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14 changed files with 143 additions and 101 deletions
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@ -9,7 +9,7 @@ type: software
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license: AGPL-3.0-or-later
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title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers
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with publication ready output'
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version: 25.4.5
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version: 25.5.1
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doi: 10.5281/zenodo.14527429
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abstract: Easily evaluate and analysis clinical health data in your browser on a server
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or on your own device. Import data from multiple sources, summarise, modify and
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@ -1,6 +1,6 @@
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Package: FreesearchR
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Title: A free and open-source browser based data analysis tool for researchers with publication ready output
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Version: 25.4.5
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Version: 25.5.1
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Authors@R: c(
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person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0002-7559-1154")),
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10
NEWS.md
10
NEWS.md
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@ -1,3 +1,13 @@
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# FreesearchR 25.5.1
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- *FIX*: correct export of single variable plot.
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- *NEW*: Include app version in report for reference.
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- *NEW*: Show progress on connecting to a REDCap database.
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- *FIX*: Data import code export.
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# FreesearchR 25.4.5
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- *BUG*: Regression results and code not returned correctly
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@ -1 +1 @@
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app_version <- function()'v25.4.5.250430'
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app_version <- function()'25.5.1'
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@ -45,15 +45,23 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
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title = "Download",
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icon = bsicons::bs_icon("download"),
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shinyWidgets::noUiSliderInput(
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inputId = ns("height"),
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inputId = ns("height_slide"),
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label = "Plot height (mm)",
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min = 50,
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max = 300,
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value = 100,
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step = 1,
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format = shinyWidgets::wNumbFormat(decimals = 0),
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color = datamods:::get_primary_color()
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color = datamods:::get_primary_color(),
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inline = TRUE
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),
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# shiny::numericInput(
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# inputId = ns("height_numeric"),
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# label = "Plot height (mm)",
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# min = 50,
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# max = 300,
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# value = 100
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# ),
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shinyWidgets::noUiSliderInput(
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inputId = ns("width"),
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label = "Plot width (mm)",
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@ -372,17 +380,32 @@ data_visuals_server <- function(id,
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}
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})
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# shiny::observeEvent(input$height_numeric, {
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# shinyWidgets::updateNoUiSliderInput(session, ns("height_slide"), value = input$height_numeric)
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# }, ignoreInit = TRUE)
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# shiny::observeEvent(input$height_slide, {
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# shiny::updateNumericInput(session, ns("height_numeric"), value = input$height_slide)
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# }, ignoreInit = TRUE)
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output$download_plot <- shiny::downloadHandler(
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filename = shiny::reactive({
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paste0("plot.", input$plot_type)
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}),
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content = function(file) {
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if (inherits(rv$plot,"patchwork")){
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plot <- rv$plot
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} else {
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plot <- rv$plot[[1]]
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}
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# browser()
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shiny::withProgress(message = "Drawing the plot. Hold on for a moment..", {
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ggplot2::ggsave(
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filename = file,
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plot = rv$plot,
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plot = plot,
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width = input$width,
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height = input$height,
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height = input$height_slide,
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dpi = 300,
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units = "mm", scale = 2
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)
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@ -517,8 +540,8 @@ supported_plots <- function() {
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fun = "plot_euler",
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descr = "Euler diagram",
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note = "Generate area-proportional Euler diagrams to display set relationships",
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primary.type = "dichotomous",
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secondary.type = "dichotomous",
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primary.type = c("dichotomous", "categorical"),
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secondary.type = c("dichotomous", "categorical"),
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secondary.multi = TRUE,
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secondary.max = 4,
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tertiary.type = c("dichotomous", "categorical"),
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@ -65,7 +65,7 @@ write_rmd <- function(data, ...) {
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## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041
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## Outputs to the same as the .qmd file
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rmarkdown::render(
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params = list(data.file = "web_data.rds"),
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params = list(data.file = "web_data.rds",version=app_version()),
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# execute_params = list(data.file = temp),
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...
