mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2025-09-12 01:49:39 +02:00
minor rev regression module
This commit is contained in:
parent
bc9a895d3b
commit
bd21cc783b
3 changed files with 352 additions and 336 deletions
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@ -322,7 +322,7 @@ regression_server <- function(id,
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##############################################################################
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#########
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######### Regression analysis
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######### Regression models
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#########
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##############################################################################
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@ -370,6 +370,179 @@ regression_server <- function(id,
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}
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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$tables <- NULL
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}
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)
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##############################################################################
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#########
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######### Regression table
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#########
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##############################################################################
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### Creating the regression table
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shiny::observeEvent(
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input$load,
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{
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shiny::req(rv$list$regression$models)
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## To avoid plotting old models on fail/error
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rv$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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p.values = input$add_regression_p == "no"
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)
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out <- lapply(rv$list$regression$models, \(.x){
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.x$model
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}) |>
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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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)
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})
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rv$list$regression$models |>
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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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})
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rv$list$regression$tables <- out
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rv$list$input <- input
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},
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warning = function(warn) {
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showNotification(paste0(warn), type = "warning")
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},
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error = function(err) {
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showNotification(paste0("Creating a regression table failed with the following error: ", err), type = "err")
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}
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)
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}
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)
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## Consider creating merged table with theming and then passing object
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## to render.
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output$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$tables)) {
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# gtsummary::theme_gtsummary_journal(journal = "jama")
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merged <- rv$list$regression$tables |>
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tbl_merge()
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if (input$add_regression_p == "no") {
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merged <- merged |>
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gtsummary::modify_column_hide(column = dplyr::starts_with("p.value"))
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}
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out <- merged |>
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gtsummary::as_gt() |>
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gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
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# rv$list$regression$table_merged <- out
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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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##############################################################################
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#########
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######### Coefficients plot
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#########
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##############################################################################
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shiny::observeEvent(list(
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input$plot_model,
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rv$list$regression
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), {
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shiny::req(input$plot_model)
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tryCatch(
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{
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p <- merge_long(
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rv$list$regression,
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sort_by(
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input$plot_model,
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c("Univariable", "Minimal", "Multivariable"),
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na.rm = TRUE
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)
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) |>
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(\(.x){
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if (length(input$plot_model) > 1) {
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plot.tbl_regression(
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x = .x,
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colour = "model",
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dodged = TRUE
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) +
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ggplot2::theme(legend.position = "bottom") +
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ggplot2::guides(color = ggplot2::guide_legend(reverse = TRUE))
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} else {
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plot.tbl_regression(
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x = .x,
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colour = "variable"
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) +
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ggplot2::theme(legend.position = "none")
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}
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})()
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rv$plot <- p +
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ggplot2::scale_y_discrete(labels = scales::label_wrap(15)) +
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gg_theme_shiny()
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},
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error = function(err) {
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showNotification(paste0(err), type = "err")
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}
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)
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})
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output$regression_plot <- shiny::renderPlot(
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{
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shiny::req(input$plot_model)
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rv$plot
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},
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alt = "Regression coefficient plot"
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)
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# plot_download_server(
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# id = ns("reg_plot_download"),
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# data = shiny::reactive(rv$plot)
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# )
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output$download_plot <- shiny::downloadHandler(
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filename = paste0("regression_plot.", input$plot_type),
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content = function(file) {
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shiny::withProgress(message = "Saving 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$plot,
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width = input$plot_width,
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height = input$plot_height,
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dpi = 300,
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units = "mm", scale = 2
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)
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})
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}
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)
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##############################################################################
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#########
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######### Model checks
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@ -477,171 +650,6 @@ regression_server <- function(id,
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alt = "Assumptions testing of the multivariable regression model"
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)
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shiny::observeEvent(
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list(
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data_r(),
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regression_vars()
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),
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{
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rv$list$regression$tables <- NULL
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}
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)
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### Creating the regression table
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shiny::observeEvent(
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input$load,
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{
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shiny::req(rv$list$regression$models)
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## To avoid plotting old models on fail/error
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rv$list$regression$tables <- NULL
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# browser()
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tryCatch(
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{
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parameters <- list(
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p.values = input$add_regression_p == "no"
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)
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out <- lapply(rv$list$regression$models, \(.x){
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.x$model
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}) |>
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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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)
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})
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rv$list$regression$models |>
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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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})
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rv$list$regression$tables <- out
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rv$list$input <- input
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},
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warning = function(warn) {
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showNotification(paste0(warn), type = "warning")
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},
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error = function(err) {
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showNotification(paste0("Creating a regression table failed with the following error: ", err), type = "err")
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}
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)
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}
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)
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## Consider creating merged table with theming and then passing object
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## to render.
