From 939abe07e240482df2e06b87e982cff6887e245e Mon Sep 17 00:00:00 2001
From: Joe Zhu <joe.zhu@roche.com>
Date: Fri, 14 Jul 2023 22:38:42 +0800
Subject: [PATCH] update example in apply_metadata to reduce run time (#284)

Fixes #283
---
 NEWS.md               |  3 ++-
 R/radqlqc.R           | 12 ++++++++++++
 R/utils.R             |  8 +++-----
 man/apply_metadata.Rd |  8 +++-----
 man/h_adqlqc.Rd       | 12 ++++++++++++
 5 files changed, 32 insertions(+), 11 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index b0e71125..f1642361 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,8 +2,9 @@
 
 ### Enhancements
 * Refactor `adpc` and `adab` following the new CDISC standard.
-
 * Refactor `abab` parameters and visits to align with `adpc`.
+* Skipping examples in `h_adqlqc` documentation.
+* Changed example in `apply_metadata` to reduce example run time. 
 
 ### Breaking changes
 * Renamed `ADSL` argument to `adsl` in `radab`, `radae`, `radaette`, `radcm`, `raddv`, `radeg`, `radex`, `radhy`, `radlb`,
diff --git a/R/radqlqc.R b/R/radqlqc.R
index 93350e15..965353a9 100644
--- a/R/radqlqc.R
+++ b/R/radqlqc.R
@@ -277,8 +277,10 @@ NULL
 #' @keywords internal
 #'
 #' @examples
+#' \dontrun{
 #' qs <- random.cdisc.data:::get_qs_data(adsl, n_assessments = 5L, seed = 1, na_percentage = 0.1)
 #' qs
+#' }
 get_qs_data <- function(adsl,
                         visit_format = "CYCLE",
                         n_assessments = 5L,
@@ -573,6 +575,7 @@ get_qs_data <- function(adsl,
 #' @keywords internal
 #'
 #' @examples
+#' \dontrun{
 #' df <- dplyr::left_join(
 #'   adsl,
 #'   qs,
@@ -586,6 +589,7 @@ get_qs_data <- function(adsl,
 #'   ) |>
 #'   dplyr::mutate(ADTM = random.cdisc.data:::get_random_dates_between(TRTSDTM, TRTEDTM, AVISITN))
 #' df
+#' }
 get_random_dates_between <- function(from, to, visit_id) {
   min_date <- min(lubridate::as_datetime(from), na.rm = TRUE)
   max_date <- max(lubridate::as_datetime(to), na.rm = TRUE)
@@ -617,8 +621,10 @@ get_random_dates_between <- function(from, to, visit_id) {
 #' @keywords internal
 #'
 #' @examples
+#' \dontrun{
 #' adqlqc1 <- random.cdisc.data:::prep_adqlqc(df = qs)
 #' adqlqc1
+#' }
 prep_adqlqc <- function(df) {
   # create PARAMCD from QSTESTCD
   adqlqc <- dplyr::mutate(
@@ -674,8 +680,10 @@ prep_adqlqc <- function(df) {
 #' @keywords internal
 #'
 #' @examples
+#' \dontrun{
 #' df_scales <- random.cdisc.data:::calc_scales(df)
 #' df_scales
+#' }
 calc_scales <- function(adqlqc1) {
   # Prep scale data ---------------------------------------------------------
   # parcat2 = scales or global health status
@@ -954,8 +962,10 @@ calc_scales <- function(adqlqc1) {
 #' @keywords internal
 #'
 #' @examples
+#' \dontrun{
 #' adqlqc <- random.cdisc.data:::derv_chgcat1(dataset = adqlqc |> dplyr::select(-CHGCAT1))
 #' adqlqc
+#' }
 derv_chgcat1 <- function(dataset) {
   # derivation of CHGCAT1
   check_vars <- c("PARCAT2", "CHG")
@@ -1118,8 +1128,10 @@ derv_chgcat1 <- function(dataset) {
