moving functions from app to fix dependencies

DESCRIPTION

@@ -29,15 +29,11 @@ Suggests:
     Hmisc,
     knitr,
     rmarkdown,
-    ggplot2,
-    here,
     styler,
     devtools,
     roxygen2,
     spelling,
-    glue,
+    rhub
-    rhub,
-    bslib
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
@@ -61,7 +57,10 @@ Imports:
     readODS,
     forcats,
     vctrs,
-    gt
+    gt,
+    bslib,
+    here,
+    glue
 Collate: 
     'REDCapCAST-package.R'
     'utils.r'

NAMESPACE

@@ -39,6 +39,7 @@ export(html_tag_wrap)
 export(is_repeated_longitudinal)
 export(match_fields_to_form)
 export(named_levels)
+export(nav_bar_page)
 export(numchar2fct)
 export(parse_data)
 export(process_user_input)

R/shiny_cast.R

@@ -89,7 +89,7 @@ cast_data_overview <- function(data){
   stopifnot("REDCapCAST" %in% class(data))
   data |>
     purrr::pluck("data") |>
-    head(20) |>
+    utils::head(20) |>
     # dplyr::tibble() |>
     gt::gt() |>
     gt::tab_style(
@@ -144,3 +144,150 @@ cast_meta_overview <- function(data){
       )
     )
 }
+
+
+#' Nav_bar defining function for shiny ui
+#'
+#' @return shiny object
+#' @export
+#'
+nav_bar_page <- function(){
+  bslib::page_navbar(
+    title = "Easy REDCap database creation",
+    sidebar = bslib::sidebar(
+      width = 300,
+      shiny::h5("Metadata casting"),
+      shiny::fileInput(
+        inputId = "ds",
+        label = "Upload spreadsheet",
+        multiple = FALSE,
+        accept = c(
+          ".csv",
+          ".xls",
+          ".xlsx",
+          ".dta",
+          ".rds",
+          ".ods"
+        )
+      ),
+      # shiny::actionButton(
+      #   inputId = "load_data",
+      #   label = "Load data",
+      #   icon = shiny::icon("circle-down")
+      # ),
+      shiny::helpText("Have a look at the preview panels to validate the data dictionary and imported data."),
+      # For some odd reason this only unfolds when the preview panel is shown..
+      # This has been solved by adding an arbitrary button to load data - which was abandoned again
+      shiny::conditionalPanel(
+        condition = "output.uploaded=='yes'",
+        shiny::radioButtons(
+          inputId = "add_id",
+          label = "Add ID, or use first column?",
+          selected = "no",
+          inline = TRUE,
+          choices = list(
+            "First column" = "no",
+            "Add ID" = "yes",
+            "No ID" = "none"
+          )
+        ),
+        shiny::radioButtons(
+          inputId = "specify_factors",
+          label = "Specify categorical variables?",
+          selected = "no",
+          inline = TRUE,
+          choices = list(
+            "No" = "no",
+            "Yes" = "yes"
+          )
+        ),
+        shiny::conditionalPanel(
+          condition = "input.specify_factors=='yes'",
+          shiny::uiOutput("factor_vars")
+        ),
+        # condition = "input.load_data",
+        #  shiny::helpText("Below you can download the dataset formatted for upload and the