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)
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1
R/hosted_version.R
Normal file
1
R/hosted_version.R
Normal file
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@ -0,0 +1 @@
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hosted_version <- function()'v25.5.1-250505'
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@ -109,6 +109,12 @@ plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
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#' ) |> plot_euler_single()
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#' mtcars[c("vs", "am")] |> plot_euler_single()
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plot_euler_single <- function(data) {
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# if (any("categorical" %in% data_type(data))){
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# shape <- "ellipse"
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# } else {
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# shape <- "circle"
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# }
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data |>
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ggeulerr(shape = "circle") +
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ggplot2::theme_void() +
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@ -112,7 +112,7 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
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tags$p(phosphoricons::ph("info", weight = "bold"), "Please specify data to download, then press 'Import'.")
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),
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dismissible = TRUE
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)#,
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) # ,
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## TODO: Use busy indicator like on download to have button activate/deactivate
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# bslib::input_task_button(
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# id = ns("data_import"),
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@ -200,7 +200,9 @@ m_redcap_readServer <- function(id) {
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)
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# browser()
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shiny::withProgress({
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imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters), silent = TRUE)
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},message = paste("Connecting to",data_rv$uri))
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## TODO: Simplify error messages
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if (inherits(imported, "try-error") || NROW(imported) < 1 || ifelse(is.list(imported), !isTRUE(imported$success), FALSE)) {
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@ -227,8 +229,10 @@ m_redcap_readServer <- function(id) {
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include_data_alert(
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see_data_text = "Click to see data dictionary",
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dataIdName = "see_data",
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extra = tags$p(tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
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glue::glue("The {data_rv$info$project_title} project is loaded.")),
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extra = tags$p(
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tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
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glue::glue("The {data_rv$info$project_title} project is loaded.")
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),
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btn_show_data = TRUE
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)
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)
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
45
SESSION.md
45
SESSION.md
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@ -11,11 +11,11 @@
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|collate |en_US.UTF-8 |
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|ctype |en_US.UTF-8 |
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|tz |Europe/Copenhagen |
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|date |2025-04-30 |
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|date |2025-05-05 |
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|rstudio |2024.12.1+563 Kousa Dogwood (desktop) |
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|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
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|quarto |1.6.40 @ /usr/local/bin/quarto |
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|FreesearchR |25.4.5.250430 |
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|FreesearchR |25.5.1.250505 |
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--------------------------------------------------------------------------------
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@ -24,10 +24,8 @@
