diff --git a/R/read_redcap_tables.R b/R/read_redcap_tables.R index b530333..b56de90 100644 --- a/R/read_redcap_tables.R +++ b/R/read_redcap_tables.R @@ -26,7 +26,7 @@ #' \link[REDCapCAST]{fct_drop} to drop empty levels. #' #' @param split_forms Whether to split "repeating" or "all" forms, default is -#' all. +#' all. Give "none" to export native semi-long REDCap format #' @param ... passed on to \link[REDCapR]{redcap_read} #' #' @return list of instruments @@ -42,22 +42,24 @@ read_redcap_tables <- function(uri, fields = NULL, events = NULL, forms = NULL, - raw_or_label = c("raw","label","both"), - split_forms = "all", + raw_or_label = c("raw", "label", "both"), + split_forms = c("all", "repeating", "none"), ...) { - - raw_or_label <- match.arg(raw_or_label, c("raw","label","both")) + raw_or_label <- match.arg(raw_or_label, c("raw", "label", "both")) + split_forms <- match.arg(split_forms) # 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")) + 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 = ", "), ".")) + print(paste0( + "The following field names are invalid: ", + paste(fields[!fields_test], collapse = ", "), "." + )) stop("Not all supplied field names are valid") } } @@ -67,8 +69,10 @@ read_redcap_tables <- function(uri, forms_test <- forms %in% unique(m$form_name) if (any(!forms_test)) { - print(paste0("The following form names are invalid: ", - paste(forms[!forms_test], collapse = ", "), ".")) + print(paste0( + "The following form names are invalid: ", + paste(forms[!forms_test], collapse = ", "), "." + )) stop("Not all supplied form names are valid") } } @@ -82,13 +86,15 @@ read_redcap_tables <- function(uri, event_test <- events %in% unique(arm_event_inst$data$unique_event_name) if (any(!event_test)) { - print(paste0("The following event names are invalid: ", - paste(events[!event_test], collapse = ", "), ".")) + print(paste0( + "The following event names are invalid: ", + paste(events[!event_test], collapse = ", "), "." + )) stop("Not all supplied event names are valid") } } - if (raw_or_label=="both"){ + if (raw_or_label == "both") { rorl <- "raw" } else { rorl <- raw_or_label @@ -106,10 +112,10 @@ read_redcap_tables <- function(uri, ... )[["data"]] - if (raw_or_label=="both"){ - d <- apply_field_label(data=d,meta=m) + if (raw_or_label == "both") { + d <- apply_field_label(data = d, meta = m) - d <- apply_factor_labels(data=d,meta=m) + d <- apply_factor_labels(data = d, meta = m) } @@ -123,15 +129,16 @@ read_redcap_tables <- function(uri, # 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) + if (split_forms != "none") { + REDCap_split(d, + m, + forms = split_forms, + primary_table_name = "" + ) |> sanitize_split() + } else { + d + } } @@ -171,7 +178,7 @@ clean_field_label <- function(data) { #' @export #' #' @examples -#' format_redcap_factor(sample(1:3,20,TRUE),"1, First. | 2, second | 3, THIRD") +#' format_redcap_factor(sample(1:3, 20, TRUE), "1, First. | 2, second | 3, THIRD") format_redcap_factor <- function(data, meta) { lvls <- strsplit(meta, " | ", fixed = TRUE) |> unlist() |> @@ -196,13 +203,13 @@ format_redcap_factor <- function(data, meta) { #' @return data.frame #' @export #' -apply_field_label <- function(data,meta){ +apply_field_label <- function(data, meta) { purrr::imap(data, \(.x, .i){ if (.i %in% meta$field_name) { # Does not handle checkboxes out <- set_attr(.x, - label = clean_field_label(meta$field_label[meta$field_name == .i]), - attr = "label" + label = clean_field_label(meta$field_label[meta$field_name == .i]), + attr = "label" ) out } else { @@ -219,8 +226,8 @@ apply_field_label <- function(data,meta){ #' @return data.frame #' @export #' -apply_factor_labels <- function(data,meta=NULL){ - if (is.list(data) && !is.data.frame(data)){ +apply_factor_labels <- function(data, meta = NULL) { + if (is.list(data) && !is.data.frame(data)) { meta <- data$meta data <- data$data } else if (is.null(meta)) { @@ -234,5 +241,3 @@ apply_factor_labels <- function(data,meta=NULL){ } }) |> dplyr::bind_cols() } - -