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https://github.com/agdamsbo/FreesearchR.git
synced 2025-09-12 09:59:39 +02:00
removed
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commit
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2 changed files with 0 additions and 1120 deletions
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@ -1,652 +0,0 @@
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library(readr)
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library(MASS)
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library(stats)
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library(gtsummary)
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library(gt)
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library(openxlsx2)
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library(haven)
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library(readODS)
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require(shiny)
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library(bslib)
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library(assertthat)
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library(dplyr)
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library(quarto)
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library(here)
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library(broom)
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library(broom.helpers)
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# library(REDCapCAST)
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library(easystats)
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library(patchwork)
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library(DHARMa)
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library(apexcharter)
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library(toastui)
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library(datamods)
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library(data.table)
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library(IDEAFilter)
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library(shinyWidgets)
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library(DT)
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# library(freesearcheR)
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# source("functions.R")
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# light <- custom_theme()
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#
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# dark <- custom_theme(bg = "#000",fg="#fff")
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server <- function(input, output, session) {
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## Listing files in www in session start to keep when ending and removing
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## everything else.
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files.to.keep <- list.files("www/")
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output$docs_file <- shiny::renderUI({
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# shiny::includeHTML("www/docs.html")
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shiny::HTML(readLines("www/docs.html"))
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})
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##############################################################################
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#########
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######### Night mode (just very popular, not really needed)
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#########
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##############################################################################
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# observeEvent(input$dark_mode,{
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# session$setCurrentTheme(
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# if (isTRUE(input$dark_mode)) dark else light
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# )})
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# observe({
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# if(input$dark_mode==TRUE)
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# session$setCurrentTheme(bs_theme_update(theme = custom_theme(version = 5)))
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# if(input$dark_mode==FALSE)
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# session$setCurrentTheme(bs_theme_update(theme = custom_theme(version = 5, bg = "#000",fg="#fff")))
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# })
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##############################################################################
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#########
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######### Setting reactive values
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#########
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##############################################################################
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rv <- shiny::reactiveValues(
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list = list(),
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ds = NULL,
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local_temp = NULL,
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ready = NULL,
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test = "no",
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data_original = NULL,
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data = NULL,
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data_filtered = NULL
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)
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##############################################################################
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#########
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######### Data import section
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#########
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##############################################################################
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data_file <- datamods::import_file_server(
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id = "file_import",
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show_data_in = "popup",
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trigger_return = "change",
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return_class = "data.frame",
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read_fns = list(
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ods = function(file) {
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readODS::read_ods(path = file)
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},
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dta = function(file) {
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haven::read_dta(file = file)
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}
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)
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)
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shiny::observeEvent(data_file$data(), {
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shiny::req(data_file$data())
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rv$data_original <- data_file$data()
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})
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data_redcap <- m_redcap_readServer(
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id = "redcap_import",
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output.format = "list"
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)
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shiny::observeEvent(data_redcap(), {
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rv$data_original <- purrr::pluck(data_redcap(), "data")()
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})
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output$redcap_prev <- DT::renderDT(
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{
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DT::datatable(head(purrr::pluck(data_redcap(), "data")(), 5),
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caption = "First 5 observations"
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)
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},
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server = TRUE
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)
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from_env <- import_globalenv_server(
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id = "env",
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trigger_return = "change",
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btn_show_data = FALSE,
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reset = reactive(input$hidden)
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)
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shiny::observeEvent(from_env$data(), {
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shiny::req(from_env$data())
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rv$data_original <- from_env$data()
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})
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##############################################################################
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#########
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######### Data modification section
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#########
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##############################################################################
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shiny::observeEvent(rv$data_original, {
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rv$data <- rv$data_original |> default_parsing()
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})
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shiny::observeEvent(input$data_reset, {
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shinyWidgets::ask_confirmation(
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inputId = "reset_confirm",
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title = "Please confirm data reset?"
