loading animation

.Rbuildignore

@@ -14,6 +14,6 @@
 ^data-raw$
 ^CITATION\.cff$
 ^app_hosted$
-^app$
+^app*$
 ^page$
 ^demo$

.gitignore

@@ -10,7 +10,8 @@ inst/shiny-examples/casting/functions.R
 functions.R
 docs
 inst/doc
-app_hosted
+app_dev
+app_stable
 app
 page
 demo

CITATION.cff

@@ -9,8 +9,11 @@ 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: 25.5.2
 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
@@ -974,6 +977,19 @@ 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'

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: 25.5.2
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154")),
@@ -62,7 +62,8 @@ Imports:
     eulerr,
     ggforce,
     RcppArmadillo,
-    ggcorrplot
+    ggcorrplot,
+    shinyjs
 Suggests: 
     styler,
     devtools,
@@ -78,7 +79,7 @@ Suggests:
     shinytest,
     covr,
     cffr
-URL: https://github.com/agdamsbo/FreesearchR, https://agdamsbo.github.io/FreesearchR/
+URL: https://github.com/agdamsbo/FreesearchR, https://agdamsbo.github.io/FreesearchR/, https://app.FreesearchR.org/
 BugReports: https://github.com/agdamsbo/FreesearchR/issues
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NEWS.md

@@ -1,3 +1,11 @@
+# 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.

R/app_version.R

@@ -1 +1 @@
-app_version <- function()'25.5.1'
+app_version <- function()'25.5.2'

R/data_plots.R

@@ -395,7 +395,9 @@ data_visuals_server <- function(id,
         content = function(file) {
           if (inherits(rv$plot,"patchwork")){
             plot <- rv$plot
-          } else {
+          } else if (inherits(rv$plot,"ggplot")){
+            plot <- rv$plot
+          }else {
             plot <- rv$plot[[1]]
 
           }
@@ -421,7 +423,6 @@ data_visuals_server <- function(id,
   )
 }
 
-
 #' Select all from vector but
 #'
 #' @param data vector

R/hosted_version.R

@@ -1 +1 @@
-hosted_version <- function()'v25.5.1-250507'
+hosted_version <- function()'v25.5.2-250508'

SESSION.md

@@ -11,11 +11,11 @@
 |collate     |en_US.UTF-8                                |
 |ctype       |en_US.UTF-8                                |
 |tz          |Europe/Copenhagen                          |
-|date        |2025-05-05                                 |
+|date        |2025-05-08                                 |
 |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 |25.5.2.250508                              |
                                                                                 
                                                                                 
 --------------------------------------------------------------------------------
@@ -24,6 +24,7 @@
 |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) |
@@ -36,6 +37,7 @@
 |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) |
@@ -43,6 +45,7 @@
 |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) |
@@ -78,10 +81,10 @@
 |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) |
@@ -96,7 +99,9 @@
 |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) |
@@ -112,9 +117,11 @@
 |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) |
@@ -127,7 +134,6 @@
 |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) |
@@ -142,11 +148,11 @@
 |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) |
-|systemfonts   |1.2.2         |2025-04-04 |CRAN (R 4.4.1) |
+|styler        |1.10.3        |2024-04-07 |CRAN (R 4.4.0) |
-|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) |
@@ -154,8 +160,8 @@
 |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()'25.5.2'
 
 
 ########
@@ -1969,7 +1969,9 @@ data_visuals_server <- function(id,
         content = function(file) {
           if (inherits(rv$plot,"patchwork")){
             plot <- rv$plot
-          } else {
+          } else if (inherits(rv$plot,"ggplot")){
+            plot <- rv$plot
+          }else {
             plot <- rv$plot[[1]]
 
           }
@@ -1995,7 +1997,6 @@ data_visuals_server <- function(id,
   )
 }
 
-
 #' Select all from vector but
 #'
 #' @param data vector
@@ -3954,7 +3955,7 @@ is_identical_to_previous <- function(data, no.name = TRUE) {
 #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R 
 ########
 
-hosted_version <- function()'v25.5.1-250507'
+hosted_version <- function()'v25.5.2-250508'
 
 
 ########
@@ -9397,7 +9398,12 @@ ui_elements <- list(
           fluidRow(
             shiny::column(
               width = 9,
-              data_summary_ui(id = "data_summary")
+              data_summary_ui(id = "data_summary"),
+              shiny::br(),
+              shiny::br(),
+              shiny::br(),
+              shiny::br(),
+              shiny::br()
             ),
             shiny::column(
               width = 3,
@@ -9735,7 +9741,7 @@ ui_elements <- list(
     # shiny::img(shiny::icon("book")),
     shiny::tags$a(
       href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8",
-      "Feedback",shiny::icon("arrow-up-right-from-square"),
+      "Feedback", shiny::icon("arrow-up-right-from-square"),
       target = "_blank",
       rel = "noopener noreferrer"
     )
@@ -9749,7 +9755,7 @@ ui_elements <- list(
     # shiny::img(shiny::icon("book")),
     shiny::tags$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"
     )
@@ -9777,10 +9783,19 @@ 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$home,
@@ -9802,14 +9817,15 @@ ui <- bslib::page_fixed(
           ),
           shiny::p(
             style = "margin: 1; color: #888;",
-        shiny::tags$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"), " | ", 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 
 ########
@@ -9840,17 +9856,26 @@ 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)

renv.lock

@@ -7930,6 +7930,40 @@
       "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",