Merge pull request #156 from aim-rsf/examples

Add examples to functions

R/browse_metadata.R

@@ -16,7 +16,7 @@
 #' for this dataset. Open the two html output files in your browser and use
 #' these as reference when running the map_metadata function.
 #' @examples
-#' # Demo run
+#' # Demo run requires no function inputs or user interaction
 #' browse_metadata()
 #' @export
 #' @importFrom dplyr %>% add_row

R/map_metadata.R

@@ -36,7 +36,7 @@
 #' mappings and 'LOG_' which contains details about the dataset and session.
 #' @examples
 #' \dontrun{
-#' # Demo run - requires user interactions
+#' # Demo run requires no function inputs but requires user interaction
 #' map_metadata()
 #' }
 #' @export

R/map_metadata_compare.R

@@ -5,15 +5,32 @@
 #'
 #' @param session_dir This directory should contain 2 csv files for each session (LOG_ and OUTPUT_), 4 csv files in total.
 #' @param session1_base Base file name for session 1 e.g. 'NationalCommunityChildHealthDatabase(NCCHD)_BLOOD_TEST_2024-07-05-16-07-38'
-#' @param session2_base Base file name for session 1 e.g. 'NationalCommunityChildHealthDatabase(NCCHD)_BLOOD_TEST_2024-07-08-12-03-30'
+#' @param session2_base Base file name for session 2 e.g. 'NationalCommunityChildHealthDatabase(NCCHD)_BLOOD_TEST_2024-07-08-12-03-30'
 #' @param json_file The full path to the metadata file used when running map_metadata (should be the same for session 1 and session 2)
 #' @param domain_file The full path to the domain file used when running map_metadata (should be the same for session 1 and session 2)
 #' @return It returns a csv output, which represents the consensus decisions between session 1 and session 2
 #' @export
 #' @importFrom utils read.csv write.csv
 #' @importFrom jsonlite fromJSON
 #' @importFrom cli cli_alert_success
-
+#' @examples
+#' \dontrun{
+#' # Locate file paths for the example files in the package
+#' demo_session_dir <- system.file("outputs", package = "browseMetadata")
+#' demo_session1_base <- "NationalCommunityChildHealthDatabase(NCCHD)_CHILD_2024-11-27-14-19-55"
+#' demo_session2_base <- "NationalCommunityChildHealthDatabase(NCCHD)_CHILD_2024-11-27-14-23-52"
+#' demo_json_file <- system.file("inputs", "national_community_child_health_database_(ncchd)_20240405T130125.json", package = "browseMetadata")
+#' demo_domain_file <- system.file("inputs", "domain_list_demo.csv", package = "browseMetadata")
+#'
+#' # Run the function - requires user interaction
+#' map_metadata_compare(
+#'   session_dir = demo_session_dir,
+#'   session1_base = demo_session1_base,
+#'   session2_base = demo_session2_base,
+#'   json_file = demo_json_file,
+#'   domain_file = demo_domain_file
+#' )
+#' }
 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")
 
@@ -110,7 +127,7 @@ map_metadata_compare <- function(session_dir, session1_base, session2_base, json
   table_find <- data.frame(table_n = numeric(length(dataset$childDataClasses)), table_label = character(length(dataset$childDataClasses)))
   for (t in 1:length(dataset$childDataClasses)) {
     table_find$table_n[t] <- t
-    table_find$table_label[t] <- dataset$childDataClasses[[t]]$label
+    table_find$table_label[t] <- dataset$childDataClasses$label[t]
   }
   table_n <- table_find$table_n[table_find$table_label == csv_1a$table[1]]
 

R/map_metadata_convert.R

@@ -8,7 +8,13 @@
 #' @return The function will return 'L-OUTPUT_' in the same output_dir
 #' @export
 #' @importFrom utils read.csv write.csv
-
+#' @examples
+#' # Locate file path and file name for the example files in the package
+#' demo_output_dir <- system.file("outputs", package = "browseMetadata")
+#' demo_output_csv <- "OUTPUT_NationalCommunityChildHealthDatabase(NCCHD)_CHILD_2024-11-27-14-19-55.csv"
+#'
+#' # Run the function
+#' map_metadata_convert(output_csv = demo_output_csv, output_dir = demo_output_dir)
 map_metadata_convert <- function(output_csv, output_dir) {
   output <- read.csv(paste0(output_dir, "/", output_csv))
   output_long <- output[0, ] # make duplicate

codemeta.json

@@ -226,7 +226,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "753.382KB",
+  "fileSize": "1085.556KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",

inst/outputs/LOG_NationalCommunityChildHealthDatabase(NCCHD)_CHILD_2024-11-27-14-19-55.csv

@@ -0,0 +1,2 @@
+"timestamp","browseMetadata","initials","metadata_version","metadata_last_updated","domain_list_desc","dataset","table","table_note"
+"2024-11-27 14:19:55",2.0.1,"demo","16.0.0","2024-03-14T17:40:57.463Z","DemoList","National Community Child Health Database (NCCHD)","CHILD","demo run"

inst/outputs/LOG_NationalCommunityChildHealthDatabase(NCCHD)_CHILD_2024-11-27-14-23-52.csv