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)
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})
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shiny::observeEvent(input$reset_confirm, {
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rv$data <- rv$data_original |> default_parsing()
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})
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######### Overview
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data_summary_server(
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id = "data_summary",
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data = shiny::reactive({
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rv$data_filtered
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}),
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color.main = "#2A004E",
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color.sec = "#C62300"
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)
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#########
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######### Modifications
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#########
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## Using modified version of the datamods::cut_variable_server function
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## Further modifications are needed to have cut/bin options based on class of variable
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## Could be defined server-side
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######### Create factor
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shiny::observeEvent(
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input$modal_cut,
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modal_cut_variable("modal_cut")
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)
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data_modal_cut <- cut_variable_server(
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id = "modal_cut",
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data_r = shiny::reactive(rv$data)
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)
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shiny::observeEvent(data_modal_cut(), rv$data <- data_modal_cut())
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######### Modify factor
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shiny::observeEvent(
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input$modal_update,
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datamods::modal_update_factor(id = "modal_update")
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)
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data_modal_update <- datamods::update_factor_server(
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id = "modal_update",
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data_r = reactive(rv$data)
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)
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shiny::observeEvent(data_modal_update(), {
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shiny::removeModal()
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rv$data <- data_modal_update()
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})
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######### Create column
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shiny::observeEvent(
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input$modal_column,
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datamods::modal_create_column(id = "modal_column")
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)
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data_modal_r <- datamods::create_column_server(
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id = "modal_column",
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data_r = reactive(rv$data)
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)
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shiny::observeEvent(data_modal_r(), rv$data <- data_modal_r())
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######### Show result
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output$table_mod <- toastui::renderDatagrid({
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shiny::req(rv$data)
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# data <- rv$data
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toastui::datagrid(
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# data = rv$data # ,
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data = data_filter()
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# bordered = TRUE,
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# compact = TRUE,
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# striped = TRUE
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)
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})
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output$code <- renderPrint({
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attr(rv$data, "code")
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})
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# updated_data <- datamods::update_variables_server(
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updated_data <- update_variables_server(
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id = "vars_update",
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data = reactive(rv$data),
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return_data_on_init = FALSE
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)
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output$original_str <- renderPrint({
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str(rv$data_original)
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})
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output$modified_str <- renderPrint({
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str(as.data.frame(rv$data_filtered) |>
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REDCapCAST::set_attr(
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label = NULL,
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attr = "code"
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))
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})
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shiny::observeEvent(updated_data(), {
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rv$data <- updated_data()
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})
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# IDEAFilter has the least cluttered UI, but might have a License issue
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data_filter <- IDEAFilter::IDEAFilter("data_filter", data = reactive(rv$data), verbose = TRUE)
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shiny::observeEvent(data_filter(), {
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rv$data_filtered <- data_filter()
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})
