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4d4403d5e5
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f45ced3083
22 changed files with 962 additions and 348 deletions
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@ -13,5 +13,3 @@
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^pkgdown$
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^data-raw$
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^CITATION\.cff$
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^app_hosted$
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^app$
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2
.gitignore
vendored
2
.gitignore
vendored
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@ -10,5 +10,3 @@ inst/shiny-examples/casting/functions.R
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functions.R
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docs
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inst/doc
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app_hosted
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app
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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: 25.4.4
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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: 25.4.4
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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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8
NEWS.md
8
NEWS.md
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@ -1,11 +1,3 @@
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# FreesearchR 25.4.5
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- *BUG*: Regression results and code not returned correctly
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- *IMPROVED*: analyses results are reset on data change
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- *NEW*: app usage tracking only in hosted app. README updated to reflect.
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# FreesearchR 25.4.4
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Minor updates in docs and easier citation.
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@ -1 +1 @@
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app_version <- function()'v25.4.5.250430'
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app_version <- function()'v25.4.4.250429'
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@ -351,25 +351,9 @@ data_visuals_server <- function(id,
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prismCodeBlock(paste0("#Plotting\n", rv$code))
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})
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shiny::observeEvent(
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list(
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data()
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),
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{
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shiny::req(data())
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rv$plot <- NULL
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}
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)
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output$plot <- shiny::renderPlot({
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# shiny::req(rv$plot)
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# rv$plot
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if (!is.null(rv$plot)) {
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shiny::req(rv$plot)
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rv$plot
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} else {
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return(NULL)
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}
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})
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output$download_plot <- shiny::downloadHandler(
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@ -331,7 +331,7 @@ regression_server <- function(id,
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"Multivariable" = "regression_model_list"
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) |>
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lapply(\(.fun){
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parameters <- list(
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parameters=list(
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data = data_r()[regression_vars()],
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outcome.str = input$outcome_var,
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fun.descr = input$regression_type
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@ -413,8 +413,6 @@ regression_server <- function(id,
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shiny::req(rv$check_plot)
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shiny::req(input$plot_checks)
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## Print checks if a regression table is present
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if (!is.null(rv$list$regression$tables)) {
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p <- rv$check_plot() +
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# patchwork::wrap_plots() +
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patchwork::plot_annotation(title = "Multivariable regression model checks")
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@ -424,7 +422,7 @@ regression_server <- function(id,
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patchwork::area(.x, 1)
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})
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p_list <- p + patchwork::plot_layout(design = Reduce(c, layout))
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out <- p + patchwork::plot_layout(design = Reduce(c, layout))
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index <- match(
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input$plot_checks,
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@ -436,45 +434,28 @@ regression_server <- function(id,
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ls <- list()
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for (i in index) {
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p <- p_list[[i]] +
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ggplot2::theme(
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axis.text = ggplot2::element_text(size = 10),
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p <- out[[i]] +
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ggplot2::theme(axis.text = ggplot2::element_text(size = 10),
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axis.title = ggplot2::element_text(size = 12),
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legend.text = ggplot2::element_text(size = 12),
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plot.subtitle = ggplot2::element_text(size = 12),
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plot.title = ggplot2::element_text(size = 18)
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)
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plot.title = ggplot2::element_text(size = 18))
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ls <- c(ls, list(p))
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}
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# browser()
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tryCatch(
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{
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out <- patchwork::wrap_plots(ls, ncol = if (length(ls) == 1) 1 else 2)
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patchwork::wrap_plots(ls, ncol = if (length(ls) == 1) 1 else 2)
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},
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error = function(err) {
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showNotification(err, type = "err")
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}
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)
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out
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} else {
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return(NULL)
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}
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},
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alt = "Assumptions testing of the multivariable regression model"
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)
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shiny::observeEvent(
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list(
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data_r(),
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regression_vars()
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),
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{
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rv$list$regression$tables <- NULL
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}
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)
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### Creating the regression table
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### Creating the regression table
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shiny::observeEvent(
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input$load,
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{
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@ -482,7 +463,6 @@ regression_server <- function(id,
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## To avoid plotting old models on fail/error
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rv$list$regression$tables <- NULL
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# browser()
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tryCatch(
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{
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parameters <- list(
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@ -495,9 +475,9 @@ regression_server <- function(id,
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purrr::map(\(.x){
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do.call(
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regression_table,
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append_list(.x, parameters, "x")
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append_list(.x,parameters,"x")
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)
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})
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})
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# if (input$add_regression_p == "no") {
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# out <- out |>
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@ -510,17 +490,23 @@ regression_server <- function(id,
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# }
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rv$list$regression$models |>
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purrr::imap(\(.x, .i){
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purrr::imap(\(.x,.i){
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rv$list$regression$models[[.i]][["code_table"]] <- paste(
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.x$code,
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expression_string(rlang::call2(.fn = "regression_table", !!!parameters, .ns = "FreesearchR"), assign.str = NULL),
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sep = "|>\n"
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)
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expression_string(rlang::call2(.fn = "regression_table",!!!parameters,.ns = "FreesearchR"),assign.str=NULL),sep="|>\n")
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})
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rv$list$regression$tables <- out
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rv$list$input <- input
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list(
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rv$code$import,
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rlang::call2(.fn = "select",!!!list(input$import_var),.ns = "dplyr"),
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rlang::call2(.fn = "default_parsing",.ns = "FreesearchR")
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) |>
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merge_expression() |>
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expression_string()
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rv$list$regression$tables <- out
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rv$list$input <- input
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},
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warning = function(warn) {
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showNotification(paste0(warn), type = "warning")
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@ -533,15 +519,11 @@ regression_server <- function(id,
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)
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output$table2 <- gt::render_gt({
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## Print checks if a regression table is present
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if (!is.null(rv$list$regression$tables)) {
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shiny::req(rv$list$regression$tables)
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rv$list$regression$tables |>
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tbl_merge() |>
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gtsummary::as_gt() |>
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gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
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} else {
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return(NULL)
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}
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})
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##############################################################################
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@ -632,8 +614,10 @@ regression_server <- function(id,
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##############################################################################
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return(shiny::reactive({
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rv$list
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return(rv$list)
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}))
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}
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)
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}
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|
||||
|
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|
|
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
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@ -54,7 +54,7 @@ FreesearchR_colors <- function(choose = NULL) {
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fg = "#000000"
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)
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if (!is.null(choose)) {
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unname(out[choose])
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out[choose]
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} else {
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out
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}
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|
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30
README.md
30
README.md
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@ -23,27 +23,23 @@ This app has the following simple goals:
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1. ease quick data overview and basic visualisations for any clinical researcher
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## Run locally on your own machine
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## Install locally
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The ***FreesearchR*** app can also run on your own machine with no data transmitted anywhere. Any data.frame available in the global environment will be accessible from the interface. Just follow the below steps:
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The ***FreesearchR***-tool can also be launched locally. Any data.frame available in the global environment will be accessible from the interface.
