Converted R code into a package

R/.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

R/.gitignore

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+.Rproj.user
+.Rhistory
+.RData

R/DESCRIPTION

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+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

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+# Generated by roxygen2: do not edit by hand
+
+export(REDCap_split)

R/R/JSON2data.frame.r

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+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

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+#' Split REDCap repeating instruments table into multiple tables
+#'
+#' 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.
+#'
+#' @param records Exported project records. May be a \code{data.frame} or
+#'   \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(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)
+#' }
+#' @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) {
+
+  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.")
+
+    return(list(records))
+
+  }
+
+  # Find the fields and associated form
+  fields <- metadata[
+    !metadata$field_type %in% c("descriptive", "checkbox"),
+    c("field_name", "form_name")
+  ]
+
+  if (any(metadata$field_type == "checkbox")) {
+
+    checkbox_basenames <- metadata[
+      metadata$field_type == "checkbox",
+      c("field_name", "form_name")
+    ]
+
+    checkbox_fields <-
+      do.call(
+        "rbind",
+        apply(
+          checkbox_basenames,
+          1,
+          function(x)
+            data.frame(
+              field_name = names(records)[grepl(paste0("^", x[1], "___.+$"), names(records))],
+              form_name = x[2],
+              stringsAsFactors = FALSE,
+              row.names = NULL
+            )
+        )
+      )
+
+    fields <- rbind(fields, checkbox_fields)
+
+  }
+
+  # Identify the subtables in the data
+  subtables <- unique(records$redcap_repeat_instrument)
+  subtables <- subtables[subtables != ""]
+
+  # Split the table based on instrument
+  out <- split.data.frame(records, records$redcap_repeat_instrument)
+
+  # Delete the variables that are not relevant
+  for (i in names(out)) {
+
+    if (i == "") {
+
+      out[[which(names(out) == "")]] <-
+        out[[which(names(out) == "")]][fields[!fields[,2] %in% subtables, 1]]
+
+    } else {
+
+      out[[i]] <-
+        out[[i]][c(names(records[1:3]),fields[fields[,2] == i, 1])]
+
+    }
+
+  }
+
+  out
+
+}

R/REDCapRITS.Rproj

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+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+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

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+% 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

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+# library(testthat)
+# library(REDCapRITS)
+#
+# test_check("REDCapRITS")