#' Download REDCap data #' #' Implementation of REDCap_split with a focused data acquisition approach using #' REDCapR::redcap_read and only downloading specified fields, forms and/or #' events using the built-in focused_metadata including some clean-up. #' Works with classical and longitudinal projects with or without repeating #' instruments. #' @param uri REDCap database API 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 split_forms Whether to split "repeating" or "all" forms, default is #' all. #' #' @return list of instruments #' @importFrom REDCapR redcap_metadata_read redcap_read redcap_event_instruments #' @include utils.r #' @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", split_forms = "all") { # Getting metadata m <- REDCapR::redcap_metadata_read(redcap_uri = uri, token = token)[["data"]] if (!is.null(fields)) { fields_test <- fields %in% c(m$field_name,paste0(unique(m$form_name),"_complete")) if (any(!fields_test)) { print(paste0("The following field names are invalid: ", paste(fields[!fields_test], collapse = ", "), ".")) stop("Not all supplied field names are valid") } } if (!is.null(forms)) { forms_test <- forms %in% unique(m$form_name) if (any(!forms_test)) { print(paste0("The following form names are invalid: ", paste(forms[!forms_test], collapse = ", "), ".")) stop("Not all supplied form names are valid") } } if (!is.null(events)) { arm_event_inst <- REDCapR::redcap_event_instruments( redcap_uri = uri, token = token ) event_test <- events %in% unique(arm_event_inst$data$unique_event_name) if (any(!event_test)) { print(paste0("The following event names are invalid: ", paste(events[!event_test], collapse = ", "), ".")) stop("Not all supplied event names are valid") } } # Getting dataset d <- REDCapR::redcap_read( redcap_uri = uri, token = token, fields = fields, events = events, forms = forms, records = records, raw_or_label = raw_or_label )[["data"]] # Process repeat instrument naming # Removes any extra characters other than a-z, 0-9 and "_", to mimic raw # instrument names. if ("redcap_repeat_instrument" %in% names(d)) { d$redcap_repeat_instrument <- clean_redcap_name(d$redcap_repeat_instrument) } # Processing metadata to reflect focused dataset m <- focused_metadata(m, names(d)) # Splitting out <- REDCap_split(d, m, forms = split_forms, primary_table_name = "" ) sanitize_split(out) }