From e41a87eee507e46a5bb5474cb58a66ff9e5acc23 Mon Sep 17 00:00:00 2001
From: "Mancini, Edoardo {MDBB~Welwyn}" <edoardo.mancini@roche.com>
Date: Wed, 19 Jul 2023 13:41:44 +0200
Subject: [PATCH] #2001 - removed for loop, changed unit in `derive_vars_aage`,
 restored `docs/pkgdown.yml`.

---
 NEWS.md                 |  2 +-
 R/compute_age_years.R   | 14 +++++++-------
 R/derive_vars_aage.R    |  8 ++++----
 docs/pkgdown.yml        | 26 ++++++++++++++++++++++++++
 man/derive_vars_aage.Rd |  4 ++--
 5 files changed, 40 insertions(+), 14 deletions(-)
 create mode 100644 docs/pkgdown.yml

diff --git a/NEWS.md b/NEWS.md
index a033778557..af1e592f72 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,7 +4,7 @@
 
 ## Updates of Existing Functions
 - The functions `derive_param_bmi()` and `derive_param_bsa()` are updated to have the option of producing more values at visits when only weight is collected (#1228).
-- The functions `derive_var_age_years` and `compute_age_years` are updated to return an `NA` age in the case that the age unit is missing (#2001).
+- The functions `derive_var_age_years` and `compute_age_years` are updated to return an `NA` age in the case that the age unit is missing. The argument `unit` for `derive_vars_aage` is also changed to `age_unit` for consistency between these age-related functions (#2001).
 
 ## Breaking Changes
 - The following functions, which were deprecated in previous `{admiral}` versions, have been removed: (#1950)
diff --git a/R/compute_age_years.R b/R/compute_age_years.R
index d847a506db..6a16759af0 100644
--- a/R/compute_age_years.R
+++ b/R/compute_age_years.R
@@ -59,16 +59,16 @@ compute_age_years <- function(age,
     ))
   }
 
-  for (i in seq_along(age_unit)) {
-    if (is.na(age_unit[i])) {
-      age[i] <- NA
-      age_unit[i] <- "years"
-    }
+  if (length(age_unit) == 1){
+    age_unit_rep <- rep(age_unit, length(age))
+  }else{
+    age_unit_rep <- age_unit
   }
 
   age_years <- time_length(
-    duration(age,
-      units = tolower(age_unit)
+    duration(
+      num = if_else(is.na(age_unit_rep), NA_real_, age),
+      units = if_else(is.na(age_unit_rep), "years", tolower(age_unit_rep))
     ),
     unit = "years"
   )
diff --git a/R/derive_vars_aage.R b/R/derive_vars_aage.R
index c8c041562c..c103486422 100644
--- a/R/derive_vars_aage.R
+++ b/R/derive_vars_aage.R
@@ -27,7 +27,7 @@
 #'
 #'   Default: `RANDDT`
 #'
-#' @param unit Unit
+#' @param age_unit Age unit
 #'
 #'   The age is derived in the specified unit
 #'
@@ -64,12 +64,12 @@
 derive_vars_aage <- function(dataset,
                              start_date = BRTHDT,
                              end_date = RANDDT,
-                             unit = "years") {
+                             age_unit = "years") {
   start_date <- assert_symbol(enexpr(start_date))
   end_date <- assert_symbol(enexpr(end_date))
   assert_data_frame(dataset, required_vars = expr_c(start_date, end_date))
   assert_character_scalar(
-    unit,
+    age_unit,
     values = c("years", "months", "weeks", "days", "hours", "minutes", "seconds")
   )
 
@@ -79,7 +79,7 @@ derive_vars_aage <- function(dataset,
     new_var_unit = AAGEU,
     start_date = !!start_date,
     end_date = !!end_date,
-    out_unit = unit,
+    out_unit = age_unit,
     add_one = FALSE,
     trunc_out = TRUE
   )
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
new file mode 100644
index 0000000000..c8fbfc66fe
--- /dev/null
+++ b/docs/pkgdown.yml
@@ -0,0 +1,26 @@
+pandoc: 2.11.4
+pkgdown: 2.0.7
+pkgdown_sha: ~
+articles:
+  admiral: admiral.html
+  adsl: adsl.html
+  bds_exposure: bds_exposure.html
+  bds_finding: bds_finding.html
+  bds_tte: bds_tte.html
+  contribution_model: contribution_model.html
+  faq: faq.html
+  generic: generic.html
+  higher_order: higher_order.html
+  hys_law: hys_law.html
+  imputation: imputation.html
+  lab_grading: lab_grading.html
+  occds: occds.html
+  pk_adnca: pk_adnca.html
+  queries_dataset: queries_dataset.html
+  questionnaires: questionnaires.html
+  visits_periods: visits_periods.html
+last_built: 2023-07-19T10:42Z
+urls:
+  reference: https://pharmaverse.github.io/admiral/reference
+  article: https://pharmaverse.github.io/admiral/articles
+
diff --git a/man/derive_vars_aage.Rd b/man/derive_vars_aage.Rd
index 6c43f19929..8eb08b1cb3 100644
--- a/man/derive_vars_aage.Rd
+++ b/man/derive_vars_aage.Rd
@@ -8,7 +8,7 @@ derive_vars_aage(
   dataset,
   start_date = BRTHDT,
   end_date = RANDDT,
-  unit = "years"
+  age_unit = "years"
 )
 }
 \arguments{
@@ -35,7 +35,7 @@ vector to a date object.
 
 Default: \code{RANDDT}}
 
-\item{unit}{Unit
+\item{age_unit}{Age unit
 
 The age is derived in the specified unit