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1. **Requirement:** You need to have [*R* installed](https://www.r-project.org/) and possibly an editor like [RStudio](https://posit.co/download/rstudio-desktop/).
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1. Then open the *R* console and copy/paste the following code, that will install the `{devtools}` package and then the `{FreesearchR}` *R*-package with its dependencies:
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```
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require("devtools")
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devtools::install_github("agdamsbo/FreesearchR")
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library(FreesearchR)
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# By loading mtcars to the environment, it will be available
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# in the interface like any other data.frame
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data(mtcars)
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launch_FreesearchR()
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```
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```
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require("devtools")
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devtools::install_github("agdamsbo/FreesearchR")
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library(FreesearchR)
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# By loading mtcars to the environment, it will be available
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# in the interface like any other data.frame
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data(mtcars)
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launch_FreesearchR()
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```
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||||
## Code of Conduct
|
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|
||||
Please note that the ***FreesearchR*** project is published with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
|
||||
Please note that the ***FreesearchR*** project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
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## Acknowledgements
|
||||
|
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@ -60,5 +56,3 @@ Like any other project, this project was never possible without the great work o
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- [IDEAfilter](https://biogen-inc.github.io/IDEAFilter/): a visually appealing data filter function based on the [{shinyDataFilter}](https://github.com/dgkf/shinyDataFilter).
|
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|
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This project was all written by a human and not by any AI-based tools.
|
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|
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The online ***FreesearchR*** app contains a tracking script, transmitting minimal data on usage. No uploaded data is transmitted anywhere. Have a look at the [tracking data here](https://analytics.gdamsbo.dk/share/2i4BNpMcDMB9lJvF/agdamsbo.shinyapps.io). No tracking data is sent running the app locally (see above).
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|
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52
SESSION.md
52
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 |2025-04-29 |
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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 |
|
||||
|FreesearchR |25.4.4.250429 |
|
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|
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|
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--------------------------------------------------------------------------------
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@ -24,10 +24,8 @@
|
|||
|package |loadedversion |date |source |
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|:-------------|:-------------|:----------|:--------------|
|
||||
|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) |
|
||||
|
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@ -37,21 +35,14 @@
|
|||
|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) |
|
||||
|
|
@ -70,47 +61,30 @@
|
|||
|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) |
|
||||
|
|
@ -120,9 +94,6 @@
|
|||
|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) |
|
||||
|performance |0.13.0 |2025-01-15 |CRAN (R 4.4.1) |
|
||||
|
|
@ -131,7 +102,6 @@
|
|||
|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) |
|
||||
|
|
@ -139,13 +109,7 @@
|
|||
|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) |
|
||||
|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) |
|
||||
|
|
@ -154,17 +118,13 @@
|
|||
|readODS |2.3.2 |2025-01-13 |CRAN (R 4.4.1) |
|
||||
|readr |2.1.5 |2024-01-10 |CRAN (R 4.4.0) |
|
||||
|readxl |1.4.5 |2025-03-07 |CRAN (R 4.4.1) |
|
||||
|REDCapCAST |25.3.2 |2025-03-10 |CRAN (R 4.4.1) |
|
||||
|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) |
|
||||
|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) |
|
||||
|
|
@ -176,12 +136,6 @@
|
|||
|shinybusy |0.3.3 |2024-03-09 |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) |
|
||||
|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) |
|
||||
|tidyr |1.3.1 |2024-01-24 |CRAN (R 4.4.1) |
|
||||
|tidyselect |1.2.1 |2024-03-11 |CRAN (R 4.4.0) |
|
||||
|
|
@ -189,7 +143,6 @@
|
|||
|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) |
|
||||
|vroom |1.6.5 |2023-12-05 |CRAN (R 4.4.0) |
|
||||
|withr |3.0.2 |2024-10-28 |CRAN (R 4.4.1) |
|
||||
|
|
@ -198,4 +151,3 @@
|
|||
|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) |
|
||||
|zip |2.3.2 |2025-02-01 |CRAN (R 4.4.1) |
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/app/functions.R
|
||||
#### Current file: /Users/au301842/FreesearchR/inst/apps/FreesearchR/functions.R
|
||||
########
|
||||
|
||||
|
||||
|
|
@ -10,7 +10,7 @@
|
|||
#### Current file: /Users/au301842/FreesearchR/R//app_version.R
|
||||
########
|
||||
|
||||
app_version <- function()'v25.4.4.250430'
|
||||
app_version <- function()'v25.4.4.250429'
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -1925,25 +1925,9 @@ data_visuals_server <- function(id,
|
|||
prismCodeBlock(paste0("#Plotting\n", rv$code))
|
||||
})
|
||||
|
||||
shiny::observeEvent(
|
||||
list(
|
||||
data()
|
||||
),
|
||||
{
|
||||
shiny::req(data())
|
||||
|
||||
rv$plot <- NULL
|
||||
}
|
||||
)
|
||||
|
||||
output$plot <- shiny::renderPlot({
|
||||
# shiny::req(rv$plot)
|
||||
# rv$plot
|
||||
if (!is.null(rv$plot)) {
|
||||
shiny::req(rv$plot)
|
||||
rv$plot
|
||||
} else {
|
||||
return(NULL)
|
||||
}
|
||||
})
|
||||
