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r-pkg: adding redcap_repeat_instrument.factor logic and improving checkbox logic

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This commit is contained in:
Egeler, Paul W 2018-06-06 17:55:01 -04:00
parent 0921a73a64
commit fc1cad40be
1 changed files with 18 additions and 9 deletions
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27
R/R/REDCap_split.r
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@ -44,8 +44,11 @@ REDCap_split <- function(records, metadata) {
records <- JSON2data.frame(records) records <- JSON2data.frame(records)
metadata <- JSON2data.frame(metadata) metadata <- JSON2data.frame(metadata)
# Get the variable names in the dataset
vars_in_data <- names(records)
# 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(vars_in_data == "redcap_repeat_instrument")) {
message("There are no repeating instruments in this data.") message("There are no repeating instruments in this data.")
@ -98,12 +101,12 @@ REDCap_split <- function(records, metadata) {
1, 1,
function(x, y) function(x, y)
data.frame( data.frame(
field_name = y[grepl(paste0("^", x[1], "___[0-9]+$"), y)], field_name = y[grepl(paste0("^", x[1], "___((?!\\.factor).)+$"), y, perl = TRUE)],
form_name = x[2], form_name = x[2],
stringsAsFactors = FALSE, stringsAsFactors = FALSE,
row.names = NULL row.names = NULL
), ),
y = names(records) y = vars_in_data
) )
) )
@ -112,7 +115,7 @@ REDCap_split <- function(records, metadata) {
} }
# Process ".*\\.factor" fields supplied by REDCap's export data R script # Process ".*\\.factor" fields supplied by REDCap's export data R script
if (any(grepl("\\.factor$", names(records)))) { if (any(grepl("\\.factor$", vars_in_data))) {
factor_fields <- factor_fields <-
do.call( do.call(
@ -130,7 +133,7 @@ REDCap_split <- function(records, metadata) {
row.names = NULL row.names = NULL
) )
}, },
y = names(records) y = vars_in_data
) )
) )
@ -142,6 +145,12 @@ REDCap_split <- function(records, metadata) {
subtables <- unique(records$redcap_repeat_instrument) subtables <- unique(records$redcap_repeat_instrument)
subtables <- subtables[subtables != ""] subtables <- subtables[subtables != ""]
# Variables to be at the beginning of each repeating instrument
repeat_instrument_fields <- c(
vars_in_data[1:3],
grep("redcap_repeat_instrument\\.factor", vars_in_data, value = TRUE)
)
# 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)
@ -150,13 +159,13 @@ REDCap_split <- function(records, metadata) {
if (i == "") { if (i == "") {
out[[which(names(out) == "")]] <- out_fields <- fields[!fields[,2] %in% subtables, 1]
out[[which(names(out) == "")]][fields[!fields[,2] %in% subtables, 1]] out[[which(names(out) == "")]] <- out[[which(names(out) == "")]][out_fields]
} else { } else {
out[[i]] <- out_fields <- c(repeat_instrument_fields, fields[fields[,2] == i, 1])
out[[i]][c(names(records[1:3]),fields[fields[,2] == i, 1])] out[[i]] <- out[[i]][out_fields]
} }