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output$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$tables)) {
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gtsummary::theme_gtsummary_journal(journal = "jama")
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merged <- rv$list$regression$tables |>
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tbl_merge()
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if (input$add_regression_p == "no") {
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merged <- merged |>
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gtsummary::modify_column_hide(column = dplyr::starts_with("p.value"))
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}
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out <- merged |>
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gtsummary::as_gt() |>
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gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
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rv$list$regression$table_merged
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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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##############################################################################
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#########
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######### Coefficients plot
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#########
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##############################################################################
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shiny::observeEvent(list(
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input$plot_model,
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rv$list$regression
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), {
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shiny::req(input$plot_model)
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tryCatch(
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{
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p <- merge_long(
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rv$list$regression,
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sort_by(
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input$plot_model,
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c("Univariable", "Minimal", "Multivariable"),
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na.rm = TRUE
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)
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) |>
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(\(.x){
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if (length(input$plot_model) > 1) {
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plot.tbl_regression(
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x = .x,
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colour = "model",
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dodged = TRUE
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) +
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ggplot2::theme(legend.position = "bottom") +
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ggplot2::guides(color = ggplot2::guide_legend(reverse = TRUE))
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} else {
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plot.tbl_regression(
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x = .x,
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colour = "variable"
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) +
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ggplot2::theme(legend.position = "none")
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}
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})()
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rv$plot <- p +
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ggplot2::scale_y_discrete(labels = scales::label_wrap(15)) +
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gg_theme_shiny()
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},
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error = function(err) {
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showNotification(paste0(err), type = "err")
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}
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)
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})
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output$regression_plot <- shiny::renderPlot(
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{
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shiny::req(input$plot_model)
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rv$plot
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},
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alt = "Regression coefficient plot"
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)
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# plot_download_server(
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# id = ns("reg_plot_download"),
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# data = shiny::reactive(rv$plot)
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# )
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output$download_plot <- shiny::downloadHandler(
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filename = paste0("regression_plot.", input$plot_type),
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content = function(file) {
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shiny::withProgress(message = "Saving 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$plot,
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width = input$plot_width,
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height = input$plot_height,
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dpi = 300,
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units = "mm", scale = 2
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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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######### Output
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@ -140,7 +140,7 @@ regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::
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}
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}
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# gtsummary::theme_gtsummary_journal(journal = theme)
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gtsummary::theme_gtsummary_journal(journal = theme)
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if (inherits(x, "polr")) {
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# browser()
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out <- do.call(getfun(fun), c(list(x = x), args.list))
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@ -49,7 +49,7 @@ library(rlang)
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#### Current file: /Users/au301842/FreesearchR/R//app_version.R
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########
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app_version <- function()'25.5.4'
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app_version <- function()'25.5.5'
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########
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@ -3996,7 +3996,7 @@ simple_snake <- function(data){
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#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R
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########
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hosted_version <- function()'v25.5.4-250513'
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hosted_version <- function()'v25.5.5-250514'
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########
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@ -7134,7 +7134,7 @@ regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::
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}
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}
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# gtsummary::theme_gtsummary_journal(journal = theme)
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gtsummary::theme_gtsummary_journal(journal = theme)
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if (inherits(x, "polr")) {
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# browser()
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out <- do.call(getfun(fun), c(list(x = x), args.list))
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@ -7505,7 +7505,7 @@ regression_server <- function(id,
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##############################################################################
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#########
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######### Regression analysis
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######### Regression models
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#########
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##############################################################################
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@ -7553,6 +7553,179 @@ regression_server <- function(id,
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}
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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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##############################################################################
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#########
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######### Regression table
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#########
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##############################################################################
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### Creating the regression table
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shiny::observeEvent(
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input$load,
|
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{
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shiny::req(rv$list$regression$models)
|
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## To avoid plotting old models on fail/error
|
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rv$list$regression$tables <- NULL
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|
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# browser()
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tryCatch(
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{
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parameters <- list(
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p.values = input$add_regression_p == "no"
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)
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out <- lapply(rv$list$regression$models, \(.x){
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.x$model
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}) |>
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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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)
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})
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rv$list$regression$models |>
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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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})
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rv$list$regression$tables <- out
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rv$list$input <- input
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},
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warning = function(warn) {
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showNotification(paste0(warn), type = "warning")
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},
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error = function(err) {
|
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showNotification(paste0("Creating a regression table failed with the following error: ", err), type = "err")
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}
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)
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}
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)
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## Consider creating merged table with theming and then passing object
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## to render.