|
||||
output$download_plot <- shiny::downloadHandler(
|
||||
|
|
@ -7386,7 +7370,7 @@ regression_server <- function(id,
|
|||
"Multivariable" = "regression_model_list"
|
||||
) |>
|
||||
lapply(\(.fun){
|
||||
parameters <- list(
|
||||
parameters=list(
|
||||
data = data_r()[regression_vars()],
|
||||
outcome.str = input$outcome_var,
|
||||
fun.descr = input$regression_type
|
||||
|
|
@ -7468,8 +7452,6 @@ regression_server <- function(id,
|
|||
shiny::req(rv$check_plot)
|
||||
shiny::req(input$plot_checks)
|
||||
|
||||
## Print checks if a regression table is present
|
||||
if (!is.null(rv$list$regression$tables)) {
|
||||
p <- rv$check_plot() +
|
||||
# patchwork::wrap_plots() +
|
||||
patchwork::plot_annotation(title = "Multivariable regression model checks")
|
||||
|
|
@ -7479,7 +7461,7 @@ regression_server <- function(id,
|
|||
patchwork::area(.x, 1)
|
||||
})
|
||||
|
||||
p_list <- p + patchwork::plot_layout(design = Reduce(c, layout))
|
||||
out <- p + patchwork::plot_layout(design = Reduce(c, layout))
|
||||
|
||||
index <- match(
|
||||
input$plot_checks,
|
||||
|
|
@ -7491,44 +7473,28 @@ regression_server <- function(id,
|
|||
ls <- list()
|
||||
|
||||
for (i in index) {
|
||||
p <- p_list[[i]] +
|
||||
ggplot2::theme(
|
||||
axis.text = ggplot2::element_text(size = 10),
|
||||
p <- out[[i]] +
|
||||
ggplot2::theme(axis.text = ggplot2::element_text(size = 10),
|
||||
axis.title = ggplot2::element_text(size = 12),
|
||||
legend.text = ggplot2::element_text(size = 12),
|
||||
plot.subtitle = ggplot2::element_text(size = 12),
|
||||
plot.title = ggplot2::element_text(size = 18)
|
||||
)
|
||||
plot.title = ggplot2::element_text(size = 18))
|
||||
ls <- c(ls, list(p))
|
||||
}
|
||||
# browser()
|
||||
tryCatch(
|
||||
{
|
||||
out <- patchwork::wrap_plots(ls, ncol = if (length(ls) == 1) 1 else 2)
|
||||
patchwork::wrap_plots(ls, ncol = if (length(ls) == 1) 1 else 2)
|
||||
},
|
||||
error = function(err) {
|
||||
showNotification(err, type = "err")
|
||||
}
|
||||
)
|
||||
|
||||
out
|
||||
} else {
|
||||
return(NULL)
|
||||
}
|
||||
},
|
||||
alt = "Assumptions testing of the multivariable regression model"
|
||||
)
|
||||
|
||||
shiny::observeEvent(
|
||||
list(
|
||||
data_r()
|
||||
),
|
||||
{
|
||||
rv$list$regression$tables <- NULL
|
||||
}
|
||||
)
|
||||
|
||||
### Creating the regression table
|
||||
### Creating the regression table
|
||||
shiny::observeEvent(
|
||||
input$load,
|
||||
{
|
||||
|
|
@ -7536,7 +7502,6 @@ regression_server <- function(id,
|
|||
## To avoid plotting old models on fail/error
|
||||
rv$list$regression$tables <- NULL
|
||||
|
||||
# browser()
|
||||
tryCatch(
|
||||
{
|
||||
parameters <- list(
|
||||
|
|
@ -7549,9 +7514,9 @@ regression_server <- function(id,
|
|||
purrr::map(\(.x){
|
||||
do.call(
|
||||
regression_table,
|
||||
append_list(.x, parameters, "x")
|
||||
append_list(.x,parameters,"x")
|
||||
)
|
||||
})
|
||||
})
|
||||
|
||||
# if (input$add_regression_p == "no") {
|
||||
# out <- out |>
|
||||
|
|
@ -7564,17 +7529,23 @@ regression_server <- function(id,
|
|||
# }
|
||||
|
||||
rv$list$regression$models |>
|
||||
purrr::imap(\(.x, .i){
|
||||
purrr::imap(\(.x,.i){
|
||||
rv$list$regression$models[[.i]][["code_table"]] <- paste(
|
||||
.x$code,
|
||||
expression_string(rlang::call2(.fn = "regression_table", !!!parameters, .ns = "FreesearchR"), assign.str = NULL),
|
||||
sep = "|>\n"
|
||||
)
|
||||
expression_string(rlang::call2(.fn = "regression_table",!!!parameters,.ns = "FreesearchR"),assign.str=NULL),sep="|>\n")
|
||||
})
|
||||
|
||||
rv$list$regression$tables <- out
|
||||
rv$list$input <- input
|
||||
list(
|
||||
rv$code$import,
|
||||
rlang::call2(.fn = "select",!!!list(input$import_var),.ns = "dplyr"),
|
||||
rlang::call2(.fn = "default_parsing",.ns = "FreesearchR")
|
||||
) |>
|
||||
merge_expression() |>
|
||||
expression_string()
|
||||
|
||||
rv$list$regression$tables <- out
|
||||
|
||||
rv$list$input <- input
|
||||
},
|
||||
warning = function(warn) {
|
||||
showNotification(paste0(warn), type = "warning")
|
||||
|
|
@ -7587,15 +7558,11 @@ regression_server <- function(id,
|
|||
)
|
||||
|
||||
output$table2 <- gt::render_gt({
|
||||
## Print checks if a regression table is present
|
||||
if (!is.null(rv$list$regression$tables)) {
|
||||
shiny::req(rv$list$regression$tables)
|
||||
rv$list$regression$tables |>
|
||||
tbl_merge() |>
|
||||
gtsummary::as_gt() |>
|
||||
gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
|
||||
} else {
|
||||
return(NULL)
|
||||
}
|
||||
})
|
||||
|
||||
##############################################################################
|
||||
|
|
@ -7686,13 +7653,15 @@ regression_server <- function(id,
|
|||
##############################################################################
|
||||
|
||||
return(shiny::reactive({
|
||||
rv$list
|
||||
return(rv$list)
|
||||
}))
|
||||
}
|
||||
)
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/R//report.R
|
||||
########
|
||||
|
|
@ -7872,7 +7841,7 @@ FreesearchR_colors <- function(choose = NULL) {
|
|||
fg = "#000000"
|
||||
)
|
||||
if (!is.null(choose)) {
|
||||
unname(out[choose])
|
||||
out[choose]
|
||||
} else {
|
||||
out
|
||||
}
|
||||
|
|
@ -9193,17 +9162,7 @@ grepl_fix <- function(data, pattern, type = c("prefix", "infix", "suffix")) {
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/dev/header_include.R
|
||||
########
|
||||
|
||||
header_include <- function(){
|
||||
shiny::tags$head(
|
||||
tags$link(rel = "stylesheet", type = "text/css", href = "style.css"))
|
||||
}
|
||||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/app/ui.R
|
||||
#### Current file: /Users/au301842/FreesearchR/inst/apps/FreesearchR/ui.R
|
||||
########
|
||||
|
||||
# ns <- NS(id)
|
||||
|
|
@ -9719,10 +9678,10 @@ dark <- custom_theme(
|
|||
ui <- bslib::page_fixed(
|
||||
prismDependencies,
|
||||
prismRDependency,
|
||||
header_include(),
|
||||
## This adds the actual favicon
|
||||
## png and ico versions are kept for compatibility
|
||||
shiny::tags$head(tags$link(rel="shortcut icon", href="favicon.svg")),
|
||||
shiny::tags$head(
|
||||
includeHTML(("www/umami-app.html")),
|
||||
tags$link(rel = "stylesheet", type = "text/css", href = "style.css")),
|
||||
tags$head(tags$link(rel="shortcut icon", href="favicon.svg")),
|
||||
title = "FreesearchR",
|
||||
theme = light,
|
||||
shiny::useBusyIndicators(),
|
||||
|
|
@ -9742,7 +9701,7 @@ ui <- bslib::page_fixed(
|
|||
style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
|
||||
shiny::p(
|
||||
style = "margin: 1",
|
||||
"Data is only stored for analyses and deleted when the app is closed.", shiny::markdown("Consider [running ***FreesearchR*** locally](https://agdamsbo.github.io/FreesearchR/#run-locally-on-your-own-machine) if working with sensitive data.")