+        # corresponding data dictionary for a new data base, if you want to upload manually."),
+        # Button
+        shiny::downloadButton(outputId = "downloadData", label = "Download renamed data"),
+
+        # Button
+        shiny::downloadButton(outputId = "downloadMeta", label = "Download data dictionary"),
+
+        # Button
+        shiny::downloadButton(outputId = "downloadInstrument", label = "Download as instrument"),
+
+        # Horizontal line ----
+        shiny::tags$hr(),
+        shiny::radioButtons(
+          inputId = "upload_redcap",
+          label = "Upload directly to REDCap server?",
+          selected = "no",
+          inline = TRUE,
+          choices = list(
+            "No" = "no",
+            "Yes" = "yes"
+          )
+        ),
+        shiny::conditionalPanel(
+          condition = "input.upload_redcap=='yes'",
+          shiny::h4("2) Data base upload"),
+          shiny::helpText("This tool is usable for now. Detailed instructions are coming."),
+          shiny::textInput(
+            inputId = "uri",
+            label = "URI",
+            value = "https://redcap.your.institution/api/"
+          ),
+          shiny::textInput(
+            inputId = "api",
+            label = "API key",
+            value = ""
+          ),
+          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."),
+          shiny::actionButton(
+            inputId = "upload.meta",
+            label = "Upload datadictionary", icon = shiny::icon("book-bookmark")
+          ),
+          shiny::helpText("Please note, that before uploading any real data, put your project
+         into production mode."),
+          shiny::actionButton(
+            inputId = "upload.data",
+            label = "Upload data", icon = shiny::icon("upload")
+          )
+        )
+      ),
+      shiny::br(),
+      shiny::br(),
+      shiny::br(),
+      shiny::p(
+        "License: ", shiny::a("GPL-3+", href = "https://agdamsbo.github.io/REDCapCAST/LICENSE.html")
+      ),
+      shiny::p(
+        shiny::a("Package documentation", href = "https://agdamsbo.github.io/REDCapCAST")
+      )
+    ),
+    bslib::nav_panel(
+      title = "Intro",
+      shiny::markdown(readLines("www/SHINYCAST.md")),
+      shiny::br()
+    ),
+    # bslib::nav_spacer(),
+    bslib::nav_panel(
+      title = "Data preview",
+      gt::gt_output(outputId = "data.tbl")
+      # shiny::htmlOutput(outputId = "data.tbl", container = shiny::span)
+    ),
+    bslib::nav_panel(
+      title = "Dictionary overview",
+      gt::gt_output(outputId = "meta.tbl")
+      # shiny::htmlOutput(outputId = "meta.tbl", container = shiny::span)
+    ),
+    bslib::nav_panel(
+      title = "Upload",
+      shiny::h3("Meta upload overview"),
+      shiny::textOutput(outputId = "upload.meta.print"),
+      shiny::h3("Data upload overview"),
+      shiny::textOutput(outputId = "upload.data.print")
+    )
+  )
+}