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output$filtered_code <- shiny::renderPrint({
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out <- gsub(
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"filter", "dplyr::filter",
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gsub(
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"\\s{2,}", " ",
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paste0(
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capture.output(attr(rv$data_filtered, "code")),
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collapse = " "
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)
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)
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)
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out <- strsplit(out, "%>%") |>
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unlist() |>
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(\(.x){
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paste(c("data", .x[-1]), collapse = "|> \n ")
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})()
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cat(out)
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})
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##############################################################################
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#########
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######### Data analyses section
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#########
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##############################################################################
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## Keep these "old" selection options as a simple alternative to the modification pane
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output$include_vars <- shiny::renderUI({
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shiny::selectizeInput(
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inputId = "include_vars",
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selected = NULL,
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label = "Covariables to include",
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choices = colnames(rv$data_filtered),
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multiple = TRUE
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)
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})
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output$outcome_var <- shiny::renderUI({
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shiny::selectInput(
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inputId = "outcome_var",
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selected = NULL,
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label = "Select outcome variable",
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choices = colnames(rv$data_filtered),
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multiple = FALSE
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)
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})
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output$factor_vars <- shiny::renderUI({
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shiny::selectizeInput(
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inputId = "factor_vars",
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selected = colnames(rv$data_filtered)[sapply(rv$data_filtered, is.factor)],
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label = "Covariables to format as categorical",
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choices = colnames(rv$data_filtered),
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multiple = TRUE
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)
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})
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base_vars <- shiny::reactive({
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if (is.null(input$include_vars)) {
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out <- colnames(rv$data_filtered)
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} else {
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out <- unique(c(input$include_vars, input$outcome_var))
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}
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return(out)
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})
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output$strat_var <- shiny::renderUI({
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shiny::selectInput(
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inputId = "strat_var",
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selected = "none",
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label = "Select variable to stratify baseline",
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choices = c(
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"none",
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rv$data_filtered[base_vars()] |>
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(\(.x){
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lapply(.x, \(.c){
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if (identical("factor", class(.c))) {
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.c
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}
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}) |>
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dplyr::bind_cols()
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})() |>
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colnames()
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),
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multiple = FALSE
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)
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})
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## Have a look at column filters at some point
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## There should be a way to use the filtering the filter data for further analyses
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## Disabled for now, as the JS is apparently not isolated
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# output$data_table <-
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# DT::renderDT(
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# {
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# DT::datatable(ds()[base_vars()])
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# },
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# server = FALSE
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# )
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#
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# output$data.classes <- gt::render_gt({
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# shiny::req(input$file)
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# data.frame(matrix(sapply(ds(), \(.x){
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# class(.x)[1]