|
||||
"Data is only stored for analyses and deleted when the app is closed."
|
||||
),
|
||||
shiny::p(
|
||||
style = "margin: 1; color: #888;",
|
||||
|
|
@ -9753,9 +9712,8 @@ ui <- bslib::page_fixed(
|
|||
)
|
||||
|
||||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/app/server.R
|
||||
#### Current file: /Users/au301842/FreesearchR/inst/apps/FreesearchR/server.R
|
||||
########
|
||||
|
||||
library(readr)
|
||||
|
|
@ -9793,7 +9751,7 @@ library(gtsummary)
|
|||
data(starwars)
|
||||
data(mtcars)
|
||||
mtcars_date <- mtcars |> append_column(as.Date(sample(1:365, nrow(mtcars))), "rand_dates")
|
||||
mtcars_date$date <- as.Date(sample(seq_len(365), nrow(mtcars)))
|
||||
mtcars_date$date <- as.Date(sample(seq_len(365),nrow(mtcars)))
|
||||
data(trial)
|
||||
|
||||
|
||||
|
|
@ -9839,7 +9797,7 @@ server <- function(input, output, session) {
|
|||
|
||||
rv <- shiny::reactiveValues(
|
||||
list = list(),
|
||||
regression = NULL,
|
||||
regression = list(),
|
||||
ds = NULL,
|
||||
local_temp = NULL,
|
||||
ready = NULL,
|
||||
|
|
@ -10224,20 +10182,6 @@ server <- function(input, output, session) {
|
|||
))
|
||||
})
|
||||
|
||||
## Evaluation table/plots reset on data change
|
||||
## This does not work (!?)
|
||||
shiny::observeEvent(
|
||||
list(
|
||||
rv$data_filtered
|
||||
),
|
||||
{
|
||||
shiny::req(rv$data_filtered)
|
||||
|
||||
rv$list$table1 <- NULL
|
||||
# rv$regression <- NULL
|
||||
}
|
||||
)
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
|
|
@ -10299,7 +10243,6 @@ server <- function(input, output, session) {
|
|||
## Just a note to self
|
||||
## This is a very rewarding couple of lines marking new insights to dynamically rendering code
|
||||
shiny::observe({
|
||||
shiny::req(rv$regression)
|
||||
rv$regression()$regression$models |> purrr::imap(\(.x, .i){
|
||||
output[[paste0("code_", tolower(.i))]] <- shiny::renderUI({
|
||||
prismCodeBlock(paste0(paste("#", .i, "regression model\n"), .x$code_table))
|
||||
|
|
@ -10376,13 +10319,11 @@ server <- function(input, output, session) {
|
|||
})
|
||||
|
||||
output$table1 <- gt::render_gt({
|
||||
if (!is.null(rv$list$table1)) {
|
||||
shiny::req(rv$list$table1)
|
||||
|
||||
rv$list$table1 |>
|
||||
gtsummary::as_gt() |>
|
||||
gt::tab_header(gt::md("**Table 1: Baseline Characteristics**"))
|
||||
} else {
|
||||
return(NULL)
|
||||
}
|
||||
})
|
||||
|
||||
data_correlations_server(
|
||||
|
|
@ -10414,22 +10355,6 @@ server <- function(input, output, session) {
|
|||
|
||||
rv$regression <- regression_server("regression", data = shiny::reactive(rv$list$data))
|
||||
|
||||
# shiny::observeEvent(rv$regression, {
|
||||
# browser()
|
||||
# if (shiny::is.reactive(rv$regression)) {
|
||||
# rv$list$regression <- rv$regression()
|
||||
# } else {
|
||||
# rv$list$regression <- rv$regression
|
||||
# }
|
||||
# # rv$list$regression <- rv$regression()
|
||||
# })
|
||||
|
||||
# output$regression_models <- renderText({
|
||||
# req(rv$list$regression)
|
||||
# browser()
|
||||
# names(rv$list$regression)
|
||||
# })
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Page navigation
|
||||
|
|
@ -10480,7 +10405,6 @@ server <- function(input, output, session) {
|
|||
paste0("report.", input$output_type)
|
||||
}),
|
||||
content = function(file, type = input$output_type) {
|
||||
# browser()
|
||||
# shiny::req(rv$list$regression)
|
||||
## Notification is not progressing
|
||||
## Presumably due to missing
|
||||
|
|
@ -10489,11 +10413,6 @@ server <- function(input, output, session) {
|
|||
format <- ifelse(type == "docx", "word_document", "odt_document")
|
||||
|
||||
# browser()
|
||||
# if (shiny::is.reactive(rv$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..", {
|
||||
|
|
@ -10547,7 +10466,7 @@ server <- function(input, output, session) {
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/FreesearchR/app/launch.R
|
||||
#### Current file: /Users/au301842/FreesearchR/inst/apps/FreesearchR/launch.R
|
||||
########
|
||||
|
||||
shinyApp(ui, server)
|
||||
|
|
|
|||
1
inst/apps/FreesearchR/launch.R
Normal file
1
inst/apps/FreesearchR/launch.R
Normal file
|
|
@ -0,0 +1 @@
|
|||
shinyApp(ui, server)
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
name: FreesearchR
|
||||
title:
|
||||
username: agdamsbo
|
||||
account: agdamsbo
|
||||
server: shinyapps.io
|
||||
hostUrl: https://api.shinyapps.io/v1
|
||||
appId: 14600805
|
||||
bundleId: 10199884
|
||||
url: https://agdamsbo.shinyapps.io/FreesearchR/
|
||||
version: 1
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
name: freesearcheR
|
||||
title:
|
||||
username: agdamsbo
|
||||
account: agdamsbo
|
||||
server: shinyapps.io
|
||||
hostUrl: https://api.shinyapps.io/v1
|
||||
appId: 13611288
|
||||
bundleId: 10164589
|
||||
url: https://agdamsbo.shinyapps.io/freesearcheR/
|
||||
version: 1
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
name: webResearch
|
||||
title:
|
||||
username: agdamsbo
|
||||
account: agdamsbo
|
||||
server: shinyapps.io
|
||||
hostUrl: https://api.shinyapps.io/v1
|
||||
appId: 13276335
|
||||
bundleId: 9436643
|
||||
url: https://agdamsbo.shinyapps.io/webResearch/
|
||||
version: 1
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
name: freesearcheR_dev
|
||||
title:
|
||||
username: cognitiveindex
|
||||
account: cognitiveindex
|
||||
server: shinyapps.io
|
||||
hostUrl: https://api.shinyapps.io/v1
|
||||
appId: 13786206
|
||||
bundleId: 9688582
|
||||
url: https://cognitiveindex.shinyapps.io/freesearcheR_dev/
|
||||
version: 1
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
name: freesearcheR_extra
|
||||
title:
|
||||
username: cognitiveindex
|
