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@ -1,6 +1,6 @@
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Package: REDCapCAST
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Title: REDCap Castellated Data Handling And Metadata Casting
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Version: 24.11.1
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Title: REDCap Castellated Data Handling and Metadata Casting
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Version: 24.11.2
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Authors@R: c(
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person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk",
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role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")),
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@ -1,32 +1,63 @@
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server <- function(input, output, session) {
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require(REDCapCAST)
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library(REDCapCAST)
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library(bslib)
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library(shiny)
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library(openxlsx2)
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library(haven)
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library(readODS)
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library(readr)
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library(dplyr)
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library(here)
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# bslib::bs_themer()
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server <- function(input, output, session) {
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v <- shiny::reactiveValues(
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file = NULL
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)
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dat <- shiny::reactive({
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shiny::req(input$ds)
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output_staging$file <- "loaded"
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read_input(input$ds$datapath)
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})
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# getData <- reactive({
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# if(is.null(input$ds$datapath)) return(NULL)
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# })
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# output$uploaded <- reactive({
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# return(!is.null(getData()))
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# })
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output$uploaded <- shiny::reactive({
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if (is.null(v$file)) {
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"no"
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} else {
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"yes"
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}
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})
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shiny::outputOptions(output, "uploaded", suspendWhenHidden = FALSE)
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dd <- shiny::reactive({
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shiny::req(input$ds)
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v$file <- "loaded"
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ds2dd_detailed(data = dat())
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})
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output$data.tbl <- shiny::renderTable({
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output$data.tbl <- gt::render_gt(
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dd() |>
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purrr::pluck("data") |>
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head(20) |>
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dplyr::tibble()
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})
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dplyr::tibble() |>
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gt::gt()
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)
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output$meta.tbl <- shiny::renderTable({
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output$meta.tbl <- gt::render_gt(
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dd() |>
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purrr::pluck("meta") |>
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dplyr::tibble()
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})
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dplyr::tibble() |>
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gt::gt()
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)
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# Downloadable csv of dataset ----
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output$downloadData <- shiny::downloadHandler(
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@ -53,17 +84,8 @@ server <- function(input, output, session) {
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)
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output_staging <- shiny::reactiveValues()
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output_staging$meta <- output_staging$data <- output_staging$file <- NA
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output$uploaded <- shiny::reactive({
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if (is.na(output_staging$file)) {
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"no"
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} else {
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"yes"
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}
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})
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shiny::outputOptions(output, "uploaded", suspendWhenHidden = FALSE)
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output_staging$meta <- output_staging$data <- NA
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shiny::observeEvent(input$upload.meta,{ upload_meta() })
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@ -4,11 +4,12 @@ ui <-
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title = "REDCap database creator",
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bslib::page_navbar(
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title = "Easy REDCap database creation",
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sidebar = bslib::sidebar(width = 300,
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sidebar = bslib::sidebar(
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width = 300,
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shiny::h5("1) Database meta data"),
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shiny::fileInput(
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inputId = "ds",
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label = "Upload spreadsheet",
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label = "Upload spreadsheet",
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multiple = FALSE,
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accept = c(
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".csv",
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@ -18,87 +19,92 @@ ui <-
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".ods"
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)
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),
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conditionalPanel(
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shiny::helpText("Have a look at the preview panels to show download options."),
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# For some odd reason this only unfolds when the preview panel is shown..