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# }), nrow = 1)) |>
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# stats::setNames(names(ds())) |>
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# gt::gt()
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# })
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shiny::observeEvent(
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{
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input$load
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},
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{
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shiny::req(input$outcome_var)
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# browser()
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# Assumes all character variables can be formatted as factors
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# data <- data_filter$filtered() |>
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tryCatch(
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{
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data <- rv$data_filtered |>
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dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |>
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REDCapCAST::fct_drop.data.frame() |>
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factorize(vars = input$factor_vars) |>
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remove_na_attr()
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if (input$strat_var == "none") {
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by.var <- NULL
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} else {
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by.var <- input$strat_var
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}
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data <- data[base_vars()]
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# model <- data |>
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# regression_model(
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# outcome.str = input$outcome_var,
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# auto.mode = input$regression_auto == 1,
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# formula.str = input$regression_formula,
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# fun = input$regression_fun,
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# args.list = eval(parse(text = paste0("list(", input$regression_args, ")")))
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# )
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models <- list(
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"Univariable" = regression_model_uv,
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"Multivariable" = regression_model
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) |>
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lapply(\(.fun){
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do.call(
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.fun,
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c(
|
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list(data = data),
|
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list(outcome.str = input$outcome_var),
|
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list(formula.str = input$regression_formula),
|
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list(fun = input$regression_fun),
|
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list(args.list = eval(parse(text = paste0("list(", input$regression_args, ")"))))
|
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)
|
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)
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})
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rv$list$data <- data
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|
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|
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|
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rv$list$check <- purrr::pluck(models, "Multivariable") |>
|
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performance::check_model()
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|
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rv$list$table1 <- data |>
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baseline_table(
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fun.args =
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list(
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by = by.var
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)
|
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) |>
|
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(\(.x){
|
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if (!is.null(by.var)) {
|
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.x |> gtsummary::add_overall()
|
||||
} else {
|
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.x
|
||||
}
|
||||
})() |>
|
||||
(\(.x){
|
||||
if (input$add_p == "yes") {
|
||||
.x |>
|
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gtsummary::add_p() |>
|
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gtsummary::bold_p()
|
||||
} else {
|
||||
.x
|
||||
}
|
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})()
|
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|
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rv$list$table2 <- models |>
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purrr::map(regression_table) |>
|
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tbl_merge()
|
||||
|
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|
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rv$list$input <- input
|
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|
||||
|
||||
# rv$list <- list(
|
||||
# data = data,
|
||||
# check = check,
|
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# table1 = data |>
|
||||
# baseline_table(
|
||||
# fun.args =
|
||||
# list(
|
||||
# by = by.var
|
||||
# )
|
||||
# ) |>
|
||||
# (\(.x){
|
||||
# if (!is.null(by.var)) {
|
||||
# .x |> gtsummary::add_overall()
|
||||
# } else {
|
||||
# .x
|
||||
# }
|
||||
# })() |>
|
||||
# (\(.x){
|
||||
# if (input$add_p == "yes") {
|
||||
# .x |>
|
||||
# gtsummary::add_p() |>
|
||||
# gtsummary::bold_p()
|
||||
# } else {
|
||||
# .x
|
||||
# }
|
||||
# })(),
|
||||
# table2 = models |>
|
||||
# purrr::map(regression_table) |>
|
||||
# tbl_merge(),
|
||||
# input = input
|
||||
# )
|
||||
|
||||
output$table1 <- gt::render_gt(
|
||||
rv$list$table1 |>
|
||||
gtsummary::as_gt()
|
||||
)
|
||||
|
||||
output$table2 <- gt::render_gt(
|
||||
rv$list$table2 |>
|
||||
gtsummary::as_gt()
|
||||
)
|
||||
|
||||
output$check <- shiny::renderPlot({
|
||||
p <- plot(rv$list$check) +
|
||||
patchwork::plot_annotation(title = "Multivariable regression model checks")
|
||||
p
|
||||
# Generate checks in one column
|
||||
# layout <- sapply(seq_len(length(p)), \(.x){
|
||||
# patchwork::area(.x, 1)
|
||||
# })
|
||||
#
|
||||
# p + patchwork::plot_layout(design = Reduce(c, layout))
|
||||
|
||||
