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JS in separate file to autohide dropdowns on navigation - new dev version
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Andreas Gammelgaard Damsbo 2025-07-03 20:26:35 +02:00
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2
CITATION.cff
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@ -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: 25.7.1
version: 25.7.2
doi: 10.5281/zenodo.14527429
identifiers:
- type: url

2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: FreesearchR
Title: A free and open-source browser based data analysis tool for researchers with publication ready output
Version: 25.7.1
Version: 25.7.2
Authors@R: c(
person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-7559-1154")),

6
NEWS.md
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@ -1,4 +1,8 @@
# FreesearchR 25.7.1 - DEV
# FreesearchR 25.7.2 - DEV
- *FIX* refining hiding drop downs. All JavaScript is now in separate file. Coded with GAI help from claude.ai.
# FreesearchR 25.7.1
- *NEW* UI overhaul and navigation update. The interface is simplified to clearly show the relationship between panels and sub-items by abandoning multiple levels on panel to instead show a drop-down menu. This also results in simplified sidebar menus with room to add more controls in the future.

2
R/app_version.R
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@ -1 +1 @@
app_version <- function()'25.7.1'
app_version <- function()'25.7.2'

2
R/hosted_version.R
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@ -1 +1 @@
hosted_version <- function()'v25.7.1-250703'
hosted_version <- function()'v25.7.2-250703'

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R/sysdata.rda
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22
SESSION.md
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@ -15,7 +15,7 @@
|rstudio |2025.05.0+496 Mariposa Orchid (desktop) |
|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
|quarto |1.7.30 @ /usr/local/bin/quarto |
|FreesearchR |25.7.1.250703 |
|FreesearchR |25.7.2.250703 |
--------------------------------------------------------------------------------
@ -26,6 +26,8 @@
|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) |
|attachment |0.4.5 |2025-03-14 |CRAN (R 4.4.1) |
|attempt |0.3.1 |2020-05-03 |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) |
@ -43,6 +45,7 @@
|cardx |0.2.4 |2025-04-12 |CRAN (R 4.4.1) |
|caTools |1.18.3 |2024-09-04 |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) |
@ -52,7 +55,9 @@
|colorspace |2.1-1 |2024-07-26 |CRAN (R 4.4.1) |
|commonmark |1.9.5 |2025-03-17 |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) |
@ -61,6 +66,7 @@
|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) |
|dockerfiler |0.2.5 |2025-05-07 |CRAN (R 4.4.1) |
|doParallel |1.0.17 |2022-02-07 |CRAN (R 4.4.0) |
|dplyr |1.1.4 |2023-11-17 |CRAN (R 4.4.0) |
|DT |0.33 |2024-04-04 |CRAN (R 4.4.0) |
@ -84,16 +90,19 @@
|foreach |1.5.2 |2022-02-02 |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) |
|FreesearchR |25.7.1 |NA |NA |
|FreesearchR |25.7.2 |NA |NA |
|fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) |
|gdtools |0.4.2 |2025-03-27 |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) |
|ggalluvial |0.12.5 |2023-02-22 |CRAN (R 4.4.0) |
|ggcorrplot |0.1.4.1 |2023-09-05 |CRAN (R 4.4.0) |
|ggforce |0.4.2 |2024-02-19 |CRAN (R 4.4.0) |
|ggplot2 |3.5.2 |2025-04-09 |CRAN (R 4.4.1) |
|ggridges |0.5.6 |2024-01-23 |CRAN (R 4.4.0) |
|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) |
@ -107,11 +116,13 @@
|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) |
|iterators |1.0.14 |2022-02-05 |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) |
@ -140,6 +151,7 @@
|opdisDownsampling |1.0.1 |2024-04-15 |CRAN (R 4.4.0) |
|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) |
|pbmcapply |1.5.1 |2022-04-28 |CRAN (R 4.4.1) |
@ -168,6 +180,7 @@
|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) |
@ -198,13 +211,16 @@
|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) |
|shiny2docker |0.0.2 |2025-02-09 |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) |
|sourcetools |0.1.7-1 |2023-02-01 |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) |
|testthat |3.2.3 |2025-01-13 |CRAN (R 4.4.1) |
|textshaping |1.0.0 |2025-01-20 |CRAN (R 4.4.1) |
@ -220,6 +236,7 @@
|urlchecker |1.0.1 |2021-11-30 |CRAN (R 4.4.1) |
|usethis |3.1.0 |2024-11-26 |CRAN (R 4.4.1) |
|uuid |1.2-1 |2024-07-29 |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) |
|vroom |1.6.5 |2023-12-05 |CRAN (R 4.4.0) |
|withr |3.0.2 |2024-10-28 |CRAN (R 4.4.1) |
@ -228,4 +245,5 @@
|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) |
|yesno |0.1.3 |2024-07-26 |CRAN (R 4.4.1) |
|zip |2.3.2 |2025-02-01 |CRAN (R 4.4.1) |

