Converted R code into a package

R/.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

R/.gitignore

@@ -0,0 +1,3 @@
+.Rproj.user
+.Rhistory
+.RData

R/DESCRIPTION

@@ -0,0 +1,22 @@
+Package: REDCapRITS
+Title: REDCap Repeating Instrument Table Splitter
+Version: 0.0.0
+Authors@R: person(
+    "Paul", 
+    "Egeler", 
+    email = "paul.egeler@spectrumhealth.org", 
+    role = c("aut", "cre"))
+Description: Split REDCap repeating instruments output into multiple tables. 
+    This will take raw output from a REDCap export and split it into a base table
+    and child tables for each repeating instrument. 
+Depends: R (>= 3.4.0)
+Suggests: RCurl, 
+    jsonlite,
+    testthat
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.0.1
+Collate: 
+    'JSON2data.frame.r'
+    'REDCap_split.r'

R/NAMESPACE

@@ -0,0 +1,3 @@
+# Generated by roxygen2: do not edit by hand
+
+export(REDCap_split)

R/R/JSON2data.frame.r

@@ -0,0 +1,37 @@
+JSON2data.frame <- function (x) {
+
+  if (inherits(x, "data.frame")) {
+
+    return(x)
+
+  } else if (inherits(x, "character")) {
+
+    if (requireNamespace("jsonlite", quietly = TRUE)) {
+
+      return(jsonlite::fromJSON(x))
+
+    } else {
+
+      stop(
+        "The package 'jsonlite' is needed to convert ",
+        deparse(substitute(x)),
+        " into a data frame.",
+        "\n       Either install 'jsonlite' or pass ",
+        deparse(substitute(x)),
+        " as a 'data.frame'.",
+        call. = FALSE
+      )
+
+    }
+
+  } else {
+
+    stop(
+      deparse(substitute(x)),
+      " must be a 'data.frame' or JSON string of class 'character'.",
+      call. = FALSE
+    )
+
+  }
+
+}

R/R/REDCap_split.r

@@ -1,15 +1,17 @@
 #' Split REDCap repeating instruments table into multiple tables
 #'
-#' This will take a raw \code{data.frame} from REDCap and split it into a base table
+#' This will take output from a REDCap export and split it into a base table
-#' and give individual tables for each repeating instrument. Metadata
+#' and child tables for each repeating instrument. Metadata
 #' is used to determine which fields should be included in each resultant table.
 #'
-#' @param records \code{data.frame} containing project records
+#' @param records Exported project records. May be a \code{data.frame} or
-#' @param metadata \code{data.frame} containing project metadata (the data dictionary)
+#'   \code{character} vector containing JSON from an API call.
+#' @param metadata Project metadata (the data dictionary). May be a
+#'   \code{data.frame} or \code{character} vector containing JSON from an API
+#'   call.
 #' @author Paul W. Egeler, M.S., GStat
 #' @examples
 #' \dontrun{
-#' library(jsonlite)
 #' library(RCurl)
 #'
 #' # Get the metadata
@@ -29,21 +31,19 @@
 #'     returnFormat = 'json'
 #' )
 #'
-#' # Convert JSON to data.frames
+#' # Convert exported JSON strings into a list of data.frames
-#' records <- fromJSON(result.record)
-#' metadata <- fromJSON(result.meta)
-#'
-#' # Split the data.frame into a list of data.frames
 #' REDCap_split(records, metadata)
 #' }
-#' @return a list of data.frames
+#' @return A list of \code{"data.frame"}s: one base table and zero or more
+#'   tables for each repeating instrument.
+#' @include JSON2data.frame.r
 #' @export
 REDCap_split <- function(records, metadata) {
 
-  stopifnot(all(sapply(list(records,metadata), inherits, "data.frame")))
+  records  <- JSON2data.frame(records)
+  metadata <- JSON2data.frame(metadata)
 
   # Check to see if there were any repeating instruments
-
   if (!any(names(records) == "redcap_repeat_instrument")) {
 
     message("There are no repeating instruments in this data.")
@@ -109,6 +109,6 @@ REDCap_split <- function(records, metadata) {
 
   }
 
-  return(out)
+  out
 
 }

R/REDCapRITS.Rproj

@@ -1,7 +1,7 @@
 Version: 1.0
 
-RestoreWorkspace: Default
+RestoreWorkspace: No
-SaveWorkspace: Default
+SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
@@ -14,3 +14,8 @@ LaTeX: pdfLaTeX
 
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

R/man/REDCap_split.Rd

@@ -0,0 +1,53 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/REDCap_split.r
+\name{REDCap_split}
+\alias{REDCap_split}
+\title{Split REDCap repeating instruments table into multiple tables}
+\usage{
+REDCap_split(records, metadata)
+}
+\arguments{
+\item{records}{Exported project records. May be a \code{data.frame} or
+\code{character} vector containing JSON from an API call.}
+
+\item{metadata}{Project metadata (the data dictionary). May be a
+\code{data.frame} or \code{character} vector containing JSON from an API
+call.}
+}
+\value{
+A list of \code{"data.frame"}s: one base table and zero or more
+  tables for each repeating instrument.
+}
+\description{
+This will take output from a REDCap export and split it into a base table
+and child tables for each repeating instrument. Metadata
+is used to determine which fields should be included in each resultant table.
+}
+\examples{
+\dontrun{
+library(RCurl)
+
+# Get the metadata
+result.meta <- postForm(
+    api_url,
+    token = api_token,
+    content = 'metadata',
+    format = 'json'
+)
+
+# Get the records
+result.record <- postForm(
+    uri = api_url,
+    token = api_token,
+    content = 'record',
+    format = 'json',
+    returnFormat = 'json'
+)
+
+# Convert exported JSON strings into a list of data.frames
+REDCap_split(records, metadata)
+}
+}
+\author{
+Paul W. Egeler, M.S., GStat
+}

R/tests/testthat.R

@@ -0,0 +1,4 @@
+# library(testthat)
+# library(REDCapRITS)
+#
+# test_check("REDCapRITS")

README.md

@@ -35,15 +35,21 @@ a solution to handle the problem in both SAS and R.
 ## Instructions
 ### R
 
-The function definition file contains [roxygen2](https://cran.r-project.org/package=roxygen2) comments to assist you.
+First you must install the package. To do so, execute the following in your R console:
+
+```r
+if (!require(devtools)) install.packages("devtools")
+devtools::install_github("SpectrumHealthResearch/REDCapRITS/R")
+```
+
+After the package is installed, follow these instructions:
 
-1. Run the function definition in the source editor or using `source()`.
 1. Download the record dataset and metadata. This can
 be accomplished either by traditional methods or using the API. The
 `read.csv()` function should be able to handle newline characters within
 records, so no pre-processing of metadata csv is needed.
 1. Call the function, pointing it to your record dataset and metadata
-`data.frame`s.
+`data.frame`s or JSON character vectors.
 
 ### SAS