including data and sorting vignette. still work to be done.

.Renviron

@@ -0,0 +1 @@
+_R_CHECK_FORCE_SUGGESTS_=FALSE

DESCRIPTION

@@ -49,5 +49,7 @@ Collate:
     'REDCap_split.r'
     'read_redcap_tables.R'
     'redcap_wider.R'
+    'redcapcast_data.R'
+    'redcapcast_meta.R'
 Language: en-US
 VignetteBuilder: knitr

R/redcapcast_data.R

@@ -0,0 +1,35 @@
+#' Data set for demonstration
+#'
+#' This is a small dataset from a REDCap database for demonstrational purposes.
+#' Contains only synthetic data.
+#'
+#' @format A data frame with 22 variables:
+#' \describe{
+#'   \item{record_id}{ID, numeric}
+#'   \item{redcap_event_name}{Event name, character}
+#'   \item{redcap_repeat_instrument}{Repeat instrument, character}
+#'   \item{redcap_repeat_instance}{Repeat instance, numeric}
+#'   \item{cpr}{CPR number, character}
+#'   \item{inclusion}{Inclusion date, date}
+#'   \item{dob}{Date of birth, date}
+#'   \item{age}{Age decimal, numeric}
+#'   \item{age_integer}{Age integer, numeric}
+#'   \item{sex}{Legal sex, character}
+#'   \item{cohabitation}{Cohabitation status, character}
+#'   \item{hypertension}{Hypertension, character}
+#'   \item{diabetes}{diabetes, character}
+#'   \item{region}{region, character}
+#'   \item{base_complete}{Completed, character}
+#'   \item{mrs_assessed}{mRS Assessed, character}
+#'   \item{mrs_date}{Assesment date, date}
+#'   \item{mrs_score}{Score, numeric}
+#'   \item{mrs_complete}{Complete, numeric}
+#'   \item{event_date}{Event date, date}
+#'   \item{event_type}{Event type, character}
+#'   \item{event_complete}{Completed, character}
+#'
+#' }
+#' @usage data(redcapcast_data)
+"redcapcast_data"
+
+

R/redcapcast_meta.R

@@ -0,0 +1,29 @@
+#' REDCap matedata from data base
+#'
+#' This metadata dataset from a REDCap database is for demonstrational purposes.
+#'
+#' @format A data frame with 22 variables:
+#' \describe{
+#'   \item{field_name}{field_name, character}
+#'   \item{form_name}{form_name, character}
+#'   \item{section_header}{section_header, character}
+#'   \item{field_type}{field_type, character}
+#'   \item{field_label}{field_label, character}
+#'   \item{select_choices_or_calculations}{select_choices_or_calculations, character}
+#'   \item{field_note}{field_note, character}
+#'   \item{text_validation_type_or_show_slider_number}{text_validation_type_or_show_slider_number, character}
+#'   \item{text_validation_min}{text_validation_min, character}
+#'   \item{text_validation_max}{text_validation_max, character}
+#'   \item{identifier}{identifier, character}
+#'   \item{branching_logic}{branching_logic, character}
+#'   \item{required_field}{required_field, character}
+#'   \item{custom_alignment}{custom_alignment, character}
+#'   \item{question_number}{question_number, character}
+#'   \item{matrix_group_name}{matrix_group_name, character}
+#'   \item{matrix_ranking}{matrix_ranking, character}
+#'   \item{field_annotation}{field_annotation, character}
+#' }
+#' @usage data(redcapcast_meta)
+"redcapcast_meta"
+
+

data-raw/redcapcast_data.R

@@ -0,0 +1,8 @@
+## code to prepare `redcapcast_data` dataset goes here
+
+redcapcast_data <- REDCapR::redcap_read(redcap_uri = uri,
+                                        token = keyring::key_get("cast_api"),
+                                        raw_or_label = "label"
+                                        )$data
+
+usethis::use_data(redcapcast_data, overwrite = TRUE)

data-raw/redcapcast_meta.R

@@ -0,0 +1,6 @@
+## code to prepare `redcapcast_meta` dataset goes here
+redcapcast_meta <- REDCapR::redcap_metadata_read(redcap_uri = uri,
+                                          token = keyring::key_get("cast_api")
+                                          )$data
+
+usethis::use_data(redcapcast_meta, overwrite = TRUE)

docs/pkgdown.yml

@@ -3,5 +3,5 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   Introduction: Introduction.html
-last_built: 2023-04-13T08:56Z
+last_built: 2023-04-13T10:14Z
 

docs/sitemap.xml

@@ -39,6 +39,12 @@
   <url>
     <loc>/reference/redcap_wider.html</loc>
   </url>
+  <url>
+    <loc>/reference/redcapcast_data.html</loc>
+  </url>
+  <url>
+    <loc>/reference/redcapcast_meta.html</loc>
+  </url>
   <url>
     <loc>/reference/sanitize_split.html</loc>
   </url>