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|package |loadedversion |date |source |
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|:-------------|:-------------|:----------|:--------------|
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|apexcharter |0.4.4 |2024-09-06 |CRAN (R 4.4.1) |
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|askpass |1.2.1 |2024-10-04 |CRAN (R 4.4.1) |
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|assertthat |0.2.1 |2019-03-21 |CRAN (R 4.4.1) |
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|backports |1.5.0 |2024-05-23 |CRAN (R 4.4.1) |
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|base64enc |0.1-3 |2015-07-28 |CRAN (R 4.4.1) |
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|bayestestR |0.15.3 |2025-04-28 |CRAN (R 4.4.1) |
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|bit |4.6.0 |2025-03-06 |CRAN (R 4.4.1) |
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|bit64 |4.6.0-1 |2025-01-16 |CRAN (R 4.4.1) |
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@ -37,21 +35,14 @@
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|bsicons |0.1.2 |2023-11-04 |CRAN (R 4.4.0) |
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|bslib |0.9.0 |2025-01-30 |CRAN (R 4.4.1) |
|
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|cachem |1.1.0 |2024-05-16 |CRAN (R 4.4.1) |
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|cards |0.6.0 |2025-04-11 |CRAN (R 4.4.1) |
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|cellranger |1.1.0 |2016-07-27 |CRAN (R 4.4.0) |
|
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|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) |
|
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|cli |3.6.5 |2025-04-23 |CRAN (R 4.4.1) |
|
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|cluster |2.1.8.1 |2025-03-12 |CRAN (R 4.4.1) |
|
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|colorspace |2.1-1 |2024-07-26 |CRAN (R 4.4.1) |
|
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|commonmark |1.9.5 |2025-03-17 |CRAN (R 4.4.1) |
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|correlation |0.8.7 |2025-03-03 |CRAN (R 4.4.1) |
|
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|crayon |1.5.3 |2024-06-20 |CRAN (R 4.4.1) |
|
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|credentials |2.0.2 |2024-10-04 |CRAN (R 4.4.1) |
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|crosstalk |1.2.1 |2023-11-23 |CRAN (R 4.4.0) |
|
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|curl |6.2.2 |2025-03-24 |CRAN (R 4.4.1) |
|
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|data.table |1.17.0 |2025-02-22 |CRAN (R 4.4.1) |
|
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|datamods |1.5.3 |2024-10-02 |CRAN (R 4.4.1) |
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|datawizard |1.0.2 |2025-03-24 |CRAN (R 4.4.1) |
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@ -70,47 +61,32 @@
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|fastmap |1.2.0 |2024-05-15 |CRAN (R 4.4.1) |
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|fontawesome |0.5.3 |2024-11-16 |CRAN (R 4.4.1) |
|
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|forcats |1.0.0 |2023-01-29 |CRAN (R 4.4.0) |
|
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|foreign |0.8-90 |2025-03-31 |CRAN (R 4.4.1) |
|
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|Formula |1.2-5 |2023-02-24 |CRAN (R 4.4.1) |
|
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|fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) |
|
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|generics |0.1.3 |2022-07-05 |CRAN (R 4.4.1) |
|
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|gert |2.1.5 |2025-03-25 |CRAN (R 4.4.1) |
|
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|ggcorrplot |0.1.4.1 |2023-09-05 |CRAN (R 4.4.0) |
|
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|ggplot2 |3.5.2 |2025-04-09 |CRAN (R 4.4.1) |
|
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|ggstats |0.9.0 |2025-03-10 |CRAN (R 4.4.1) |
|
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|gh |1.4.1 |2024-03-28 |CRAN (R 4.4.0) |
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|gitcreds |0.1.2 |2022-09-08 |CRAN (R 4.4.1) |
|
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|glue |1.8.0 |2024-09-30 |CRAN (R 4.4.1) |
|
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|gridExtra |2.3 |2017-09-09 |CRAN (R 4.4.1) |
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|gt |1.0.0 |2025-04-05 |CRAN (R 4.4.1) |
|
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|gtable |0.3.6 |2024-10-25 |CRAN (R 4.4.1) |
|
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|gtsummary |2.2.0 |2025-04-14 |CRAN (R 4.4.1) |
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|haven |2.5.4 |2023-11-30 |CRAN (R 4.4.0) |
|
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|here |1.0.1 |2020-12-13 |CRAN (R 4.4.1) |
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|Hmisc |5.2-3 |2025-03-16 |CRAN (R 4.4.1) |
|
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|hms |1.1.3 |2023-03-21 |CRAN (R 4.4.0) |
|
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|htmlTable |2.4.3 |2024-07-21 |CRAN (R 4.4.0) |
|
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|htmltools |0.5.8.1 |2024-04-04 |CRAN (R 4.4.1) |
