stRoke/R/read_redcap_tables.R
2022-12-21 08:06:05 +01:00

55 lines
1.9 KiB
R

#' Download REDCap data
#'
#' Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split including some clean-up.
#' Handles
#' @param uri REDCap database uri
#' @param token API token
#' @param records records to download
#' @param fields fields to download
#' @param events events to download
#' @param forms forms to download
#' @param generics vector of auto-generated generic variable names to ignore when discarding empty rows
#'
#' @return list of instruments
#' @export
#'
#' @examples
#' # Examples will be provided later
read_redcap_tables <- function(uri,
token,
records=NULL,
fields=NULL,
events=NULL,
forms=NULL,
generics=c("record_id", "redcap_event_name", "redcap_repeat_instrument", "redcap_repeat_instance")){
if (requireNamespace("REDCapRITS", quietly = FALSE)) {
cli::cli_abort(
c("x" = "The package REDCapRITS is not installed.",
"i" = "Please install REDCapRITS by running \"remotes::install_github('agdamsbo/REDCapRITS/R')\".")
)
}
# Notes to self: Based on the metadata, this functionality could be introduced without using the REDCapRITS package.. To be tried..
d <- REDCapR::redcap_read (redcap_uri = uri,
token = token,
fields=fields,
events=events,
forms=forms,
records=records)
m <- REDCapR::redcap_metadata_read (redcap_uri = uri,token = token)
l <- REDCapRITS::REDCap_split(d$data, m$data[m$data$field_name %in% names(d$data),], forms = "all")
lapply(l, function(i){
if (ncol(i) > 2){
s <- data.frame(i[,!colnames(i) %in% generics])
i[!apply(is.na(s),MARGIN=1, FUN=all), ]
} else {i}
} )
}