man/redcapcast_data.Rd

@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/redcapcast_data.R
+\docType{data}
+\name{redcapcast_data}
+\alias{redcapcast_data}
+\title{Data set for demonstration}
+\format{
+A data frame with 22 variables:
+\describe{
+  \item{record_id}{ID, numeric}
+  \item{redcap_event_name}{Event name, character}
+  \item{redcap_repeat_instrument}{Repeat instrument, character}
+  \item{redcap_repeat_instance}{Repeat instance, numeric}
+  \item{cpr}{CPR number, character}
+  \item{inclusion}{Inclusion date, date}
+  \item{dob}{Date of birth, date}
+  \item{age}{Age decimal, numeric}
+  \item{age_integer}{Age integer, numeric}
+  \item{sex}{Legal sex, character}
+  \item{cohabitation}{Cohabitation status, character}
+  \item{hypertension}{Hypertension, character}
+  \item{diabetes}{diabetes, character}
+  \item{region}{region, character}
+  \item{base_complete}{Completed, character}
+  \item{mrs_assessed}{mRS Assessed, character}
+  \item{mrs_date}{Assesment date, date}
+  \item{mrs_score}{Score, numeric}
+  \item{mrs_complete}{Complete, numeric}
+  \item{event_date}{Event date, date}
+  \item{event_type}{Event type, character}
+  \item{event_complete}{Completed, character}
+
+}
+}
+\usage{
+data(redcapcast_data)
+}
+\description{
+This is a small dataset from a REDCap database for demonstrational purposes.
+Contains only synthetic data.
+}
+\keyword{datasets}

man/redcapcast_meta.Rd

@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/redcapcast_meta.R
+\docType{data}
+\name{redcapcast_meta}
+\alias{redcapcast_meta}
+\title{REDCap matedata from data base}
+\format{
+A data frame with 22 variables:
+\describe{
+  \item{field_name}{field_name, character}
+  \item{form_name}{form_name, character}
+  \item{section_header}{section_header, character}
+  \item{field_type}{field_type, character}
+  \item{field_label}{field_label, character}
+  \item{select_choices_or_calculations}{select_choices_or_calculations, character}
+  \item{field_note}{field_note, character}
+  \item{text_validation_type_or_show_slider_number}{text_validation_type_or_show_slider_number, character}
+  \item{text_validation_min}{text_validation_min, character}
+  \item{text_validation_max}{text_validation_max, character}
+  \item{identifier}{identifier, character}
+  \item{branching_logic}{branching_logic, character}
+  \item{required_field}{required_field, character}
+  \item{custom_alignment}{custom_alignment, character}
+  \item{question_number}{question_number, character}
+  \item{matrix_group_name}{matrix_group_name, character}
+  \item{matrix_ranking}{matrix_ranking, character}
+  \item{field_annotation}{field_annotation, character}
+}
+}
+\usage{
+data(redcapcast_meta)
+}
+\description{
+This metadata dataset from a REDCap database is for demonstrational purposes.
+}
+\keyword{datasets}

vignettes/Introduction.Rmd

@@ -20,57 +20,49 @@ library(REDCapCAST)
 
 This vignette covers the included functions and basic functionality.
 
+A dataset and a meta data file are provided with the package for demonstration of the functions.
+
 ## Splitting the dataset
 
-```{r eval=FALSE}
-keyring::key_set("handbook_api")
-keyring::key_set("cast_api")
-```
-
-```{r include=FALSE}
-uri <- keyring::key_get("DB_URI")
-```
-
-
 ```{r}
-dataset <- REDCapR::redcap_read_oneshot(redcap_uri = uri,
+redcapcast_data |> gt::gt()
-                                   token = keyring::key_get("cast_api"))$data
-
-dataset |> gt::gt()
 ```
 
 ```{r}
-metadata <- REDCapR::redcap_metadata_read(redcap_uri = uri,
+redcapcast_meta |> gt::gt()
-                                   token = keyring::key_get("cast_api"))$data
-metadata |> gt::gt()
 ```
 ```{r}
 list <-
-  REDCapCAST::REDCap_split(records = dataset,
+  REDCapCAST::REDCap_split(records = redcapcast_data,
-                           metadata = metadata,
+                           metadata = redcapcast_meta,
                            forms = "repeating")
 str(list)
 ```
 
 ```{r}
 list <-
-  REDCapCAST::REDCap_split(records = dataset,
+  REDCapCAST::REDCap_split(records = redcapcast_data,
-                           metadata = metadata,
+                           metadata = redcapcast_meta,
                            forms = "all")
 str(list)
 ```
 
 ## Reading data from REDCap
 
-```{r}
+This function wraps all the above demonstrated function to get the dataset, the metadata, apply the `REDCap_split`function and then a bit of cleaning.
-ds <- read_redcap_tables(uri = uri, token = keyring::key_get("cast_api"))
+
-str(ds)
+The function works verysimilarly as the `REDCapR::redcap_read()`.
+
+```{r eval=FALSE}
+# read_redcap_tables(uri = "YOUR URI", token = "YOUR TOKEN")
+
+# ds <- read_redcap_tables(uri = key_get("DB_URI"), token = key_get("cast_api"))
 ```
 
 ## Pivotting to wider format
 
 ```{r}
-redcap_wider(ds) |> gt::gt()
+# redcap_wider(ds)
 ```