|
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|htmlwidgets |1.6.4 |2023-12-06 |CRAN (R 4.4.0) |
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|httpuv |1.6.16 |2025-04-16 |CRAN (R 4.4.1) |
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|httr2 |1.1.2 |2025-03-26 |CRAN (R 4.4.1) |
|
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|IDEAFilter |0.2.0 |2024-04-15 |CRAN (R 4.4.0) |
|
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|insight |1.2.0 |2025-04-22 |CRAN (R 4.4.1) |
|
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|jquerylib |0.1.4 |2021-04-26 |CRAN (R 4.4.0) |
|
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|jsonlite |2.0.0 |2025-03-27 |CRAN (R 4.4.1) |
|
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|jsonvalidate |1.5.0 |2025-02-07 |CRAN (R 4.4.1) |
|
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|KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.4.1) |
|
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|keyring |1.3.2 |2023-12-11 |CRAN (R 4.4.0) |
|
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|knitr |1.50 |2025-03-16 |CRAN (R 4.4.1) |
|
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|labeling |0.4.3 |2023-08-29 |CRAN (R 4.4.1) |
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|labelled |2.14.0 |2025-01-08 |CRAN (R 4.4.1) |
|
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|later |1.4.2 |2025-04-08 |CRAN (R 4.4.1) |
|
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|lattice |0.22-7 |2025-04-02 |CRAN (R 4.4.1) |
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|lifecycle |1.0.4 |2023-11-07 |CRAN (R 4.4.1) |
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|litedown |0.7 |2025-04-08 |CRAN (R 4.4.1) |
|
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|lme4 |1.1-37 |2025-03-26 |CRAN (R 4.4.1) |
|
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|magrittr |2.0.3 |2022-03-30 |CRAN (R 4.4.1) |
|
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|markdown |2.0 |2025-03-23 |CRAN (R 4.4.1) |
|
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|MASS |7.3-65 |2025-02-28 |CRAN (R 4.4.1) |
|
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|Matrix |1.7-3 |2025-03-11 |CRAN (R 4.4.1) |
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|memoise |2.0.1 |2021-11-26 |CRAN (R 4.4.0) |
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@ -120,8 +96,6 @@
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|modelbased |0.10.0 |2025-03-10 |CRAN (R 4.4.1) |
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|nlme |3.1-168 |2025-03-31 |CRAN (R 4.4.1) |
|
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|nloptr |2.2.1 |2025-03-17 |CRAN (R 4.4.1) |
|
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|nnet |7.3-20 |2025-01-01 |CRAN (R 4.4.1) |
|
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|openssl |2.3.2 |2025-02-03 |CRAN (R 4.4.1) |
|
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|openxlsx2 |1.15 |2025-04-25 |CRAN (R 4.4.1) |
|
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|parameters |0.24.2 |2025-03-04 |CRAN (R 4.4.1) |
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|patchwork |1.3.0 |2024-09-16 |CRAN (R 4.4.1) |
|
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|
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@ -131,7 +105,6 @@
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|pkgbuild |1.4.7 |2025-03-24 |CRAN (R 4.4.1) |
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|pkgconfig |2.0.3 |2019-09-22 |CRAN (R 4.4.1) |
|
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|pkgload |1.4.0 |2024-06-28 |CRAN (R 4.4.0) |
|
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|plyr |1.8.9 |2023-10-02 |CRAN (R 4.4.1) |
|
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|processx |3.8.6 |2025-02-21 |CRAN (R 4.4.1) |
|
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|profvis |0.4.0 |2024-09-20 |CRAN (R 4.4.1) |
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|promises |1.3.2 |2024-11-28 |CRAN (R 4.4.1) |
|
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|
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@ -139,13 +112,9 @@
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|ps |1.9.1 |2025-04-12 |CRAN (R 4.4.1) |
|
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|purrr |1.0.4 |2025-02-05 |CRAN (R 4.4.1) |
|
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|quarto |1.4.4 |2024-07-20 |CRAN (R 4.4.0) |
|
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|R.cache |0.16.0 |2022-07-21 |CRAN (R 4.4.0) |
|
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|R.methodsS3 |1.8.2 |2022-06-13 |CRAN (R 4.4.1) |
|
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|R.oo |1.27.0 |2024-11-01 |CRAN (R 4.4.1) |
|
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|R.utils |2.13.0 |2025-02-24 |CRAN (R 4.4.1) |
|
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|R6 |2.6.1 |2025-02-15 |CRAN (R 4.4.1) |
|
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|ragg |1.4.0 |2025-04-10 |CRAN (R 4.4.1) |
|
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|rappdirs |0.3.3 |2021-01-31 |CRAN (R 4.4.1) |
|
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|rankinPlot |1.1.0 |2023-01-30 |CRAN (R 4.4.0) |
|