# patchwork::wrap_plots(ncol=1) +
|
||||
# patchwork::plot_annotation(title = 'Multivariable regression model checks')
|
||||
})
|
||||
},
|
||||
warning = function(warn) {
|
||||
showNotification(paste0(warn), type = "warning")
|
||||
},
|
||||
error = function(err) {
|
||||
showNotification(paste0("There was the following error. Inspect your data and adjust settings. Error: ", err), type = "err")
|
||||
}
|
||||
)
|
||||
rv$ready <- "ready"
|
||||
}
|
||||
)
|
||||
|
||||
|
||||
shiny::conditionalPanel(
|
||||
condition = "output.uploaded == 'yes'",
|
||||
)
|
||||
|
||||
# observeEvent(input$act_start, {
|
||||
# nav_show(id = "overview",target = "Import"
|
||||
# )
|
||||
# })
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### 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$ready)) {
|
||||
"no"
|
||||
} else {
|
||||
"yes"
|
||||
}
|
||||
})
|
||||
|
||||
shiny::outputOptions(output, "ready", suspendWhenHidden = FALSE)
|
||||
|
||||
# Reimplement from environment at later time
|
||||
# output$has_input <- shiny::reactive({
|
||||
# if (rv$input) {
|
||||
# "yes"
|
||||
# } else {
|
||||
# "no"
|
||||
# }
|
||||
# })
|
||||
|
||||
# shiny::outputOptions(output, "has_input", suspendWhenHidden = FALSE)
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Downloads
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
# Could be rendered with other tables or should show progress
|
||||
# Investigate quarto render problems
|
||||
# On temp file handling: https://github.com/quarto-dev/quarto-cli/issues/3992
|
||||
output$report <- downloadHandler(
|
||||
filename = shiny::reactive({
|
||||
paste0("report.", input$output_type)
|
||||
}),
|
||||
content = function(file, type = input$output_type) {
|
||||
## Notification is not progressing
|
||||
## Presumably due to missing
|
||||
shiny::withProgress(message = "Generating the report. Hold on for a moment..", {
|
||||
rv$list |>
|
||||
write_quarto(
|
||||
output_format = type,
|
||||
input = file.path(getwd(), "www/report.qmd")
|
||||
)
|
||||
})
|
||||
file.rename(paste0("www/report.", type), file)
|
||||
}
|
||||
)
|
||||
|
||||
output$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 {
|
||||
haven::write_dta(as.data.frame(rv$list$data), path = 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"))
|
||||
})
|
||||
})
|
||||
}
|
||||
|
|
@ -1,468 +0,0 @@
|
|||
# ns <- NS(id)
|
||||
|
||||
ui_elements <- list(
|
||||
##############################################################################
|
||||
#########
|
||||
######### Home panel
|
||||
#########
|
||||
##############################################################################
|
||||
"home" = bslib::nav_panel(
|
||||
title = "freesearcheR",
|
||||
shiny::markdown(readLines("www/intro.md")),
|
||||
icon = shiny::icon("home")
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
######### Import panel
|
||||
#########
|
||||
##############################################################################
|
||||
"import" = bslib::nav_panel(
|
||||
title = "Import",
|
||||
shiny::tagList(
|
||||
shiny::h4("Choose your data source"),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "output.has_input=='yes'",
|
||||
# # Input: Select a file ----
|
||||
# shiny::helpText("Analyses are performed on provided data")
|
||||
# ),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "output.has_input=='no'",
|
||||
# Input: Select a file ----
|
||||
shinyWidgets::radioGroupButtons(
|
||||
inputId = "source",
|
||||
selected = "env",
|
||||
# label = "Choice: ",
|
||||
choices = c(
|
||||
"File upload" = "file",
|
||||
"REDCap server" = "redcap",
|
||||
"Local data" = "env"
|
||||
),
|
||||
# checkIcon = list(
|
||||
# yes = icon("square-check"),
|
||||
# no = icon("square")
|
||||
# ),
|
||||
width = "100%"
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.source=='file'",
|
||||
datamods::import_file_ui("file_import",
|
||||
title = "Choose a datafile to upload",
|
||||
file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav", ".ods", ".dta")
|
||||
)
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.source=='redcap'",
|
||||
m_redcap_readUI("redcap_import")
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.source=='env'",
|
||||
import_globalenv_ui(id = "env", title = NULL)
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.source=='redcap'",
|
||||
DT::DTOutput(outputId = "redcap_prev")
|
||||
),
|
||||
shiny::br(),
|
||||
shiny::actionButton(
|
||||
inputId = "act_start",
|
||||
label = "Start",
|
||||
width = "100%",
|
||||
icon = shiny::icon("play")
|
||||
),
|
||||
shiny::helpText('After importing, hit "Start" or navigate to the desired tab.'),
|
||||
shiny::br(),
|
||||
shiny::br()
|
||||
)
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data overview panel
|
||||
#########
|
||||
##############################################################################
|
||||
"overview" =
|
||||
# bslib::nav_panel_hidden(
|
||||
bslib::nav_panel(
|
||||
# value = "overview",
|
||||
title = "Data",
|
||||
bslib::navset_bar(
|
||||
fillable = TRUE,
|
||||
bslib::nav_panel(
|
||||
title = "Summary & filter",
|
||||
tags$h3("Data summary and filtering"),
|
||||
fluidRow(
|
||||
shiny::column(
|
||||
width = 9,
|
||||
shiny::tags$p(
|
||||
"Below is a short summary table of the provided data.
|
||||
On the right hand side you have the option to create filters.
|
||||
At the bottom you'll find a raw overview of the original vs the modified data."
|
||||
)
|
||||
)
|
||||
),
|
||||
fluidRow(
|
||||
# column(
|
||||
# width = 3,
|
||||
# shiny::uiOutput("filter_vars"),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "(typeof input.filter_vars !== 'undefined' && input.filter_vars.length > 0)",
|
||||
# datamods::filter_data_ui("filtering", max_height = "500px")
|
||||
# )
|
||||
# ),
|
||||
# column(
|
||||
# width = 9,
|
||||
# DT::DTOutput(outputId = "filtered_table"),
|
||||
# tags$b("Code dplyr:"),
|
||||
# verbatimTextOutput(outputId = "filtered_code")
|
||||
# ),
|
||||
shiny::column(
|
||||
width = 9,
|
||||
data_summary_ui(id = "data_summary")
|
||||
),
|
||||
shiny::column(
|
||||
width = 3,
|
||||
IDEAFilter::IDEAFilter_ui("data_filter"),
|
||||
shiny::tags$br(),
|
||||
shiny::tags$b("Filter code:"),
|
||||
shiny::verbatimTextOutput(outputId = "filtered_code"),
|
||||
shiny::tags$br()
|
||||
)
|
||||
),
|
||||
fluidRow(
|
||||
column(
|
||||
width = 6,
|
||||
tags$b("Original data:"),
|
||||
# verbatimTextOutput("original"),
|
||||
verbatimTextOutput("original_str")
|
||||
),
|
||||
column(
|
||||
width = 6,
|
||||
tags$b("Modified data:"),
|
||||
# verbatimTextOutput("modified"),
|
||||
verbatimTextOutput("modified_str")
|
||||
)
|
||||
)
|
||||
),
|
||||
# bslib::nav_panel(
|
||||
# title = "Overview",
|
||||
# DT::DTOutput(outputId = "table")
|
||||
# ),
|
||||
bslib::nav_panel(
|
||||
title = "Modify",
|
||||
tags$h3("Subset, rename and convert variables"),
|
||||
fluidRow(
|
||||
shiny::column(
|
||||
width = 9,
|
||||
shiny::tags$p("Below, you can subset the data (by not selecting the variables to exclude on applying changes), rename variables, set new labels (for nicer tables in the analysis report) and change variable classes.
