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new tests and removed notes

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AG Damsbo 2023-03-06 14:37:06 +01:00
parent c7b61cb19e
commit b57e130395
1 changed files with 28 additions and 11 deletions
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39
R/read_redcap_tables.R
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@ -12,10 +12,10 @@
#' @param raw_or_label raw or label tags #' @param raw_or_label raw or label tags
#' @param generics vector of auto-generated generic variable names to #' @param generics vector of auto-generated generic variable names to
#' ignore when discarding empty rows #' ignore when discarding empty rows
#' @param ... extra parameters for internal REDCapR::redcap_read
#' #'
#' @return list of instruments #' @return list of instruments
#' @importFrom REDCapR redcap_metadata_read redcap_read #' @importFrom REDCapR redcap_metadata_read redcap_read redcap_event_instruments
#' @include utils.r
#' @export #' @export
#' #'
#' @examples #' @examples
@ -32,12 +32,30 @@ read_redcap_tables <- function(uri,
"redcap_event_name", "redcap_event_name",
"redcap_repeat_instrument", "redcap_repeat_instrument",
"redcap_repeat_instance" "redcap_repeat_instance"
), )) {
...) {
# Notes to self: Based on the metadata, this functionality could be
# introduced without using the REDCapRITS package.. To be tried.. if (!is.null(forms) | !is.null(events)){
# arm_event_inst <- REDCapR::redcap_event_instruments(redcap_uri = uri,
# This does not handle repeated instruments!! This should be implemented. token = token)
if (!is.null(forms)){
forms_test <- forms %in% unique(arm_event_inst$data$form)
if (any(!forms_test)){
stop("Not all supplied forms are valid")
}
}
if (!is.null(events)){
event_test <- events %in% unique(arm_event_inst$data$unique_event_name)
if (any(!forms_test)){
stop("Not all supplied event names are valid")
}
}
}
d <- REDCapR::redcap_read( d <- REDCapR::redcap_read(
redcap_uri = uri, redcap_uri = uri,
@ -46,15 +64,14 @@ read_redcap_tables <- function(uri,
events = events, events = events,
forms = forms, forms = forms,
records = records, records = records,
raw_or_label = raw_or_label, raw_or_label = raw_or_label
...
) )
m <- m <-
REDCapR::redcap_metadata_read (redcap_uri = uri, token = token) REDCapR::redcap_metadata_read (redcap_uri = uri, token = token)
l <- REDCap_split(d$data, l <- REDCap_split(d$data,
m$data[m$data$field_name %in% names(d$data), ], focused_metadata(m$data,names(d$data)),
forms = "all") forms = "all")
lapply(l, function(i) { lapply(l, function(i) {