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|rbibutils |2.3 |2024-10-04 |CRAN (R 4.4.1) |
|
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|RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.4.1) |
|
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|Rcpp |1.0.14 |2025-01-12 |CRAN (R 4.4.1) |
|
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|
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@ -158,13 +127,12 @@
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|REDCapR |1.4.0 |2025-01-11 |CRAN (R 4.4.1) |
|
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|reformulas |0.4.0 |2024-11-03 |CRAN (R 4.4.1) |
|
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|remotes |2.5.0 |2024-03-17 |CRAN (R 4.4.1) |
|
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|rempsyc |0.1.9 |2025-02-01 |CRAN (R 4.4.1) |
|
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|renv |1.1.4 |2025-03-20 |CRAN (R 4.4.1) |
|
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|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) |
|
||||
|
|
@ -177,9 +145,6 @@
|
|||
|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) |
|
||||
|
|
@ -189,8 +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) |
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
#### Current file: /Users/au301842/FreesearchR/R//app_version.R
|
||||
########
|
||||
|
||||
app_version <- function()'v25.4.4.250430'
|
||||
app_version <- function()'25.5.1'
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -1619,15 +1619,23 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
|
|||
title = "Download",
|
||||
icon = bsicons::bs_icon("download"),
|
||||
shinyWidgets::noUiSliderInput(
|
||||
inputId = ns("height"),
|
||||
inputId = ns("height_slide"),
|
||||
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)",
|
||||
|
|
@ -1946,17 +1954,32 @@ 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$plot[[1]]
|
||||
|
||||
}
|
||||
# browser()
|
||||
shiny::withProgress(message = "Drawing the plot. Hold on for a moment..", {
|
||||
ggplot2::ggsave(
|
||||
filename = file,
|
||||
plot = rv$plot,
|
||||
plot = plot,
|
||||
width = input$width,
|
||||
height = input$height,
|
||||
height = input$height_slide,
|
||||
dpi = 300,
|
||||
units = "mm", scale = 2
|
||||
)
|
||||
|
|
@ -2091,8 +2114,8 @@ supported_plots <- function() {
|
|||
fun = "plot_euler",
|
||||
descr = "Euler diagram",
|
||||
note = "Generate area-proportional Euler diagrams to display set relationships",
|
||||
primary.type = "dichotomous",
|
||||
secondary.type = "dichotomous",
|
||||
primary.type = c("dichotomous", "categorical"),
|
||||
secondary.type = c("dichotomous", "categorical"),
|
||||
secondary.multi = TRUE,
|
||||
secondary.max = 4,
|
||||
tertiary.type = c("dichotomous", "categorical"),
|
||||
|
|
@ -3338,7 +3361,7 @@ write_rmd <- function(data, ...) {
|
|||
## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041
|
||||
## Outputs to the same as the .qmd file
|
||||
rmarkdown::render(
|
||||
params = list(data.file = "web_data.rds"),
|
||||
params = list(data.file = "web_data.rds",version=app_version()),
|
||||
# execute_params = list(data.file = temp),
|
||||
...
|
||||
)
|
||||
|
|
@ -3927,6 +3950,13 @@ is_identical_to_previous <- function(data, no.name = TRUE) {
|
|||
}
|
||||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R
|
||||
########
|
||||
|
||||
hosted_version <- function()'v25.5.1-250505'
|
||||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/R//html_dependency_freesearchr.R
|
||||
########
|
||||
|
|
@ -4784,6 +4814,12 @@ plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
|
|||
#' ) |> plot_euler_single()
|
||||
#' mtcars[c("vs", "am")] |> plot_euler_single()
|
||||
plot_euler_single <- function(data) {
|
||||
# if (any("categorical" %in% data_type(data))){
|
||||
# shape <- "ellipse"
|
||||
# } else {
|
||||
# shape <- "circle"
|
||||
# }
|
||||
|
||||
data |>
|
||||
ggeulerr(shape = "circle") +
|
||||
ggplot2::theme_void() +
|
||||
|
|
@ -5441,7 +5477,7 @@ m_redcap_readUI <- function(id, title = TRUE, url = NULL) {
|
|||
tags$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"),
|
||||
|
|
@ -5529,7 +5565,9 @@ m_redcap_readServer <- function(id) {
|
|||
)
|
||||
|
||||
# browser()
|
||||
shiny::withProgress({
|
||||
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)) {
|
||||
|
|
@ -5556,8 +5594,10 @@ m_redcap_readServer <- function(id) {
|
|||
include_data_alert(
|
||||
see_data_text = "Click to see data dictionary",
|
||||
dataIdName = "see_data",
|
||||
extra = tags$p(tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
|
||||
glue::glue("The {data_rv$info$project_title} project is loaded.")),
|
||||
extra = tags$p(
|
||||
tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"),
|
||||
glue::glue("The {data_rv$info$project_title} project is loaded.")
|
||||
),
|
||||
btn_show_data = TRUE
|
||||
)
|
||||
)
|
||||
|
|
@ -7521,7 +7561,8 @@ regression_server <- function(id,
|
|||
|
||||
shiny::observeEvent(
|
||||
list(
|
||||
data_r()
|
||||
data_r(),
|
||||
regression_vars()
|
||||
),
|
||||
{
|
||||
rv$list$regression$tables <- NULL
|
||||
|
|
@ -9397,8 +9438,8 @@ ui_elements <- list(
|
|||
width = 9,
|
||||
shiny::tags$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 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 data or variable filtering is applied.")
