includes read_redcap_table

R/read_redcap_tables.R

@@ -0,0 +1,71 @@
+#' Download REDCap data
+#'
+#' Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split
+#' including some clean-up. Works with longitudinal projects with repeating
+#' instruments.
+#' @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 raw_or_label raw or label tags
+#' @param generics vector of auto-generated generic variable names to
+#' ignore when discarding empty rows
+#' @param ... ekstra parameters for REDCapR::redcap_read_oneshot
+#'
+#' @return list of instruments
+#' @importFrom REDCapR redcap_metadata_read redcap_read
+#' @export
+#'
+#' @examples
+#' # Examples will be provided later
+read_redcap_tables <- function(uri,
+                               token,
+                               records = NULL,
+                               fields = NULL,
+                               events = NULL,
+                               forms = NULL,
+                               raw_or_label = "label",
+                               generics = c(
+                                 "record_id",
+                                 "redcap_event_name",
+                                 "redcap_repeat_instrument",
+                                 "redcap_repeat_instance"
+                               ),
+                               ...) {
+  # Notes to self: Based on the metadata, this functionality could be
+  # introduced without using the REDCapRITS package.. To be tried..
+  #
+  # This does not handle repeated instruments!! This should be implemented.
+
+  d <- REDCapR::redcap_read_oneshot(
+    redcap_uri = uri,
+    token = token,
+    fields = fields,
+    events = events,
+    forms = forms,
+    records = records,
+    raw_or_label = raw_or_label,
+    ...
+  )
+
+  m <-
+    REDCapR::redcap_metadata_read (redcap_uri = uri, token = token)
+
+  l <- 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
+    }
+  })
+
+}
+
+