49
inst/apps/FreesearchR/app.R
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@ -49,7 +49,7 @@ library(rlang)
#### Current file: /Users/au301842/FreesearchR/R//app_version.R
########
app_version <- function()'25.7.1'
app_version <- function()'25.7.2'
########
@ -4026,7 +4026,7 @@ simple_snake <- function(data){
#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R
########
hosted_version <- function()'v25.7.1-250703'
hosted_version <- function()'v25.7.2-250703'
########
@ -9867,7 +9867,8 @@ grepl_fix <- function(data, pattern, type = c("prefix", "infix", "suffix")) {
header_include <- function(){
shiny::tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "style.css"))
tags$link(rel = "stylesheet", type = "text/css", href = "style.css"),
tags$script(src="scripts.js"))
}
@ -9918,7 +9919,7 @@ ui_elements <- list(
##############################################################################
"import" = bslib::nav_panel(
title = "Get started",
icon = shiny::icon("upload"),
icon = shiny::icon("play"),
shiny::fluidRow(
shiny::column(width = 2),
shiny::column(
@ -10486,17 +10487,35 @@ ui <- bslib::page_fixed(
header_include(),
## Automatically close drop-downs on navigation
## Thanks to claude.ai
tags$script("
$(document).on('shown.bs.tab', '#main_panel', function(e) {
// Close dropdown in this specific navset only
$('#main_panel .dropdown-menu').removeClass('show');
$('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false');
// Close navbar collapse (burger menu)
$('#main_panel .navbar-collapse collapse').removeClass('show');
$('#main_panel .navbar-toggle').removeClass('collapsed').attr('aria-expanded', 'false');
});
"),
# tags$script("
# $(document).on('shown.bs.tab', '#main_panel', function(e) {
# // Close dropdown in this specific navset only
# $('#main_panel .dropdown-menu').removeClass('show');
# $('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false');
# });
#
# $(document).on('shiny:sessioninitialized', function() {
# // Function to collapse navbar on mobile
# function collapseNavbar() {
# var navbar = $('.navbar-collapse');
# if (navbar.hasClass('show')) {
# navbar.removeClass('show');
# $('.navbar-toggler').addClass('collapsed');
# $('.navbar-toggler').attr('aria-expanded', 'false');
# }
# }
#
# // Add click event to navigation tabs
# $(document).on('click', '.nav-link[data-bs-toggle=\"tab\"]', function() {
# setTimeout(collapseNavbar, 10);
# });
#
# // Also handle direct clicks on nav items
# $(document).on('click', '.navbar-nav .nav-link', function() {
# setTimeout(collapseNavbar, 10);
# });
# });
# "),
## This adds the actual favicon
## png and ico versions are kept for compatibility
shiny::tags$head(tags$link(rel = "shortcut icon", href = "favicon.svg")),

29
inst/apps/FreesearchR/www/scripts.js Normal file
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@ -0,0 +1,29 @@
// Automatically close drop-downs on navigation
// Thanks to claude.ai
$(document).on('shown.bs.tab', '#main_panel', function(e) {
// Close dropdown in this specific navset only
$('#main_panel .dropdown-menu').removeClass('show');
$('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false');
});
$(document).on('shiny:sessioninitialized', function() {
// Function to collapse navbar on mobile
function collapseNavbar() {
var navbar = $('.navbar-collapse');
if (navbar.hasClass('show')) {
navbar.removeClass('show');
$('.navbar-toggler').addClass('collapsed');
$('.navbar-toggler').attr('aria-expanded', 'false');
}
}
// Add click event to navigation tabs
$(document).on('click', '.nav-link[data-bs-toggle=\"tab\"]', function() {
setTimeout(collapseNavbar, 10);
});
// Also handle direct clicks on nav items
$(document).on('click', '.navbar-nav .nav-link', function() {
setTimeout(collapseNavbar, 10);
});
});

29
inst/assets/js/FreesearchR.js Normal file
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@ -0,0 +1,29 @@
// Automatically close drop-downs on navigation
// Thanks to claude.ai
$(document).on('shown.bs.tab', '#main_panel', function(e) {
// Close dropdown in this specific navset only
$('#main_panel .dropdown-menu').removeClass('show');
$('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false');
});
$(document).on('shiny:sessioninitialized', function() {
// Function to collapse navbar on mobile
function collapseNavbar() {
var navbar = $('.navbar-collapse');
if (navbar.hasClass('show')) {
navbar.removeClass('show');
$('.navbar-toggler').addClass('collapsed');
$('.navbar-toggler').attr('aria-expanded', 'false');
}
}
// Add click event to navigation tabs
$(document).on('click', '.nav-link[data-bs-toggle=\"tab\"]', function() {
setTimeout(collapseNavbar, 10);
});
// Also handle direct clicks on nav items
$(document).on('click', '.navbar-nav .nav-link', function() {
setTimeout(collapseNavbar, 10);
});
});