|
||||
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("Please note that data modifications are applied before any filtering.")
|
||||
)
|
||||
)
|
||||
),
|
||||
|
|
@ -9687,14 +9728,28 @@ ui_elements <- list(
|
|||
),
|
||||
##############################################################################
|
||||
#########
|
||||
######### Documentation panel
|
||||
######### Feedback link
|
||||
#########
|
||||
##############################################################################
|
||||
"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 (external)",
|
||||
"Docs",shiny::icon("arrow-up-right-from-square"),
|
||||
target = "_blank",
|
||||
rel = "noopener noreferrer"
|
||||
)
|
||||
|
|
@ -9736,6 +9791,7 @@ ui <- bslib::page_fixed(
|
|||
ui_elements$analyze,
|
||||
ui_elements$download,
|
||||
bslib::nav_spacer(),
|
||||
ui_elements$feedback,
|
||||
ui_elements$docs,
|
||||
fillable = FALSE,
|
||||
footer = shiny::tags$footer(
|
||||
|
|
@ -9746,7 +9802,7 @@ ui <- bslib::page_fixed(
|
|||
),
|
||||
shiny::p(
|
||||
style = "margin: 1; color: #888;",
|
||||
shiny::tags$a("Docs", href = "https://agdamsbo.github.io/FreesearchR/", target = "_blank", rel = "noopener noreferrer")," | ", 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$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer")
|
||||
shiny::tags$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$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer")
|
||||
),
|
||||
)
|
||||
)
|
||||
|
|
@ -9773,9 +9829,7 @@ library(quarto)
|
|||
library(here)
|
||||
library(broom)
|
||||
library(broom.helpers)
|
||||
# library(REDCapCAST)
|
||||
library(easystats)
|
||||
# library(esquisse)
|
||||
library(patchwork)
|
||||
library(DHARMa)
|
||||
library(apexcharter)
|
||||
|
|
@ -9786,32 +9840,17 @@ library(shinyWidgets)
|
|||
library(DT)
|
||||
library(data.table)
|
||||
library(gtsummary)
|
||||
# library(FreesearchR)
|
||||
|
||||
# source("functions.R")
|
||||
|
||||
data(starwars)
|
||||
data(mtcars)
|
||||
mtcars_date <- mtcars |> append_column(as.Date(sample(1:365, nrow(mtcars))), "rand_dates")
|
||||
mtcars_date$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$docs_file <- shiny::renderUI({
|
||||
# shiny::includeHTML("www/docs.html")
|
||||
shiny::HTML(readLines("www/docs.html"))
|
||||
})
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Night mode (just very popular, not really needed)
|
||||
|
|
@ -10254,10 +10293,12 @@ server <- function(input, output, session) {
|
|||
# })
|
||||
|
||||
output$code_import <- shiny::renderUI({
|
||||
shiny::req(rv$code$import)
|
||||
prismCodeBlock(paste0("#Data import\n", rv$code$import))
|
||||
})
|
||||
|
||||
output$code_import <- shiny::renderUI({
|
||||
output$code_format <- shiny::renderUI({
|
||||
shiny::req(rv$code$format)
|
||||
prismCodeBlock(paste0("#Data import formatting\n", rv$code$format))
|
||||
})
|
||||
|
||||
|
|
@ -10480,20 +10521,11 @@ 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..", {
|
||||
|
|
|
|||
|
|
@ -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), or share on [GitHub](https://github.com/agdamsbo/FreesearchR/issues).
|
||||
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).
|
||||
|
|
|
|||
|
|
@ -6,6 +6,7 @@ author: FreesearchR data analysis tool
|
|||
toc: false
|
||||
params:
|
||||
data.file: NA
|
||||
version: NA
|
||||
---
|
||||
|
||||
```{r setup, echo = FALSE}
|
||||
|
|
@ -46,7 +47,7 @@ Research should be free and open with easy access for all. The FreesearchR tool
|
|||
|
||||
## Methods
|
||||
|
||||
Analyses were conducted in the *FreesearchR* data analysis web-tool based on R version 4.4.1.
|
||||
Analyses were conducted using the *FreesearchR* data analysis web-tool version `r params$version` based on *R* version 4.4.1.
|
||||
|
||||
## Results
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue