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https://github.com/agdamsbo/REDCapCAST.git
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moving functions from app to fix dependencies
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parent
a896bf4e76
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11
DESCRIPTION
11
DESCRIPTION
@ -29,15 +29,11 @@ Suggests:
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Hmisc,
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knitr,
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rmarkdown,
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ggplot2,
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here,
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styler,
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devtools,
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roxygen2,
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spelling,
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glue,
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rhub,
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bslib
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rhub
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License: GPL (>= 3)
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Encoding: UTF-8
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LazyData: true
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@ -61,7 +57,10 @@ Imports:
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readODS,
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forcats,
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vctrs,
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gt
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gt,
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bslib,
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here,
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glue
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Collate:
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'REDCapCAST-package.R'
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'utils.r'
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@ -39,6 +39,7 @@ export(html_tag_wrap)
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export(is_repeated_longitudinal)
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export(match_fields_to_form)
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export(named_levels)
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export(nav_bar_page)
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export(numchar2fct)
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export(parse_data)
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export(process_user_input)
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149
R/shiny_cast.R
149
R/shiny_cast.R
@ -89,7 +89,7 @@ cast_data_overview <- function(data){
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stopifnot("REDCapCAST" %in% class(data))
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data |>
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purrr::pluck("data") |>
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head(20) |>
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utils::head(20) |>
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# dplyr::tibble() |>
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gt::gt() |>
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gt::tab_style(
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@ -144,3 +144,150 @@ cast_meta_overview <- function(data){
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)
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)
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}
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#' Nav_bar defining function for shiny ui
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#'
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#' @return shiny object
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#' @export
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#'
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nav_bar_page <- function(){
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bslib::page_navbar(
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title = "Easy REDCap database creation",
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sidebar = bslib::sidebar(
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width = 300,
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shiny::h5("Metadata casting"),
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shiny::fileInput(
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inputId = "ds",
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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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".xls",
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".xlsx",
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".dta",
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".rds",
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".ods"
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)
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),
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# shiny::actionButton(
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# inputId = "load_data",
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# label = "Load data",
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# icon = shiny::icon("circle-down")
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# ),
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shiny::helpText("Have a look at the preview panels to validate the data dictionary and imported data."),
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# For some odd reason this only unfolds when the preview panel is shown..
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# This has been solved by adding an arbitrary button to load data - which was abandoned again
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shiny::conditionalPanel(
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condition = "output.uploaded=='yes'",
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shiny::radioButtons(
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inputId = "add_id",
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label = "Add ID, or use first column?",
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selected = "no",
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inline = TRUE,
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choices = list(
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"First column" = "no",
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"Add ID" = "yes",
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"No ID" = "none"
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)
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),
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shiny::radioButtons(
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inputId = "specify_factors",
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label = "Specify categorical variables?",
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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.specify_factors=='yes'",
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shiny::uiOutput("factor_vars")
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),
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# condition = "input.load_data",
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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(outputId = "downloadData", label = "Download renamed data"),
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# Button
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shiny::downloadButton(outputId = "downloadMeta", label = "Download data dictionary"),
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# Button
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shiny::downloadButton(outputId = "downloadInstrument", label = "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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)
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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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),
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shiny::p(
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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_panel(
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title = "Data preview",
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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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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::textOutput(outputId = "upload.meta.print"),
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shiny::h3("Data upload overview"),
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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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@ -5,6 +5,6 @@ account: agdamsbo
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server: shinyapps.io
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hostUrl: https://api.shinyapps.io/v1
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appId: 11351429
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bundleId: 9392220
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bundleId: 9392320
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url: https://agdamsbo.shinyapps.io/redcapcast/
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version: 1
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@ -5,7 +5,6 @@ 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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library(devtools)
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if (!requireNamespace("REDCapCAST")) {
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devtools::install_github("agdamsbo/REDCapCAST", quiet = TRUE, upgrade = "never")
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@ -2,143 +2,6 @@ ui <-
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bslib::page(
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theme = bslib::bs_theme(preset = "united"),
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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(
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width = 300,
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shiny::h5("Metadata casting"),
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shiny::fileInput(
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inputId = "ds",
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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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".xls",
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".xlsx",
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".dta",
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".rds",
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".ods"
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)
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),
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# shiny::actionButton(
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# inputId = "load_data",
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# label = "Load data",
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# icon = shiny::icon("circle-down")
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# ),
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shiny::helpText("Have a look at the preview panels to validate the data dictionary and imported data."),
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# For some odd reason this only unfolds when the preview panel is shown..
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# This has been solved by adding an arbitrary button to load data - which was abandoned again
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shiny::conditionalPanel(
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condition = "output.uploaded=='yes'",
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shiny::radioButtons(
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inputId = "add_id",
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label = "Add ID, or use first column?",
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selected = "no",
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inline = TRUE,
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choices = list(
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"First column" = "no",
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"Add ID" = "yes",
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"No ID" = "none"
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)
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),
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shiny::radioButtons(
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inputId = "specify_factors",
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label = "Specify categorical variables?",
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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.specify_factors=='yes'",
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uiOutput("factor_vars")
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),
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# condition = "input.load_data",
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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(outputId = "downloadData", label = "Download renamed data"),
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# Button
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shiny::downloadButton(outputId = "downloadMeta", label = "Download data dictionary"),
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# Button
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shiny::downloadButton(outputId = "downloadInstrument", label = "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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)
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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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),
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shiny::p(
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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_panel(
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title = "Data preview",
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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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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::textOutput(outputId = "upload.meta.print"),
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shiny::h3("Data upload overview"),
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shiny::textOutput(outputId = "upload.data.print")
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)
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)
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nav_bar_page()
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)
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14
man/nav_bar_page.Rd
Normal file
14
man/nav_bar_page.Rd
Normal file
@ -0,0 +1,14 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/shiny_cast.R
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\name{nav_bar_page}
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\alias{nav_bar_page}
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\title{Nav_bar defining function for shiny ui}
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\usage{
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nav_bar_page()
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}
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\value{
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shiny object
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}
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\description{
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Nav_bar defining function for shiny ui
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}
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