",
      rel = "noopener noreferrer"
    )
@ -9783,49 +9777,39 @@ ui <- bslib::page_fixed(
  header_include(),
  ## This adds the actual favicon
  ## png and ico versions are kept for compatibility
-  shiny::tags$head(tags$link(rel = "shortcut icon", href = "favicon.svg")),
+  shiny::tags$head(tags$link(rel="shortcut icon", href="favicon.svg")),
  title = "FreesearchR",
  theme = light,
  shiny::useBusyIndicators(),
-  shinyjs::useShinyjs(),
-  shiny::div(
-    id = "loading_page",
-    # shiny::h1("Loading the FreesearchR app..."),
-    shinybusy::add_busy_spinner(position = "full-page")
-  ),
-  shinyjs::hidden(
-    shiny::div(
-      id = "main_content",
-      bslib::page_navbar(
-        id = "main_panel",
-        ui_elements$home,
-        ui_elements$import,
-        ui_elements$overview,
-        ui_elements$describe,
-        ui_elements$visuals,
-        ui_elements$analyze,
-        ui_elements$download,
-        bslib::nav_spacer(),
-        ui_elements$feedback,
-        ui_elements$docs,
-        fillable = FALSE,
-        footer = shiny::tags$footer(
-          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 when the app is closed.", shiny::markdown("Consider [running ***FreesearchR*** locally](https://agdamsbo.github.io/FreesearchR/#run-locally-on-your-own-machine) if working with sensitive data.")
-          ),
-          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")
-          ),
-        )
-      )
+  bslib::page_navbar(
+    id = "main_panel",
+    ui_elements$home,
+    ui_elements$import,
+    ui_elements$overview,
+    ui_elements$describe,
+    ui_elements$visuals,
+    ui_elements$analyze,
+    ui_elements$download,
+    bslib::nav_spacer(),
+    ui_elements$feedback,
+    ui_elements$docs,
+    fillable = FALSE,
+    footer = shiny::tags$footer(
+      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 when the app is closed.", shiny::markdown("Consider [running ***FreesearchR*** locally](https://agdamsbo.github.io/FreesearchR/#run-locally-on-your-own-machine) if working with sensitive data.")
+      ),
+      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")
+      ),
    )
  )
 )


+
 ########
 #### Current file: /Users/au301842/FreesearchR/app/server.R 
 ########
@ -9856,26 +9840,17 @@ library(shinyWidgets)
 library(DT)
 library(data.table)
 library(gtsummary)
-library(shinyjs)

 data(starwars)
 data(mtcars)
 data(trial)

-load_data <- function() {
-  Sys.sleep(1)
-  hide("loading_page")
-  show("main_content")
-}
-

 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/")

-  load_data()
-
  ##############################################################################
  #########
  #########  Night mode (just very popular, not really needed)
--- a/renv.lock
+++ b/renv.lock
@ -7930,40 +7930,6 @@
      "Maintainer": "Victor Perrier <victor.perrier@dreamrs.fr>",
      "Repository": "CRAN"
    },
-    "shinyjs": {
-      "Package": "shinyjs",
-      "Version": "2.1.0",
-      "Source": "Repository",
-      "Title": "Easily Improve the User Experience of Your Shiny Apps in Seconds",
-      "Authors@R": "person(\"Dean\", \"Attali\",  email = \"daattali@gmail.com\", role = c(\"aut\", \"cre\"), comment= c(ORCID=\"0000-0002-5645-3493\"))",
-      "Description": "Perform common useful JavaScript operations in Shiny apps that will greatly improve your apps without having to know any JavaScript. Examples include: hiding an element, disabling an input, resetting an input back to its original value, delaying code execution by a few seconds, and many more useful functions for both the end user and the developer. 'shinyjs' can also be used to easily call your own custom JavaScript functions from R.",
-      "URL": "https://deanattali.com/shinyjs/",
-      "BugReports": "https://github.com/daattali/shinyjs/issues",
-      "Depends": [
-        "R (>= 3.1.0)"
-      ],
-      "Imports": [
-        "digest (>= 0.6.8)",
-        "jsonlite",
-        "shiny (>= 1.0.0)"
-      ],
-      "Suggests": [
-        "htmltools (>= 0.2.9)",
-        "knitr (>= 1.7)",
-        "rmarkdown",
-        "shinyAce",
-        "shinydisconnect",
-        "testthat (>= 0.9.1)"
-      ],
-      "License": "MIT + file LICENSE",
-      "VignetteBuilder": "knitr",
-      "RoxygenNote": "7.1.1",
-      "Encoding": "UTF-8",
-      "NeedsCompilation": "no",
-      "Author": "Dean Attali [aut, cre] (<https://orcid.org/0000-0002-5645-3493>)",
-      "Maintainer": "Dean Attali <daattali@gmail.com>",
-      "Repository": "CRAN"
-    },
    "sodium": {
      "Package": "sodium",
      "Version": "1.4.0",