|
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|
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output$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$tables)) {
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# gtsummary::theme_gtsummary_journal(journal = "jama")
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merged <- rv$list$regression$tables |>
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tbl_merge()
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if (input$add_regression_p == "no") {
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merged <- merged |>
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gtsummary::modify_column_hide(column = dplyr::starts_with("p.value"))
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}
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out <- merged |>
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gtsummary::as_gt() |>
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gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
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# rv$list$regression$table_merged <- out
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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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##############################################################################
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#########
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######### Coefficients plot
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#########
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##############################################################################
|
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|
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shiny::observeEvent(list(
|
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input$plot_model,
|
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rv$list$regression
|
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), {
|
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shiny::req(input$plot_model)
|
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|
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tryCatch(
|
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{
|
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p <- merge_long(
|
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rv$list$regression,
|
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sort_by(
|
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input$plot_model,
|
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c("Univariable", "Minimal", "Multivariable"),
|
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na.rm = TRUE
|
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)
|
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) |>
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(\(.x){
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if (length(input$plot_model) > 1) {
|
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plot.tbl_regression(
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x = .x,
|
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colour = "model",
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dodged = TRUE
|
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) +
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ggplot2::theme(legend.position = "bottom") +
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ggplot2::guides(color = ggplot2::guide_legend(reverse = TRUE))
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} else {
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plot.tbl_regression(
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x = .x,
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colour = "variable"
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||||
) +
|
||||
ggplot2::theme(legend.position = "none")
|
||||
}
|
||||
})()
|
||||
|
||||
rv$plot <- p +
|
||||
ggplot2::scale_y_discrete(labels = scales::label_wrap(15)) +
|
||||
gg_theme_shiny()
|
||||
},
|
||||
error = function(err) {
|
||||
showNotification(paste0(err), type = "err")
|
||||
}
|
||||
)
|
||||
})
|
||||
|
||||
|
||||
output$regression_plot <- shiny::renderPlot(
|
||||
{
|
||||
shiny::req(input$plot_model)
|
||||
|
||||
rv$plot
|
||||
},
|
||||
alt = "Regression coefficient plot"
|
||||
)
|
||||
|
||||
# plot_download_server(
|
||||
# id = ns("reg_plot_download"),
|
||||
# data = shiny::reactive(rv$plot)
|
||||
# )
|
||||
|
||||
output$download_plot <- shiny::downloadHandler(
|
||||
filename = paste0("regression_plot.", input$plot_type),
|
||||
content = function(file) {
|
||||
shiny::withProgress(message = "Saving the plot. Hold on for a moment..", {
|
||||
ggplot2::ggsave(
|
||||
filename = file,
|
||||
plot = rv$plot,
|
||||
width = input$plot_width,
|
||||
height = input$plot_height,
|
||||
dpi = 300,
|
||||
units = "mm", scale = 2
|
||||
)
|
||||
})
|
||||
}
|
||||
)
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Model checks
|
||||
|
|
@ -7660,171 +7833,6 @@ regression_server <- function(id,
|
|||
alt = "Assumptions testing of the multivariable regression model"
|
||||
)
|
||||
|
||||
shiny::observeEvent(
|
||||
list(
|
||||
data_r(),
|
||||
regression_vars()
|
||||
),
|
||||
{
|
||||
rv$list$regression$tables <- NULL
|
||||
}
|
||||
)
|
||||
|
||||
### Creating the regression table
|
||||
shiny::observeEvent(
|
||||
input$load,
|
||||
{
|
||||
shiny::req(rv$list$regression$models)
|
||||
## To avoid plotting old models on fail/error
|
||||
rv$list$regression$tables <- NULL
|
||||
|
||||
# browser()
|
||||
tryCatch(
|
||||
{
|
||||
parameters <- list(
|
||||
p.values = input$add_regression_p == "no"
|
||||
)
|
||||
|
||||
out <- lapply(rv$list$regression$models, \(.x){
|
||||
.x$model
|
||||
}) |>
|
||||
purrr::map(\(.x){
|
||||
do.call(
|
||||
regression_table,
|
||||
append_list(.x, parameters, "x")
|
||||
)
|
||||
})
|
||||
|
||||
rv$list$regression$models |>
|
||||
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"
|
||||
)
|
||||
})
|
||||
|
||||
rv$list$regression$tables <- out
|
||||
rv$list$input <- input
|
||||
},
|
||||
warning = function(warn) {
|
||||
showNotification(paste0(warn), type = "warning")
|
||||
},
|
||||
error = function(err) {
|
||||
showNotification(paste0("Creating a regression table failed with the following error: ", err), type = "err")
|
||||
}
|
||||
)
|
||||
}
|
||||
)
