add examples to functions

R/browse_metadata.R

@@ -153,7 +153,7 @@ browse_metadata <- function(json_file = NULL, output_dir = NULL) {
   # SAVE PLOTS ----
 
   original_wd <- getwd()
-  setwd(output_dir) # saveWidget has a bug with paths & saving
+  on.exit(output_dir) # saveWidget has a bug with paths & saving
   base_fname <- paste0(gsub(" ", "", dataset_name), "_V", dataset_version)
 
   ## Save the table plot to a HTML file
@@ -168,7 +168,7 @@ browse_metadata <- function(json_file = NULL, output_dir = NULL) {
   bar_fname <- paste0("BROWSE_bar_", base_fname, ".csv")
   write.csv(count_empty_long, bar_fname, row.names = FALSE)
 
-  setwd(original_wd) # saveWidget has a bug with paths & saving
+  on.exit(original_wd) # saveWidget has a bug with paths & saving
 
   # OUTPUTS ----
   cat("\n")

R/map_metadata_compare.R

@@ -13,6 +13,65 @@
 #' @importFrom utils read.csv write.csv
 #' @importFrom jsonlite fromJSON
 #' @importFrom cli cli_alert_success
+#' @examples
+#' # Create a temporary directory for the example
+#' temp_dir <- tempdir()
+#'
+#' # Create example LOG_ and OUTPUT_ CSV files for two sessions with primary care data
+#' # Session 1 data
+#' session1_data <- data.frame(
+#'   patient_id = c(101, 102),
+#'   condition_code = c("A01", "B02"),
+#'   medication = c("Medication1", "Medication2"),
+#'   visit_date = c("2023-01-15", "2023-02-20")
+#' )
+#' write.csv(session1_data, file = file.path(temp_dir, "LOG_NationalCommunityChildHealthDatabase(NCCHD)_BLOOD_TEST_2024-07-05-16-07-38.csv"), row.names = FALSE)
+#' write.csv(session1_data, file = file.path(temp_dir, "OUTPUT_NationalCommunityChildHealthDatabase(NCCHD)_BLOOD_TEST_2024-07-05-16-07-38.csv"), row.names = FALSE)
+#'
+#' # Session 2 data (slightly different to simulate mismatch)
+#' session2_data <- data.frame(
+#'   patient_id = c(101, 103),
+#'   condition_code = c("A01", "A01,C03"),
+#'   medication = c("Medication1", "Medication3"),
+#'   visit_date = c("2023-01-15", "2023-03-25")
+#' )
+#' write.csv(session2_data, file = file.path(temp_dir, "LOG_NationalCommunityChildHealthDatabase(NCCHD)_BLOOD_TEST_2024-07-08-12-03-30.csv"), row.names = FALSE)
+#' write.csv(session2_data, file = file.path(temp_dir, "OUTPUT_NationalCommunityChildHealthDatabase(NCCHD)_BLOOD_TEST_2024-07-08-12-03-30.csv"), row.names = FALSE)
+#'
+#' # Create mock metadata JSON and domain file
+#' json_file <- file.path(temp_dir, "metadata.json")
+#' domain_file <- file.path(temp_dir, "domain.csv")
+#'
+#' # Example metadata json (mock structure)
+#' meta_data <- list(
+#'   dataModel = list(
+#'     label = "NationalCommunityChildHealthDatabase",
+#'     childDataClasses = list(list(label = "Blood Test Data"))
+#'   ),
+#'   data = list()
+#' )
+#' jsonlite::write_json(meta_data, json_file)
+#'
+#' # Example domain file (mock domain codes)
+#' domain_data <- data.frame(
+#'   code = c("A01", "B02", "C03", "D04"),
+#'   description = c("Blood Test A01", "Blood Test B02", "Blood Test C03", "Blood Test D04")
+#' )
+#' write.csv(domain_data, domain_file, row.names = FALSE)
+#'
+#' # Use the map_metadata_compare function to compare the sessions and get consensus
+#' map_metadata_compare(
+#'   session_dir = temp_dir,
+#'   session1_base = "NationalCommunityChildHealthDatabase(NCCHD)_BLOOD_TEST_2024-07-05-16-07-38",
+#'   session2_base = "NationalCommunityChildHealthDatabase(NCCHD)_BLOOD_TEST_2024-07-08-12-03-30",
+#'   json_file = json_file,
+#'   domain_file = domain_file
+#' )
+#'
+#' # Check the consensus output
+#' consensus_output <- read.csv(file.path(temp_dir, "CONSENSUS_OUTPUT_NationalCommunityChildHealthDatabase_BloodTestData_2024-07-05-16-07-38.csv"))
+#' print(consensus_output)
+
 
 map_metadata_compare <- function(session_dir, session1_base, session2_base, json_file, domain_file) {
   timestamp_now_fname <- format(Sys.time(), "%Y-%m-%d-%H-%M-%S")

R/map_metadata_convert.R

@@ -8,7 +8,23 @@
 #' @return The function will return 'L-OUTPUT_' in the same output_dir
 #' @export
 #' @importFrom utils read.csv write.csv
-
+#' @examples
+#' # Create a temporary directory for the example
+#' temp_dir <- tempdir()
+#'
+#' # Create an example OUTPUT_ CSV file with primary care data
+#' example_data <- data.frame(
+#'   patient_id = c(101, 102, 103, 104),
+#'   condition_code = c("A01", "B02", "A01,C03", "D04"),
+#'   medication = c("Medication1", "Medication2", "Medication3", "Medication4")
+#' )
+#' write.csv(example_data, file = file.path(temp_dir, "OUTPUT_example.csv"), row.names = FALSE)
+#'
+#' # Use the function to process the example file
+#' map_metadata_convert("OUTPUT_example.csv", temp_dir)
+#'
+#' # Check the output
+#' read.csv(file.path(temp_dir, "L-OUTPUT_example.csv"))
 map_metadata_convert <- function(output_csv, output_dir) {
   output <- read.csv(paste0(output_dir, "/", output_csv))
   output_long <- output[0, ] # make duplicate