|
||||
Italic text can be edited/changed.
|
||||
On the right, you can create and modify factor/categorical variables as well as resetting the data to the originally imported data.")
|
||||
)
|
||||
),
|
||||
fluidRow(
|
||||
shiny::column(
|
||||
width = 9,
|
||||
update_variables_ui("vars_update"),
|
||||
shiny::tags$br()
|
||||
),
|
||||
shiny::column(
|
||||
width = 3,
|
||||
tags$h4("Create new variables"),
|
||||
shiny::tags$br(),
|
||||
shiny::actionButton(
|
||||
inputId = "modal_cut",
|
||||
label = "Create factor variable",
|
||||
width = "100%"
|
||||
),
|
||||
shiny::tags$br(),
|
||||
shiny::helpText("Create factor/categorical variable from an other value."),
|
||||
shiny::tags$br(),
|
||||
shiny::tags$br(),
|
||||
shiny::actionButton(
|
||||
inputId = "modal_update",
|
||||
label = "Reorder factor levels",
|
||||
width = "100%"
|
||||
),
|
||||
shiny::tags$br(),
|
||||
shiny::helpText("Reorder the levels of factor/categorical variables."),
|
||||
shiny::tags$br(),
|
||||
shiny::tags$br(),
|
||||
shiny::actionButton(
|
||||
inputId = "modal_column",
|
||||
label = "New variable",
|
||||
width = "100%"
|
||||
),
|
||||
shiny::tags$br(),
|
||||
shiny::helpText("Create a new variable/column based on an R-expression."),
|
||||
shiny::tags$br(),
|
||||
shiny::tags$br(),
|
||||
tags$h4("Restore"),
|
||||
shiny::actionButton(
|
||||
inputId = "data_reset",
|
||||
label = "Restore original data",
|
||||
width = "100%"
|
||||
),
|
||||
shiny::tags$br(),
|
||||
shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
|
||||
shiny::tags$br() # ,
|
||||
# shiny::tags$br(),
|
||||
# shiny::tags$br(),
|
||||
# IDEAFilter::IDEAFilter_ui("data_filter") # ,
|
||||
# shiny::actionButton("save_filter", "Apply the filter")
|
||||
)
|
||||
# datamods::update_variables_ui("vars_update")
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Browser",
|
||||
tags$h3("Browse the provided data"),
|
||||
shiny::tags$p(
|
||||
"Below is a data table with all the modified data provided to browse and understand data."