|
||||
|
||||
## Consider creating merged table with theming and then passing object
|
||||
## to render.
|
||||
|
||||
output$table2 <- gt::render_gt({
|
||||
## Print checks if a regression table is present
|
||||
if (!is.null(rv$list$regression$tables)) {
|
||||
gtsummary::theme_gtsummary_journal(journal = "jama")
|
||||
merged <- rv$list$regression$tables |>
|
||||
tbl_merge()
|
||||
|
||||
if (input$add_regression_p == "no") {
|
||||
merged <- merged |>
|
||||
gtsummary::modify_column_hide(column = dplyr::starts_with("p.value"))
|
||||
}
|
||||
|
||||
out <- merged |>
|
||||
gtsummary::as_gt() |>
|
||||
gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
|
||||
|
||||
rv$list$regression$table_merged
|
||||
|
||||
out
|
||||
} else {
|
||||
return(NULL)
|
||||
}
|
||||
})
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Coefficients plot
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
shiny::observeEvent(list(
|
||||
input$plot_model,
|
||||
rv$list$regression
|
||||
), {
|
||||
shiny::req(input$plot_model)
|
||||
|
||||
tryCatch(
|
||||
{
|
||||
p <- merge_long(
|
||||
rv$list$regression,
|
||||
sort_by(
|
||||
input$plot_model,
|
||||
c("Univariable", "Minimal", "Multivariable"),
|
||||
na.rm = TRUE
|
||||
)
|
||||
) |>
|
||||
(\(.x){
|
||||
if (length(input$plot_model) > 1) {
|
||||
plot.tbl_regression(
|
||||
x = .x,
|
||||
colour = "model",
|
||||
dodged = TRUE
|
||||
) +
|
||||
ggplot2::theme(legend.position = "bottom") +
|
||||
ggplot2::guides(color = ggplot2::guide_legend(reverse = TRUE))
|
||||
} else {
|
||||
plot.tbl_regression(
|
||||
x = .x,
|
||||
colour = "variable"
|
||||
) +
|
||||
ggplot2::theme(legend.position = "none")
|
||||
}
|
||||
})()
|
||||
|
||||
rv$plot <- p +
|
||||
ggplot2::scale_y_discrete(labels = scales::label_wrap(15)) +
|
||||
gg_theme_shiny()
|
||||
},
|
||||
error = function(err) {
|
||||
showNotification(paste0(err), type = "err")
|
||||
}
|
||||
)
|
||||
})
|
||||
|
||||
|
||||
output$regression_plot <- shiny::renderPlot(
|
||||
{
|
||||
shiny::req(input$plot_model)
|
||||
|
||||
rv$plot
|
||||
},
|
||||
alt = "Regression coefficient plot"
|
||||
)
|
||||
|
||||
# plot_download_server(
|
||||
# id = ns("reg_plot_download"),
|
||||
# data = shiny::reactive(rv$plot)
|
||||
# )
|
||||
|
||||
output$download_plot <- shiny::downloadHandler(
|
||||
filename = paste0("regression_plot.", input$plot_type),
|
||||
content = function(file) {
|
||||
shiny::withProgress(message = "Saving the plot. Hold on for a moment..", {
|
||||
ggplot2::ggsave(
|
||||
filename = file,
|
||||
plot = rv$plot,
|
||||
width = input$plot_width,
|
||||
height = input$plot_height,
|
||||
dpi = 300,
|
||||
units = "mm", scale = 2
|
||||
)
|
||||
})
|
||||
}
|
||||
)
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Output
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue