andreas/REDCapCAST
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Cleaning up R code and adding RStudio project.

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Egeler, Paul W 2018-05-25 12:02:21 -04:00
parent f25319366c
commit cbc39e288e
3 changed files with 47 additions and 28 deletions
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1
.gitignore vendored
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*.html *.html
.Rhistory .Rhistory
.Rproj.user

16
REDCapRITS.Rproj Normal file
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Version: 1.0
RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8
RnwWeave: Sweave
LaTeX: pdfLaTeX
AutoAppendNewline: Yes
StripTrailingWhitespace: Yes

16
REDCap_split.r
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# v0.0.0
#' Split REDCap repeating instruments table into multiple tables #' Split REDCap repeating instruments table into multiple tables
#' #'
#' This will take a raw data frame from REDCap and split it into a base table #' This will take a raw \code{data.frame} from REDCap and split it into a base table
#' and give individual tables for each repeating instrument. Metadata #' and give individual tables for each repeating instrument. Metadata
#' is used to determine which fields should be included in each resultant table. #' is used to determine which fields should be included in each resultant table.
#' #'
@ -45,25 +44,28 @@
#' @export #' @export
REDCap_split <- function(records, metadata) { REDCap_split <- function(records, metadata) {
stopifnot(all(sapply(list(records,metadata), inherits, "data.frame")))
# Check to see if there were any repeating instruments # Check to see if there were any repeating instruments
if (!any(names(records) == "redcap_repeat_instrument")) { if (!any(names(records) == "redcap_repeat_instrument")) {
warning("There are no repeating instruments.\n") message("There are no repeating instruments in this data.")
return(list(records)) return(list(records))
} }
# Clean the metadata # Clean the metadata
metadata <- metadata[metadata["field_type"] != "descriptive", 1:4] metadata <-
metadata[metadata$field_type != "descriptive", c("field_name", "form_name")]
# Identify the subtables in the data # Identify the subtables in the data
subtables <- unique(records["redcap_repeat_instrument"]) subtables <- unique(records$redcap_repeat_instrument)
subtables <- subtables[subtables != ""] subtables <- subtables[subtables != ""]
# Split the table based on instrument # Split the table based on instrument
out <- split.data.frame(records, records["redcap_repeat_instrument"]) out <- split.data.frame(records, records$redcap_repeat_instrument)
# Delete the variables that are not relevant # Delete the variables that are not relevant
for (i in names(out)) { for (i in names(out)) {
@ -71,7 +73,7 @@ REDCap_split <- function(records, metadata) {
if (i == "") { if (i == "") {
out[[which(names(out) == "")]] <- out[[which(names(out) == "")]] <-
out[[which(names(out) == "")]][metadata[`!`(metadata[,2] %in% subtables), 1]] out[[which(names(out) == "")]][metadata[!metadata[,2] %in% subtables, 1]]
} else { } else {