|
||||
),
|
||||
shinyWidgets::html_dependency_winbox(),
|
||||
# fluidRow(
|
||||
# column(
|
||||
# width = 3,
|
||||
# shiny::uiOutput("filter_vars"),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "(typeof input.filter_vars !== 'undefined' && input.filter_vars.length > 0)",
|
||||
# datamods::filter_data_ui("filtering", max_height = "500px")
|
||||
# )
|
||||
# ),
|
||||
# column(
|
||||
# width = 9,
|
||||
# DT::DTOutput(outputId = "filtered_table"),
|
||||
# tags$b("Code dplyr:"),
|
||||
# verbatimTextOutput(outputId = "filtered_code")
|
||||
# ),
|
||||
# shiny::column(
|
||||
# width = 8,
|
||||
toastui::datagridOutput(outputId = "table_mod") # ,
|
||||
# shiny::tags$b("Reproducible code:"),
|
||||
# shiny::verbatimTextOutput(outputId = "filtered_code")
|
||||
# ),
|
||||
# shiny::column(
|
||||
# width = 4,
|
||||
# shiny::actionButton("modal_cut", "Create factor from a variable"),
|
||||
# shiny::tags$br(),
|
||||
# shiny::tags$br(),
|
||||
# shiny::actionButton("modal_update", "Reorder factor levels")#,
|
||||
# # shiny::tags$br(),
|
||||
# # shiny::tags$br(),
|
||||
# # IDEAFilter::IDEAFilter_ui("data_filter") # ,
|
||||
# # shiny::actionButton("save_filter", "Apply the filter")
|
||||
# )
|
||||
# )
|
||||
)
|
||||
|
||||
|
||||
# column(
|
||||
# 8,
|
||||
# shiny::verbatimTextOutput("filtered_code"),
|
||||
# DT::DTOutput("filtered_table")
|
||||
# ),
|
||||
# column(4, IDEAFilter::IDEAFilter_ui("data_filter"))
|
||||
)
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data analyses panel
|
||||
#########
|
||||
##############################################################################
|
||||
"analyze" =
|
||||
# bslib::nav_panel_hidden(
|
||||
bslib::nav_panel(
|
||||
# value = "analyze",
|
||||
title = "Analyses",
|
||||
bslib::navset_bar(
|
||||
title = "",
|
||||
# bslib::layout_sidebar(
|
||||
# fillable = TRUE,
|
||||
sidebar = bslib::sidebar(
|
||||
shiny::helpText(em("Please specify relevant settings for your data, and press 'Analyse'")),
|
||||
shiny::uiOutput("outcome_var"),
|
||||
shiny::radioButtons(
|
||||
inputId = "all",
|
||||
label = "Specify covariables",
|
||||
inline = TRUE, selected = 2,
|
||||
choiceNames = c(
|
||||
"Yes",
|
||||
"No"
|
||||
),
|
||||
choiceValues = c(1, 2)
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.all==1",
|
||||
shiny::uiOutput("include_vars")
|
||||
),
|
||||
shiny::uiOutput("strat_var"),
|
||||
shiny::helpText("Only factor/categorical variables are available for stratification. Go back to the 'Data' tab to reclass a variable if it's not on the list."),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.strat_var!='none'",
|
||||
shiny::radioButtons(
|
||||
inputId = "add_p",
|
||||
label = "Compare strata?",
|
||||
selected = "no",
|
||||
inline = TRUE,
|
||||
choices = list(
|
||||
"No" = "no",
|
||||
"Yes" = "yes"
|
||||
)
|
||||
),
|
||||
shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
|
||||
),
|
||||
shiny::radioButtons(
|
||||
inputId = "specify_factors",
|
||||
label = "Specify categorical variables?",
|
||||
selected = "no",
|
||||
inline = TRUE,
|
||||
choices = list(
|
||||
"Yes" = "yes",
|
||||
"No" = "no"
|
||||
)
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.specify_factors=='yes'",
|
||||
shiny::uiOutput("factor_vars")
|
||||
),
|
||||
bslib::input_task_button(
|
||||
id = "load",
|
||||
label = "Analyse",
|
||||
icon = shiny::icon("pencil", lib = "glyphicon"),
|
||||
label_busy = "Working...",
|
||||
icon_busy = fontawesome::fa_i("arrows-rotate",
|
||||
class = "fa-spin",
|
||||
"aria-hidden" = "true"
|
||||
),
|
||||
type = "secondary",
|
||||
auto_reset = TRUE
|
||||
),
|
||||
shiny::helpText("If you change the parameters, press 'Analyse' again to update the tables"),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "output.ready=='yes'",
|
||||
shiny::tags$hr(),
|
||||
shiny::h4("Download results"),