||||
account: cognitiveindex
|
||||
server: shinyapps.io
|
||||
hostUrl: https://api.shinyapps.io/v1
|
||||
appId: 13622743
|
||||
bundleId: 9544828
|
||||
url: https://cognitiveindex.shinyapps.io/freesearcheR_extra/
|
||||
version: 1
|
||||
747
inst/apps/FreesearchR/server.R
Normal file
747
inst/apps/FreesearchR/server.R
Normal file
|
|
@ -0,0 +1,747 @@
|
|||
library(readr)
|
||||
library(MASS)
|
||||
library(stats)
|
||||
library(gt)
|
||||
# library(openxlsx2)
|
||||
library(haven)
|
||||
library(readODS)
|
||||
require(shiny)
|
||||
library(bslib)
|
||||
library(assertthat)
|
||||
library(dplyr)
|
||||
library(quarto)
|
||||
library(here)
|
||||
library(broom)
|
||||
library(broom.helpers)
|
||||
# library(REDCapCAST)
|
||||
library(easystats)
|
||||
# library(esquisse)
|
||||
library(patchwork)
|
||||
library(DHARMa)
|
||||
library(apexcharter)
|
||||
library(toastui)
|
||||
library(datamods)
|
||||
library(IDEAFilter)
|
||||
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$docs_file <- shiny::renderUI({
|
||||
# shiny::includeHTML("www/docs.html")
|
||||
shiny::HTML(readLines("www/docs.html"))
|
||||
})
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Night mode (just very popular, not really needed)
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
# observeEvent(input$dark_mode,{
|
||||
# session$setCurrentTheme(
|
||||
# if (isTRUE(input$dark_mode)) dark else light
|
||||
# )})
|
||||
|
||||
# observe({
|
||||
# if(input$dark_mode==TRUE)
|
||||
# session$setCurrentTheme(bs_theme_update(theme = custom_theme(version = 5)))
|
||||
# if(input$dark_mode==FALSE)
|
||||
# session$setCurrentTheme(bs_theme_update(theme = custom_theme(version = 5, bg = "#000",fg="#fff")))
|
||||
# })
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Setting reactive values
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
rv <- shiny::reactiveValues(
|
||||
list = list(),
|
||||
regression = list(),
|
||||
ds = NULL,
|
||||
local_temp = NULL,
|
||||
ready = NULL,
|
||||
test = "no",
|
||||
data_original = NULL,
|
||||
data_temp = NULL,
|
||||
data = NULL,
|
||||
data_variables = NULL,
|
||||
data_filtered = NULL,
|
||||
models = NULL,
|
||||
code = list()
|
||||
)
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data import section
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
data_file <- import_file_server(
|
||||
id = "file_import",
|
||||
show_data_in = "popup",
|
||||
trigger_return = "change",
|
||||
return_class = "data.frame"
|
||||
)
|
||||
|
||||
shiny::observeEvent(data_file$data(), {
|
||||
shiny::req(data_file$data())
|
||||
rv$data_temp <- data_file$data()
|
||||
rv$code <- modifyList(x = rv$code, list(import = data_file$code()))
|
||||
})
|
||||
|
||||
from_redcap <- m_redcap_readServer(
|
||||
id = "redcap_import"
|
||||
)
|
||||
|
||||
shiny::observeEvent(from_redcap$data(), {
|
||||
rv$data_temp <- from_redcap$data()
|
||||
rv$code <- modifyList(x = rv$code, list(import = from_redcap$code()))
|
||||
})
|
||||
|
||||
## This is used to ensure the reactive data is retrieved
|
||||
output$redcap_prev <- DT::renderDT(
|
||||
{
|
||||
DT::datatable(head(from_redcap$data(), 5),
|
||||
caption = "First 5 observations"
|
||||
)
|
||||
},
|
||||
server = TRUE
|
||||
)
|
||||
|
||||
from_env <- datamods::import_globalenv_server(
|
||||
id = "env",
|
||||
trigger_return = "change",
|
||||
btn_show_data = FALSE,
|
||||
reset = reactive(input$hidden)
|
||||
)
|
||||
|
||||
shiny::observeEvent(from_env$data(), {
|
||||
shiny::req(from_env$data())
|
||||
|
||||
rv$data_temp <- from_env$data()
|
||||
rv$code <- modifyList(x = rv$code, list(import = from_env$name()))
|
||||
})
|
||||
|
||||
output$import_var <- shiny::renderUI({
|
||||
shiny::req(rv$data_temp)
|
||||
|
||||
preselect <- names(rv$data_temp)[sapply(rv$data_temp, missing_fraction) <= input$complete_cutoff / 100]
|
||||
|
||||
shinyWidgets::virtualSelectInput(
|
||||
inputId = "import_var",
|
||||
label = "Select variables to include",
|
||||
selected = preselect,
|
||||
choices = names(rv$data_temp),
|
||||
updateOn = "change",
|
||||
multiple = TRUE,
|
||||
search = TRUE,
|
||||
showValueAsTags = TRUE
|
||||
)
|
||||
})
|
||||
|
||||
output$data_loaded <- shiny::reactive({
|
||||
!is.null(rv$data_temp)
|
||||
})
|
||||
|
||||
shiny::observeEvent(input$source, {
|
||||
rv$data_temp <- NULL
|
||||
})
|
||||
|
||||
shiny::outputOptions(output, "data_loaded", suspendWhenHidden = FALSE)
|
||||
|
||||
shiny::observeEvent(
|
||||
eventExpr = list(
|
||||
input$import_var,
|
||||
input$complete_cutoff,
|
||||
rv$data_temp
|
||||
),
|
||||
handlerExpr = {
|
||||
shiny::req(rv$data_temp)
|
||||
shiny::req(input$import_var)
|
||||
# browser()
|
||||
temp_data <- rv$data_temp
|
||||
if (all(input$import_var %in% names(temp_data))) {
|
||||
temp_data <- temp_data |> dplyr::select(input$import_var)
|
||||
}
|
||||
|
||||
rv$data_original <- temp_data |>
|
||||
default_parsing()
|
||||
|
||||
rv$code$import <- rv$code$import |>
|
||||
expression_string(assign.str = "df <-")
|
||||
|
||||
rv$code$format <- list(
|
||||
"df",
|
||||
rlang::expr(dplyr::select(dplyr::all_of(!!input$import_var))),
|
||||
rlang::call2(.fn = "default_parsing", .ns = "FreesearchR")
|
||||
) |>
|
||||
lapply(expression_string) |>
|
||||
pipe_string() |>
|
||||
expression_string(assign.str = "df <-")
|
||||
|
||||
rv$code$filter <- NULL
|
||||
rv$code$modify <- NULL
|
||||
}, ignoreNULL = FALSE
|
||||
)
|
||||
|
||||
output$data_info_import <- shiny::renderUI({
|
||||
shiny::req(rv$data_original)
|
||||
data_description(rv$data_original)
|
||||
})
|
||||
|
||||
## Activating action buttons on data imported
|