 #' @keywords internal
 #'
 #' @examples
+#' \dontrun{
 #' compliance_data <- random.cdisc.data:::comp_derv(adqlqc, 80, 2)
 #' compliance_data
+#' }
 comp_derv <- function(dataset, percent, number) {
   # original items data
   orig_data <- filter(
diff --git a/R/utils.R b/R/utils.R
index eecd4f66..10af6c3b 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -231,15 +231,13 @@ var_relabel <- function(x, ...) {
 #' @examples
 #' seed <- 1
 #' adsl <- radsl(seed = seed)
-#' adlb <- radlb(adsl, seed = seed)
-#' \dontrun{
+#' adsub <- radsub(adsl, seed = seed)
 #' yaml_path <- file.path(path.package("random.cdisc.data"), "inst", "metadata")
 #' adsl <- random.cdisc.data:::apply_metadata(adsl, file.path(yaml_path, "ADSL.yml"), FALSE)
-#' adlb <- random.cdisc.data:::apply_metadata(
-#'   adlb, file.path(yaml_path, "ADLB.yml"), TRUE,
+#' adsub <- random.cdisc.data:::apply_metadata(
+#'   adsub, file.path(yaml_path, "ADSUB.yml"), TRUE,
 #'   file.path(yaml_path, "ADSL.yml")
 #' )
-#' }
 apply_metadata <- function(df, filename, add_adsl = TRUE, adsl_filename = "metadata/ADSL.yml") {
   checkmate::assert_data_frame(df)
   checkmate::assert_string(filename)
diff --git a/man/apply_metadata.Rd b/man/apply_metadata.Rd
index 7a762cac..abebecd5 100644
--- a/man/apply_metadata.Rd
+++ b/man/apply_metadata.Rd
@@ -26,14 +26,12 @@ Apply label and variable ordering attributes to domains.
 \examples{
 seed <- 1
 adsl <- radsl(seed = seed)
-adlb <- radlb(adsl, seed = seed)
-\dontrun{
+adsub <- radsub(adsl, seed = seed)
 yaml_path <- file.path(path.package("random.cdisc.data"), "inst", "metadata")
 adsl <- random.cdisc.data:::apply_metadata(adsl, file.path(yaml_path, "ADSL.yml"), FALSE)
-adlb <- random.cdisc.data:::apply_metadata(
-  adlb, file.path(yaml_path, "ADLB.yml"), TRUE,
+adsub <- random.cdisc.data:::apply_metadata(
+  adsub, file.path(yaml_path, "ADSUB.yml"), TRUE,
   file.path(yaml_path, "ADSL.yml")
 )
 }
-}
 \keyword{internal}
diff --git a/man/h_adqlqc.Rd b/man/h_adqlqc.Rd
index 8b55239c..e6aad8e4 100644
--- a/man/h_adqlqc.Rd
+++ b/man/h_adqlqc.Rd
@@ -107,8 +107,11 @@ Function for generating random Questionnaires SDTM domain
 adsl <- radsl(N = 10, study_duration = 2, seed = 1)
 adqlqc <- radqlqc(adsl, seed = 1, percent = 80, number = 2)
 
+\dontrun{
 qs <- random.cdisc.data:::get_qs_data(adsl, n_assessments = 5L, seed = 1, na_percentage = 0.1)
 qs
+}
+\dontrun{
 df <- dplyr::left_join(
   adsl,
   qs,
@@ -122,13 +125,22 @@ df <- dplyr::left_join(
   ) |>
   dplyr::mutate(ADTM = random.cdisc.data:::get_random_dates_between(TRTSDTM, TRTEDTM, AVISITN))
 df
+}
+\dontrun{
 adqlqc1 <- random.cdisc.data:::prep_adqlqc(df = qs)
 adqlqc1
+}
+\dontrun{
 df_scales <- random.cdisc.data:::calc_scales(df)
 df_scales
+}
+\dontrun{
 adqlqc <- random.cdisc.data:::derv_chgcat1(dataset = adqlqc |> dplyr::select(-CHGCAT1))
 adqlqc
+}
+\dontrun{
 compliance_data <- random.cdisc.data:::comp_derv(adqlqc, 80, 2)
 compliance_data
 }
+}
 \keyword{internal}