|
||||
shiny::helpText("Choose your favourite output file format for further work, and download, when the analyses are done."),
|
||||
shiny::selectInput(
|
||||
inputId = "output_type",
|
||||
label = "Output format",
|
||||
selected = NULL,
|
||||
choices = list(
|
||||
"MS Word" = "docx",
|
||||
"LibreOffice" = "odt"
|
||||
# ,
|
||||
# "PDF" = "pdf",
|
||||
# "All the above" = "all"
|
||||
)
|
||||
),
|
||||
shiny::br(),
|
||||
# Button
|
||||
shiny::downloadButton(
|
||||
outputId = "report",
|
||||
label = "Download report",
|
||||
icon = shiny::icon("download")
|
||||
),
|
||||
shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."),
|
||||
shiny::tags$hr(),
|
||||
shiny::h4("Download data"),
|
||||
shiny::helpText("Choose your favourite output data format to download the modified data."),
|
||||
shiny::selectInput(
|
||||
inputId = "data_type",
|
||||
label = "Data format",
|
||||
selected = NULL,
|
||||
choices = list(
|
||||
"R" = "rds",
|
||||
"stata" = "dta"
|
||||
)
|
||||
),
|
||||
shiny::br(),
|
||||
# Button
|
||||
shiny::downloadButton(
|
||||
outputId = "data_modified",
|
||||
label = "Download data",
|
||||
icon = shiny::icon("download")
|
||||
)
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Baseline characteristics",
|
||||
gt::gt_output(outputId = "table1")
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Regression table",
|
||||
gt::gt_output(outputId = "table2")
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Regression checks",
|
||||
shiny::plotOutput(outputId = "check")
|
||||
)
|
||||
)
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
######### Documentation panel
|
||||
#########
|
||||
##############################################################################
|
||||
"docs" = bslib::nav_item(
|
||||
# shiny::img(shiny::icon("book")),
|
||||
shiny::tags$a(
|
||||
href = "https://agdamsbo.github.io/freesearcheR/",
|
||||
"Docs (external)",
|
||||
target = "_blank",
|
||||
rel = "noopener noreferrer"
|
||||
)
|
||||
)
|
||||
# bslib::nav_panel(
|
||||
# title = "Documentation",
|
||||
# # shiny::tags$iframe("www/docs.html", height=600, width=535),
|
||||
# shiny::htmlOutput("docs_file"),
|
||||
# shiny::br()
|
||||
# )
|
||||
)
|
||||
|
||||
# Initial attempt at creating light and dark versions
|
||||
light <- custom_theme()
|
||||
dark <- custom_theme(
|
||||
bg = "#000",
|
||||
fg = "#fff"
|
||||
)
|
||||
|
||||
# Fonts to consider:
|
||||
# https://webdesignerdepot.com/17-open-source-fonts-youll-actually-love/
|
||||
|
||||
ui <- bslib::page_fixed(
|
||||
shiny::tags$head(includeHTML(("www/umami-app.html"))),
|
||||
shiny::tags$style(
|
||||
type = "text/css",
|
||||
# add the name of the tab you want to use as title in data-value
|
||||
shiny::HTML(
|
||||
".container-fluid > .nav > li >
|
||||
a[data-value='freesearcheR'] {font-size: 28px}"
|
||||
)
|
||||
),
|
||||
title = "freesearcheR",
|
||||
theme = light,
|
||||
shiny::useBusyIndicators(),
|
||||
bslib::page_navbar(
|
||||
# title = "freesearcheR",
|
||||
id = "main_panel",
|
||||
# header = shiny::tags$header(shiny::p("Data is only stored temporarily for analysis and deleted immediately afterwards.")),
|
||||
ui_elements$home,
|
||||
ui_elements$import,
|
||||
ui_elements$overview,
|
||||
ui_elements$analyze,
|
||||
bslib::nav_spacer(),
|
||||
ui_elements$docs,
|
||||
# bslib::nav_spacer(),
|
||||
# bslib::nav_item(shinyWidgets::circleButton(inputId = "mode", icon = icon("moon"),status = "primary")),
|
||||
fillable = FALSE,
|
||||
footer = shiny::tags$footer(
|
||||
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 immediately afterwards."
|
||||
),
|
||||
shiny::p(
|
||||
style = "margin: 1; color: #888;",
|
||||
"Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target = "_blank", rel = "noopener noreferrer")
|
||||
),
|
||||
)
|
||||
)
|
||||
)
|
||||
Loading…
Add table
Reference in a new issue