||||
shiny::observeEvent(rv$data_original, {
|
||||
if (is.null(rv$data_original) | NROW(rv$data_original) == 0) {
|
||||
shiny::updateActionButton(inputId = "act_start", disabled = TRUE)
|
||||
shiny::updateActionButton(inputId = "modal_browse", disabled = TRUE)
|
||||
shiny::updateActionButton(inputId = "act_eval", disabled = TRUE)
|
||||
} else {
|
||||
shiny::updateActionButton(inputId = "act_start", disabled = FALSE)
|
||||
shiny::updateActionButton(inputId = "modal_browse", disabled = FALSE)
|
||||
shiny::updateActionButton(inputId = "act_eval", disabled = FALSE)
|
||||
}
|
||||
})
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data modification section
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
shiny::observeEvent(
|
||||
eventExpr = list(
|
||||
rv$data_original
|
||||
),
|
||||
handlerExpr = {
|
||||
shiny::req(rv$data_original)
|
||||
|
||||
rv$data <- rv$data_original
|
||||
}
|
||||
)
|
||||
|
||||
## For now this solution work, but I would prefer to solve this with the above
|
||||
shiny::observeEvent(input$reset_confirm,
|
||||
{
|
||||
if (isTRUE(input$reset_confirm)) {
|
||||
shiny::req(rv$data_original)
|
||||
rv$data <- rv$data_original
|
||||
rv$code$filter <- NULL
|
||||
rv$code$variables <- NULL
|
||||
rv$code$modify <- NULL
|
||||
}
|
||||
},
|
||||
ignoreNULL = TRUE
|
||||
)
|
||||
|
||||
|
||||
shiny::observeEvent(input$data_reset, {
|
||||
shinyWidgets::ask_confirmation(
|
||||
cancelOnDismiss = TRUE,
|
||||
inputId = "reset_confirm",
|
||||
title = "Please confirm data reset?",
|
||||
type = "warning"
|
||||
)
|
||||
})
|
||||
|
||||
|
||||
#########
|
||||
######### Modifications
|
||||
#########
|
||||
|
||||
## Using modified version of the datamods::cut_variable_server function
|
||||
## Further modifications are needed to have cut/bin options based on class of variable
|
||||
## Could be defined server-side
|
||||
|
||||
output$data_info <- shiny::renderUI({
|
||||
shiny::req(data_filter())
|
||||
data_description(data_filter(), "The filtered data")
|
||||
})
|
||||
|
||||
######### Create factor
|
||||
|
||||
shiny::observeEvent(
|
||||
input$modal_cut,
|
||||
modal_cut_variable("modal_cut", title = "Create new factor")
|
||||
)
|
||||
|
||||
data_modal_cut <- cut_variable_server(
|
||||
id = "modal_cut",
|
||||
data_r = shiny::reactive(rv$data)
|
||||
)
|
||||
|
||||
shiny::observeEvent(data_modal_cut(), {
|
||||
rv$data <- data_modal_cut()
|
||||
rv$code$modify[[length(rv$code$modify) + 1]] <- attr(rv$data, "code")
|
||||
})
|
||||
|
||||
######### Modify factor
|
||||
|
||||
shiny::observeEvent(
|
||||
input$modal_update,
|
||||
datamods::modal_update_factor(id = "modal_update", title = "Reorder factor levels")
|
||||
)
|
||||
|
||||
data_modal_update <- datamods::update_factor_server(
|
||||
id = "modal_update",
|
||||
data_r = reactive(rv$data)
|
||||
)
|
||||
|
||||
shiny::observeEvent(data_modal_update(), {
|
||||
shiny::removeModal()
|
||||
rv$data <- data_modal_update()
|
||||
rv$code$modify[[length(rv$code$modify) + 1]] <- attr(rv$data, "code")
|
||||
})
|
||||
|
||||
######### Create column
|
||||
|
||||
shiny::observeEvent(
|
||||
input$modal_column,
|
||||
modal_create_column(
|
||||
id = "modal_column",
|
||||
footer = shiny::markdown("This window is aimed at advanced users and require some *R*-experience!"),
|
||||
title = "Create new variables"
|
||||
)
|
||||
)
|
||||
data_modal_r <- create_column_server(
|
||||
id = "modal_column",
|
||||
data_r = reactive(rv$data)
|
||||
)
|
||||
shiny::observeEvent(
|
||||
data_modal_r(),
|
||||
{
|
||||
rv$data <- data_modal_r()
|
||||
rv$code$modify[[length(rv$code$modify) + 1]] <- attr(rv$data, "code")
|
||||
}
|
||||
)
|
||||
|
||||
######### Subset, rename, reclass
|
||||
|
||||
updated_data <- update_variables_server(
|
||||
id = "modal_variables",
|
||||
data = shiny::reactive(rv$data),
|
||||
return_data_on_init = FALSE
|
||||
)
|
||||
|
||||
shiny::observeEvent(updated_data(), {
|
||||
rv$data <- updated_data()
|
||||
rv$code$modify[[length(rv$code$modify) + 1]] <- attr(rv$data, "code")
|
||||
})
|
||||
|
||||
### Column filter
|
||||
### Completely implemented, but it takes a little considering where in the
|
||||
### data flow to implement, as it will act destructively on previous
|
||||
### manipulations
|
||||
|
||||
output$column_filter <- shiny::renderUI({
|
||||
shiny::req(rv$data)
|
||||
# c("dichotomous", "ordinal", "categorical", "datatime", "continuous")
|
||||
shinyWidgets::virtualSelectInput(
|
||||
inputId = "column_filter",
|
||||
label = "Select variable types to include",
|
||||
selected = unique(data_type(rv$data)),
|
||||
choices = unique(data_type(rv$data)),
|
||||
updateOn = "change",
|
||||
multiple = TRUE,
|
||||
search = FALSE,
|
||||
showValueAsTags = TRUE
|
||||
)
|
||||
})
|
||||
|
||||
shiny::observe({
|
||||
# shiny::req(input$column_filter)
|
||||
out <- data_type_filter(rv$data, input$column_filter)
|
||||
rv$data_variables <- out
|
||||
if (!is.null(input$column_filter)) {
|
||||
rv$code$variables <- attr(out, "code")
|
||||
}
|
||||
# rv$code$modify[[length(rv$code$modify) + 1]] <- attr(rv$data, "code")
|
||||
})
|
||||
|
||||
|
||||
######### Data filter
|
||||
# IDEAFilter has the least cluttered UI, but might have a License issue
|
||||
# Consider using shinyDataFilter, though not on CRAN
|
||||
data_filter <- IDEAFilter::IDEAFilter("data_filter",
|
||||
data = shiny::reactive(rv$data_variables),
|
||||
verbose = TRUE
|
||||
)
|
||||
|
||||
shiny::observeEvent(
|
||||
list(
|
||||
shiny::reactive(rv$data_variables),
|
||||
shiny::reactive(rv$data_original),
|
||||
data_filter(),
|
||||
