From 9d53f84427e119c10fb79746ccedb619618dd8ac Mon Sep 17 00:00:00 2001
From: Andreas Gammelgaard Damsbo <andreas@gdamsbo.dk>
Date: Mon, 18 Nov 2024 14:41:44 +0100
Subject: [PATCH] docs and name update

---
 DESCRIPTION                          |  3 ++-
 NAMESPACE                            |  6 ++++++
 inst/shiny-examples/casting/server.R |  3 ++-
 man/REDCapCAST-package.Rd            |  2 +-
 vignettes/Database-creation.Rmd      |  2 +-
 vignettes/REDCapCAST.Rmd             |  2 +-
 vignettes/Shiny-app.Rmd              | 31 +++++++++++++++++++++++-----
 7 files changed, 39 insertions(+), 10 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d231029..28ad56f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -58,7 +58,8 @@ Imports:
     zip,
     assertthat,
     openxlsx2,
-    readODS
+    readODS,
+    forcats
 Collate: 
     'REDCapCAST-package.R'
     'utils.r'
diff --git a/NAMESPACE b/NAMESPACE
index 36cc88d..42d9bc1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -20,10 +20,14 @@ export(file_extension)
 export(focused_metadata)
 export(format_subheader)
 export(get_api_key)
+export(guess_time_only)
 export(guess_time_only_filter)
+export(haven_all_levels)
 export(html_tag_wrap)
 export(is_repeated_longitudinal)
 export(match_fields_to_form)
+export(numchar2fct)
+export(parse_data)
 export(process_user_input)
 export(read_input)
 export(read_redcap_instrument)
@@ -33,9 +37,11 @@ export(sanitize_split)
 export(shiny_cast)
 export(split_non_repeating_forms)
 export(strsplitx)
+export(var2fct)
 importFrom(REDCapR,redcap_event_instruments)
 importFrom(REDCapR,redcap_metadata_read)
 importFrom(REDCapR,redcap_read)
+importFrom(forcats,as_factor)
 importFrom(keyring,key_get)
 importFrom(keyring,key_list)
 importFrom(keyring,key_set)
diff --git a/inst/shiny-examples/casting/server.R b/inst/shiny-examples/casting/server.R
index 161976d..119e198 100644
--- a/inst/shiny-examples/casting/server.R
+++ b/inst/shiny-examples/casting/server.R
@@ -17,7 +17,8 @@ server <- function(input, output, session) {
   dat <- shiny::reactive({
     shiny::req(input$ds)
 
-    read_input(input$ds$datapath)
+    read_input(input$ds$datapath) |>
+      parse_data()
   })
 
   # getData <- reactive({
diff --git a/man/REDCapCAST-package.Rd b/man/REDCapCAST-package.Rd
index f0117d7..da4a544 100644
--- a/man/REDCapCAST-package.Rd
+++ b/man/REDCapCAST-package.Rd
@@ -4,7 +4,7 @@
 \name{REDCapCAST-package}
 \alias{REDCapCAST}
 \alias{REDCapCAST-package}
-\title{REDCapCAST: REDCap Castellated Data Handling And Metadata Casting}
+\title{REDCapCAST: REDCap Castellated Data Handling and Metadata Casting}
 \description{
 \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}}
 
diff --git a/vignettes/Database-creation.Rmd b/vignettes/Database-creation.Rmd
index 4967051..7c7327c 100644
--- a/vignettes/Database-creation.Rmd
+++ b/vignettes/Database-creation.Rmd
@@ -45,7 +45,7 @@ The more advanced `ds2dd_detailed()` is a natural development. It will try to ap
 
 The dataset should be correctly formatted for the data dictionary to preserve as much information as possible.
 
-```{r eval=TRUE}
+```{r eval=FALSE}
 d2 <- REDCapCAST::redcapcast_data |> 
   dplyr::mutate(record_id = seq_len(dplyr::n()),
                 region=factor(region)) |>
diff --git a/vignettes/REDCapCAST.Rmd b/vignettes/REDCapCAST.Rmd
index c9ea11a..0b782a3 100644
--- a/vignettes/REDCapCAST.Rmd
+++ b/vignettes/REDCapCAST.Rmd
@@ -2,7 +2,7 @@
 title: "REDCapCAST"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Introduction}
+  %\VignetteIndexEntry{REDCapCAST}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
diff --git a/vignettes/Shiny-app.Rmd b/vignettes/Shiny-app.Rmd
index acb4dd7..34a43b6 100644
--- a/vignettes/Shiny-app.Rmd
+++ b/vignettes/Shiny-app.Rmd
@@ -14,13 +14,34 @@ knitr::opts_chunk$set(
 )
 ```
 
-To make the easiest possible transition from spreadsheet/dataset to REDCap, I have created a small Shiny app, which adds a graphical interface to the casting of a data dictionary and data upload. Install the package and run the app as follows:
+To make the easiest possible transition from spreadsheet/dataset to REDCap, I have created a small app, which adds a graphical interface to the casting of a data dictionary and data upload. Install the package and launch the app as follows:
 
 ```{r eval=FALSE}
-require(REDCapCAST)
-shiny_cast()
+REDCapCAST::shiny_cast()
+```
+
+The app primarily wraps one function: `ds2dd_detailed()`.
+
+```{r}
+REDCap_split(
+    records = redcapcast_data,
+    metadata = redcapcast_meta,
+    forms = "all"
+  ) |> 
+  sanitize_split() |> 
+  redcap_wider() |> 
+  ds2dd_detailed()|>  
+  purrr::pluck("data") |> 
+  readr::type_convert( 
+      col_types = readr::cols(.default = readr::col_guess()))
+```
+
+
+```{r}
+redcapcast_data |> 
+  dplyr::mutate(dplyr::across(dplyr::everything(),as.character)) |>  
+  readr::type_convert( 
+      col_types = readr::cols(.default = readr::col_guess()))
 ```
 
-The app will launch in a new window and the interface should be fairly self-explanatory.
-The app only provides the most basic functionality, but might be extended in the future.