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