@@ -0,0 +1,2 @@
+"timestamp","browseMetadata","initials","metadata_version","metadata_last_updated","domain_list_desc","dataset","table","table_note"
+"2024-11-27 14:23:52",2.0.1,"demo2","16.0.0","2024-03-14T17:40:57.463Z","DemoList","National Community Child Health Database (NCCHD)","CHILD","demo2"

inst/outputs/OUTPUT_NationalCommunityChildHealthDatabase(NCCHD)_CHILD_2024-11-27-14-19-55.csv

@@ -0,0 +1,21 @@
+"timestamp","table","data_element_n","data_element","domain_code","note"
+"2024-11-27 14:19:55","CHILD","1 of 35","ALF_E","2","AUTO CATEGORISED"
+"2024-11-27 14:19:55","CHILD","2 of 35","ALF_MTCH_PCT","2","AUTO CATEGORISED"
+"2024-11-27 14:19:55","CHILD","3 of 35","ALF_STS_CD","2","AUTO CATEGORISED"
+"2024-11-27 14:19:55","CHILD","4 of 35","APGAR_1","7",""
+"2024-11-27 14:19:55","CHILD","5 of 35","APGAR_2","7",""
+"2024-11-27 14:19:55","CHILD","6 of 35","AVAIL_FROM_DT","1","AUTO CATEGORISED"
+"2024-11-27 14:19:55","CHILD","7 of 35","BIRTH_ORDER","7","10% missingess"
+"2024-11-27 14:19:55","CHILD","8 of 35","BIRTH_TM","1,7","20% missingess"
+"2024-11-27 14:19:55","CHILD","9 of 35","BIRTH_WEIGHT","7",""
+"2024-11-27 14:19:55","CHILD","10 of 35","BIRTH_WEIGHT_DEC","7",""
+"2024-11-27 14:19:55","CHILD","11 of 35","BREASTFEED_8_WKS_FLG","7",""
+"2024-11-27 14:19:55","CHILD","12 of 35","BREASTFEED_BIRTH_FLG","7",""
+"2024-11-27 14:19:55","CHILD","13 of 35","CHILD_ID_E","2",""
+"2024-11-27 14:19:55","CHILD","14 of 35","CURR_LHB_CD_BIRTH","5,7","Place of birth"
+"2024-11-27 14:19:55","CHILD","15 of 35","DEL_CD","7",""
+"2024-11-27 14:19:55","CHILD","16 of 35","DOD","3,7",""
+"2024-11-27 14:19:55","CHILD","17 of 35","ETHNIC_GRP_CD","3",""
+"2024-11-27 14:19:55","CHILD","18 of 35","GEST_AGE","3,7",""
+"2024-11-27 14:19:55","CHILD","19 of 35","GNDR_CD","3","AUTO CATEGORISED"
+"2024-11-27 14:19:55","CHILD","20 of 35","HEALTH_VISITOR_CD_E","2",""

inst/outputs/OUTPUT_NationalCommunityChildHealthDatabase(NCCHD)_CHILD_2024-11-27-14-23-52.csv

@@ -0,0 +1,21 @@
+"timestamp","table","data_element_n","data_element","domain_code","note"
+"2024-11-27 14:23:52","CHILD","1 of 35","ALF_E","2","AUTO CATEGORISED"
+"2024-11-27 14:23:52","CHILD","2 of 35","ALF_MTCH_PCT","2","AUTO CATEGORISED"
+"2024-11-27 14:23:52","CHILD","3 of 35","ALF_STS_CD","2","AUTO CATEGORISED"
+"2024-11-27 14:23:52","CHILD","4 of 35","APGAR_1","7",""
+"2024-11-27 14:23:52","CHILD","5 of 35","APGAR_2","7",""
+"2024-11-27 14:23:52","CHILD","6 of 35","AVAIL_FROM_DT","1","AUTO CATEGORISED"
+"2024-11-27 14:23:52","CHILD","7 of 35","BIRTH_ORDER","1,7",""
+"2024-11-27 14:23:52","CHILD","8 of 35","BIRTH_TM","7",""
+"2024-11-27 14:23:52","CHILD","9 of 35","BIRTH_WEIGHT","7",""
+"2024-11-27 14:23:52","CHILD","10 of 35","BIRTH_WEIGHT_DEC","7",""
+"2024-11-27 14:23:52","CHILD","11 of 35","BREASTFEED_8_WKS_FLG","7",""
+"2024-11-27 14:23:52","CHILD","12 of 35","BREASTFEED_BIRTH_FLG","7",""
+"2024-11-27 14:23:52","CHILD","13 of 35","CHILD_ID_E","2",""
+"2024-11-27 14:23:52","CHILD","14 of 35","CURR_LHB_CD_BIRTH","5,7",""
+"2024-11-27 14:23:52","CHILD","15 of 35","DEL_CD","7",""
+"2024-11-27 14:23:52","CHILD","16 of 35","DOD","3",""
+"2024-11-27 14:23:52","CHILD","17 of 35","ETHNIC_GRP_CD","3",""
+"2024-11-27 14:23:52","CHILD","18 of 35","GEST_AGE","7",""
+"2024-11-27 14:23:52","CHILD","19 of 35","GNDR_CD","3","AUTO CATEGORISED"
+"2024-11-27 14:23:52","CHILD","20 of 35","HEALTH_VISITOR_CD_E","0,1",""