inst/shiny-examples/casting/rsconnect/shinyapps.io/agdamsbo/redcapcast.dcf

@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 11351429
-bundleId: 9392220
+bundleId: 9392320
 url: https://agdamsbo.shinyapps.io/redcapcast/
 version: 1

inst/shiny-examples/casting/server.R

@@ -5,7 +5,6 @@ library(haven)
 library(readODS)
 library(readr)
 library(dplyr)
-library(here)
 library(devtools)
 if (!requireNamespace("REDCapCAST")) {
   devtools::install_github("agdamsbo/REDCapCAST", quiet = TRUE, upgrade = "never")

inst/shiny-examples/casting/ui.R

@@ -2,143 +2,6 @@ ui <-
   bslib::page(
     theme = bslib::bs_theme(preset = "united"),
     title = "REDCap database creator",
-    bslib::page_navbar(
+nav_bar_page()
-      title = "Easy REDCap database creation",
-      sidebar = bslib::sidebar(
-        width = 300,
-        shiny::h5("Metadata casting"),
-        shiny::fileInput(
-          inputId = "ds",
-          label = "Upload spreadsheet",
-          multiple = FALSE,
-          accept = c(
-            ".csv",
-            ".xls",
-            ".xlsx",
-            ".dta",
-            ".rds",
-            ".ods"
-          )
-        ),
-        # shiny::actionButton(
-        #   inputId = "load_data",
-        #   label = "Load data",
-        #   icon = shiny::icon("circle-down")
-        # ),
-        shiny::helpText("Have a look at the preview panels to validate the data dictionary and imported data."),
-        # For some odd reason this only unfolds when the preview panel is shown..
-        # This has been solved by adding an arbitrary button to load data - which was abandoned again
-        shiny::conditionalPanel(
-          condition = "output.uploaded=='yes'",
-          shiny::radioButtons(
-            inputId = "add_id",
-            label = "Add ID, or use first column?",
-            selected = "no",
-            inline = TRUE,
-            choices = list(
-              "First column" = "no",
-              "Add ID" = "yes",
-              "No ID" = "none"
-            )
-          ),
-          shiny::radioButtons(
-            inputId = "specify_factors",
-            label = "Specify categorical variables?",
-            selected = "no",
-            inline = TRUE,
-            choices = list(
-              "No" = "no",
-              "Yes" = "yes"
-            )
-          ),
-          shiny::conditionalPanel(
-            condition = "input.specify_factors=='yes'",
-            uiOutput("factor_vars")
-          ),
-          # condition = "input.load_data",
-         #  shiny::helpText("Below you can download the dataset formatted for upload and the
-         # corresponding data dictionary for a new data base, if you want to upload manually."),
-          # Button
-          shiny::downloadButton(outputId = "downloadData", label = "Download renamed data"),
-
-          # Button
-          shiny::downloadButton(outputId = "downloadMeta", label = "Download data dictionary"),
-
-          # Button
-          shiny::downloadButton(outputId = "downloadInstrument", label = "Download as instrument"),
-
-          # Horizontal line ----
-          shiny::tags$hr(),
-          shiny::radioButtons(
-            inputId = "upload_redcap",
-            label = "Upload directly to REDCap server?",
-            selected = "no",
-            inline = TRUE,
-            choices = list(
-              "No" = "no",
-              "Yes" = "yes"
-            )
-          ),
-          shiny::conditionalPanel(
-            condition = "input.upload_redcap=='yes'",
-            shiny::h4("2) Data base upload"),
-            shiny::helpText("This tool is usable for now. Detailed instructions are coming."),
-            shiny::textInput(
-              inputId = "uri",
-              label = "URI",
-              value = "https://redcap.your.institution/api/"
-            ),
-            shiny::textInput(
-              inputId = "api",
-              label = "API key",
-              value = ""
-            ),
-            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."),
-            shiny::actionButton(
-              inputId = "upload.meta",
-              label = "Upload datadictionary", icon = shiny::icon("book-bookmark")
-            ),
-            shiny::helpText("Please note, that before uploading any real data, put your project
-         into production mode."),
-            shiny::actionButton(
-              inputId = "upload.data",
-              label = "Upload data", icon = shiny::icon("upload")
-            )
-          )
-        ),
-        shiny::br(),
-        shiny::br(),
-        shiny::br(),
-        shiny::p(
-          "License: ", shiny::a("GPL-3+", href = "https://agdamsbo.github.io/REDCapCAST/LICENSE.html")
-        ),
-        shiny::p(
-          shiny::a("Package documentation", href = "https://agdamsbo.github.io/REDCapCAST")
-        )
-      ),
-      bslib::nav_panel(
-        title = "Intro",
-        shiny::markdown(readLines("www/SHINYCAST.md")),
-        shiny::br()
-      ),
-      # bslib::nav_spacer(),
-      bslib::nav_panel(
-        title = "Data preview",
-        gt::gt_output(outputId = "data.tbl")
-        # shiny::htmlOutput(outputId = "data.tbl", container = shiny::span)
-      ),
-      bslib::nav_panel(
-        title = "Dictionary overview",
-        gt::gt_output(outputId = "meta.tbl")
-        # shiny::htmlOutput(outputId = "meta.tbl", container = shiny::span)
-      ),
-      bslib::nav_panel(
-        title = "Upload",
-        shiny::h3("Meta upload overview"),
-        shiny::textOutput(outputId = "upload.meta.print"),
-        shiny::h3("Data upload overview"),
-        shiny::textOutput(outputId = "upload.data.print")
-      )
-    )
   )
 

man/nav_bar_page.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/shiny_cast.R
+\name{nav_bar_page}
+\alias{nav_bar_page}
+\title{Nav_bar defining function for shiny ui}
+\usage{
+nav_bar_page()
+}
+\value{
+shiny object
+}
+\description{
+Nav_bar defining function for shiny ui
+}