# regression_vars(),
|
||||
input$complete_cutoff
|
||||
),
|
||||
{
|
||||
### Save filtered data
|
||||
rv$data_filtered <- data_filter()
|
||||
|
||||
### Save filtered data
|
||||
### without empty factor levels
|
||||
rv$list$data <- data_filter() |>
|
||||
REDCapCAST::fct_drop() |>
|
||||
(\(.x){
|
||||
.x[!sapply(.x, is.character)]
|
||||
})()
|
||||
|
||||
## This looks messy!! But it works as intended for now
|
||||
|
||||
out <- gsub(
|
||||
"filter", "dplyr::filter",
|
||||
gsub(
|
||||
"\\s{2,}", " ",
|
||||
paste0(
|
||||
capture.output(attr(rv$data_filtered, "code")),
|
||||
collapse = " "
|
||||
)
|
||||
)
|
||||
)
|
||||
|
||||
out <- strsplit(out, "%>%") |>
|
||||
unlist() |>
|
||||
(\(.x){
|
||||
paste(c("df <- df", .x[-1], "REDCapCAST::fct_drop()"),
|
||||
collapse = "|> \n "
|
||||
)
|
||||
})()
|
||||
|
||||
rv$code <- append_list(data = out, list = rv$code, index = "filter")
|
||||
}
|
||||
)
|
||||
|
||||
######### Data preview
|
||||
|
||||
### Overview
|
||||
|
||||
data_summary_server(
|
||||
id = "data_summary",
|
||||
data = shiny::reactive({
|
||||
rv$data_filtered
|
||||
}),
|
||||
color.main = "#2A004E",
|
||||
color.sec = "#C62300",
|
||||
pagination = 10
|
||||
)
|
||||
|
||||
observeEvent(input$modal_browse, {
|
||||
show_data(REDCapCAST::fct_drop(rv$data_filtered), title = "Uploaded data overview", type = "modal")
|
||||
})
|
||||
|
||||
output$original_str <- renderPrint({
|
||||
str(rv$data_original)
|
||||
})
|
||||
|
||||
output$modified_str <- renderPrint({
|
||||
str(as.data.frame(rv$data_filtered) |>
|
||||
REDCapCAST::set_attr(
|
||||
label = NULL,
|
||||
attr = "code"
|
||||
))
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Code export
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
## This really should be collapsed to only one call, but I'll leave it for now
|
||||
## as a working example of dynamically defining outputs and rendering.
|
||||
|
||||
# output$code_import <- shiny::renderPrint({
|
||||
# shiny::req(rv$code$import)
|
||||
# cat(c("#Data import\n", rv$code$import))
|
||||
# })
|
||||
|
||||
output$code_import <- shiny::renderUI({
|
||||
prismCodeBlock(paste0("#Data import\n", rv$code$import))
|
||||
})
|
||||
|
||||
output$code_import <- shiny::renderUI({
|
||||
prismCodeBlock(paste0("#Data import formatting\n", rv$code$format))
|
||||
})
|
||||
|
||||
output$code_data <- shiny::renderUI({
|
||||
shiny::req(rv$code$modify)
|
||||
# browser()
|
||||
## This will create three lines for each modification
|
||||
# ls <- rv$code$modify
|
||||
## This will remove all non-unique entries
|
||||
# ls <- rv$code$modify |> unique()
|
||||
## This will only remove all non-repeating entries
|
||||
ls <- rv$code$modify[!is_identical_to_previous(rv$code$modify)]
|
||||
|
||||
out <- ls |>
|
||||
lapply(expression_string) |>
|
||||
pipe_string() |>
|
||||
expression_string(assign.str = "df <- df |>\n")
|
||||
|
||||
prismCodeBlock(paste0("#Data modifications\n", out))
|
||||
})
|
||||
|
||||
output$code_variables <- shiny::renderUI({
|
||||
shiny::req(rv$code$variables)
|
||||
out <- expression_string(rv$code$variables, assign.str = "df <- df |>\n")
|
||||
prismCodeBlock(paste0("#Variables filter\n", out))
|
||||
})
|
||||
|
||||
output$code_filter <- shiny::renderUI({
|
||||
shiny::req(rv$code$filter)
|
||||
prismCodeBlock(paste0("#Data filter\n", rv$code$filter))
|
||||
})
|
||||
|
||||
output$code_table1 <- shiny::renderUI({
|
||||
shiny::req(rv$code$table1)
|
||||
prismCodeBlock(paste0("#Data characteristics table\n", rv$code$table1))
|
||||
})
|
||||
|
||||
|
||||
## Just a note to self
|
||||
## This is a very rewarding couple of lines marking new insights to dynamically rendering code
|
||||
shiny::observe({
|
||||
rv$regression()$regression$models |> purrr::imap(\(.x, .i){
|
||||
output[[paste0("code_", tolower(.i))]] <- shiny::renderUI({
|
||||
prismCodeBlock(paste0(paste("#", .i, "regression model\n"), .x$code_table))
|
||||
})
|
||||
})
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data analyses Inputs
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
output$strat_var <- shiny::renderUI({
|
||||
columnSelectInput(
|
||||
inputId = "strat_var",
|
||||
selected = "none",
|
||||
label = "Select variable to stratify baseline",
|
||||
data = shiny::reactive(rv$data_filtered)(),
|
||||
col_subset = c(
|
||||
"none",
|
||||
names(rv$data_filtered)[unlist(lapply(rv$data_filtered, data_type)) %in% c("dichotomous", "categorical", "ordinal")]
|
||||
)
|
||||
)
|
||||
})
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Descriptive evaluations
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
|
||||
output$data_info_nochar <- shiny::renderUI({
|
||||
shiny::req(rv$list$data)
|
||||
data_description(rv$list$data, data_text = "The dataset without text variables")
|
||||
})
|
||||
|
||||
shiny::observeEvent(
|
||||
list(
|
||||
input$act_eval
|
||||
),
|
||||
{
|
||||
shiny::req(input$strat_var)
|
||||
shiny::req(rv$list$data)
|
||||
|
||||
parameters <- list(
|
||||
by.var = input$strat_var,
|
||||
add.p = input$add_p == "yes",
|
||||
add.overall = TRUE
|
||||
)
|
||||
|
||||
shiny::withProgress(message = "Creating the table. Hold on for a moment..", {
|
||||
rv$list$table1 <- rlang::exec(create_baseline, !!!append_list(rv$list$data, parameters, "data"))
|
||||
})
|
||||
|
||||
rv$code$table1 <- glue::glue("FreesearchR::create_baseline(data,{list2str(parameters)})")
|
||||
}
|
||||
)
|
||||
|
||||
output$outcome_var_cor <- shiny::renderUI({
|
||||
columnSelectInput(
|
||||
inputId = "outcome_var_cor",
|
||||
selected = "none",
|
||||
data = rv$list$data,
|
||||
label = "Select outcome variable",