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shiny::conditionalPanel(
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condition = "output.uploaded=='yes'",
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shiny::helpText("Below you can download the dataset formatted for upload and the
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shiny::helpText("Below you can download the dataset formatted for upload and the
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corresponding data dictionary for a new data base, if you want to upload manually."),
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# Button
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shiny::downloadButton("downloadData", "Download adjusted data"),
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# Button
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shiny::downloadButton("downloadData", "Download renamed data"),
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# Button
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shiny::downloadButton("downloadMeta", "Download data dictionary"),
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# Button
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shiny::downloadButton("downloadMeta", "Download data dictionary"),
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# Button
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shiny::downloadButton("downloadInstrument", "Download as instrument"),
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# Button
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shiny::downloadButton("downloadInstrument", "Download as instrument"),
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# Horizontal line ----
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shiny::tags$hr(),
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shiny::radioButtons(
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inputId = "upload_redcap",
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label = "Upload directly to REDCap server?",
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selected = "no",
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inline = TRUE,
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choices = list(
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"No" = "no",
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"Yes" = "yes"
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# Horizontal line ----
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shiny::tags$hr(),
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shiny::radioButtons(
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inputId = "upload_redcap",
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label = "Upload directly to REDCap server?",
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selected = "no",
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inline = TRUE,
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choices = list(
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"No" = "no",
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"Yes" = "yes"
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)
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),
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shiny::conditionalPanel(
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condition = "input.upload_redcap=='yes'",
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shiny::h4("2) Data base upload"),
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shiny::helpText("This tool is usable for now. Detailed instructions are coming."),
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shiny::textInput(
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inputId = "uri",
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label = "URI",
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value = "https://redcap.your.institution/api/"
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),
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shiny::textInput(
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inputId = "api",
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label = "API key",
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value = ""
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),
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shiny::helpText("An API key is an access key to the REDCap database. Please", shiny::a("see here for directions", href = "https://www.iths.org/news/redcap-tip/redcap-api-101/"), " to obtain an API key for your project."),
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shiny::actionButton(
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inputId = "upload.meta",
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label = "Upload datadictionary", icon = shiny::icon("book-bookmark")
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),
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shiny::helpText("Please note, that before uploading any real data, put your project
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into production mode."),
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shiny::actionButton(
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inputId = "upload.data",
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label = "Upload data", icon = shiny::icon("upload")
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)
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)
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),
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shiny::conditionalPanel(
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condition = "input.upload_redcap=='yes'",
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shiny::h4("2) Data base upload"),
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shiny::helpText("This tool is usable for now. Detailed instructions are coming."),
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shiny::textInput(
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inputId = "uri",
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label = "URI",
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value = "https://redcap.your.institution/api/"
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),
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shiny::textInput(
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inputId = "api",
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label = "API key",
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value = ""
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),
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shiny::helpText("An API key is an access key to the REDCap database. Please", shiny::a("see here for directions", href = "https://www.iths.org/news/redcap-tip/redcap-api-101/"), " to obtain an API key for your project."),
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shiny::actionButton(
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inputId = "upload.meta",
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label = "Upload datadictionary", icon = shiny::icon("book-bookmark")
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),
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shiny::helpText("Please note, that before uploading any real data, put your project
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into production mode."),
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shiny::actionButton(
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inputId = "upload.data",
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label = "Upload data", icon = shiny::icon("upload")
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)
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)
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),
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shiny::br(),
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shiny::br(),
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shiny::br(),
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shiny::p(
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"License: ",shiny::a("GPL-3+", href = "https://agdamsbo.github.io/REDCapCAST/LICENSE.html")),
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"License: ", shiny::a("GPL-3+", href = "https://agdamsbo.github.io/REDCapCAST/LICENSE.html")
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),
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shiny::p(
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shiny::a("Package documentation", href = "https://agdamsbo.github.io/REDCapCAST"))
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shiny::a("Package documentation", href = "https://agdamsbo.github.io/REDCapCAST")
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)
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),
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bslib::nav_panel(
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title = "Intro",
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shiny::markdown(readLines("www/SHINYCAST.md")),
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shiny::br()
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),
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bslib::nav_spacer(),
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# bslib::nav_spacer(),
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bslib::nav_panel(
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title = "Data preview",
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shiny::htmlOutput(outputId = "data.tbl", container = shiny::span)
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gt::gt_output(outputId = "data.tbl")
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# shiny::htmlOutput(outputId = "data.tbl", container = shiny::span)
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),
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bslib::nav_panel(
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title = "Dictionary overview",
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shiny::htmlOutput(outputId = "meta.tbl", container = shiny::span)
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gt::gt_output(outputId = "meta.tbl")
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# shiny::htmlOutput(outputId = "meta.tbl", container = shiny::span)
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),
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bslib::nav_panel(
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title = "Upload",
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shiny::h3("Meta upload overview"),
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shiny::htmlOutput(outputId = "upload.meta.print", container = shiny::span),
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shiny::textOutput(outputId = "upload.meta.print"),
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shiny::h3("Data upload overview"),
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shiny::htmlOutput(outputId = "upload.data.print", container = shiny::span)
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shiny::textOutput(outputId = "upload.data.print")
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)
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)
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)
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