|
||||
col_subset = c(
|
||||
"none",
|
||||
colnames(rv$list$data)
|
||||
),
|
||||
multiple = FALSE
|
||||
)
|
||||
})
|
||||
|
||||
output$table1 <- gt::render_gt({
|
||||
shiny::req(rv$list$table1)
|
||||
|
||||
rv$list$table1 |>
|
||||
gtsummary::as_gt() |>
|
||||
gt::tab_header(gt::md("**Table 1: Baseline Characteristics**"))
|
||||
})
|
||||
|
||||
data_correlations_server(
|
||||
id = "correlations",
|
||||
data = shiny::reactive({
|
||||
shiny::req(rv$list$data)
|
||||
out <- rv$list$data
|
||||
if (!is.null(input$outcome_var_cor) && input$outcome_var_cor != "none") {
|
||||
out <- out[!names(out) %in% input$outcome_var_cor]
|
||||
}
|
||||
out
|
||||
}),
|
||||
cutoff = shiny::reactive(input$cor_cutoff)
|
||||
)
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data visuals
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
pl <- data_visuals_server("visuals", data = shiny::reactive(rv$list$data))
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Regression model analyses
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
rv$regression <- regression_server("regression", data = shiny::reactive(rv$list$data))
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Page navigation
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
shiny::observeEvent(input$act_start, {
|
||||
bslib::nav_select(id = "main_panel", selected = "Data")
|
||||
})
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Reactivity
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
output$uploaded <- shiny::reactive({
|
||||
if (is.null(rv$ds)) {
|
||||
"no"
|
||||
} else {
|
||||
"yes"
|
||||
}
|
||||
})
|
||||
|
||||
shiny::outputOptions(output, "uploaded", suspendWhenHidden = FALSE)
|
||||
|
||||
output$ready <- shiny::reactive({
|
||||
if (is.null(rv$ready)) {
|
||||
"no"
|
||||
} else {
|
||||
"yes"
|
||||
}
|
||||
})
|
||||
|
||||
shiny::outputOptions(output, "ready", suspendWhenHidden = FALSE)
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Downloads
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
# Could be rendered with other tables or should show progress
|
||||
# Investigate quarto render problems
|
||||
# On temp file handling: https://github.com/quarto-dev/quarto-cli/issues/3992
|
||||
output$report <- downloadHandler(
|
||||
filename = shiny::reactive({
|
||||
paste0("report.", input$output_type)
|
||||
}),
|
||||
content = function(file, type = input$output_type) {
|
||||
# shiny::req(rv$list$regression)
|
||||
## Notification is not progressing
|
||||
## Presumably due to missing
|
||||
# browser()
|
||||
# Simplified for .rmd output attempt
|
||||
format <- ifelse(type == "docx", "word_document", "odt_document")
|
||||
|
||||
# browser()
|
||||
rv$list$regression <- rv$regression()
|
||||
|
||||
shiny::withProgress(message = "Generating the report. Hold on for a moment..", {
|
||||
tryCatch(
|
||||
{
|
||||
rv$list |>
|
||||
write_rmd(
|
||||
output_format = format,
|
||||
input = file.path(getwd(), "www/report.rmd")
|
||||
)
|
||||
},
|
||||
error = function(err) {
|
||||
showNotification(paste0("We encountered the following error creating your report: ", err), type = "err")
|
||||
}
|
||||
)
|
||||
})
|
||||
file.rename(paste0("www/report.", type), file)
|
||||
}
|
||||
)
|
||||
|
||||
output$data_modified <- downloadHandler(
|
||||
filename = shiny::reactive({
|
||||
paste0("modified_data.", input$data_type)
|
||||
}),
|
||||
content = function(file, type = input$data_type) {
|
||||
if (type == "rds") {
|
||||
readr::write_rds(rv$list$data, file = file)
|
||||
} else if (type == "dta") {
|
||||
haven::write_dta(as.data.frame(rv$list$data), path = file)
|
||||
} else if (type == "csv") {
|
||||
readr::write_csv(rv$list$data, file = file)
|
||||
}
|
||||
}
|
||||
)
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Clearing the session on end
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
session$onSessionEnded(function() {
|
||||
cat("Session Ended\n")
|
||||
files <- list.files("www/")
|
||||
lapply(files[!files %in% files.to.keep], \(.x){
|
||||
unlink(paste0("www/", .x), recursive = FALSE)
|
||||
print(paste(.x, "deleted"))
|
||||
})
|
||||
})
|
||||
}
|
||||
|
|
@ -508,10 +508,13 @@ dark <- custom_theme(
|
|||
# Fonts to consider:
|
||||
# https://webdesignerdepot.com/17-open-source-fonts-youll-actually-love/
|
||||
|
||||
ui_list <- shiny::tagList(
|
||||
ui <- bslib::page_fixed(
|
||||
prismDependencies,
|
||||
prismRDependency,
|
||||
header_include(),
|
||||
## Basic Umami page tracking
|
||||
shiny::tags$head(
|
||||
includeHTML(("www/umami-app.html")),
|
||||
tags$link(rel = "stylesheet", type = "text/css", href = "style.css")),
|
||||
## This adds the actual favicon
|
||||
## png and ico versions are kept for compatibility
|
||||
shiny::tags$head(tags$link(rel="shortcut icon", href="favicon.svg")),
|
||||
|
|
@ -543,12 +546,3 @@ ui_list <- shiny::tagList(
|
|||
)
|
||||
)
|
||||
)
|
||||
|
||||
# ui_list <- shiny::tagAppendChild(ui_list,list(
|
||||
# ## Basic Umami page tracking
|
||||
# shiny::tags$head(includeHTML("www/umami-app.html"))
|
||||
# # shiny::tags$head(shiny::tags$script(rel="defer", src="https://analytics.gdamsbo.dk/script.js", "data-website-id"="e7d4e13a-5824-4778-bbc0-8f92fb08303a"))
|
||||
# ))
|
||||
|
||||
ui <- do.call(
|
||||
bslib::page_fixed,ui_list)
|
||||
|
|
|
|||
1
inst/apps/FreesearchR/www/umami-app.html
Normal file
1
inst/apps/FreesearchR/www/umami-app.html
Normal file
|
|
@ -0,0 +1 @@
|
|||
<script defer src="https://analytics.gdamsbo.dk/script.js" data-website-id="e7d4e13a-5824-4778-bbc0-8f92fb08303a"></script>
|
||||
Loading…
Add table
Reference in a new issue