From 4275530843a16e5f655c1d153aac26eb86f943bf Mon Sep 17 00:00:00 2001
From: StefanThoma <40463122+StefanThoma@users.noreply.github.com>
Date: Thu, 3 Aug 2023 08:01:03 +0200
Subject: [PATCH 1/7] code updated

---
 NEWS.md                              |  2 ++
 R/compute_kidney.R                   | 33 ++++++++++++++++++----------
 tests/testthat/test-compute_kidney.R | 18 +++++++++++----
 vignettes/pk_adnca.Rmd               |  4 ++--
 4 files changed, 40 insertions(+), 17 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index d5103d24e4..16eb55b810 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -34,6 +34,8 @@
 - The arguments `dataset_adsl` in the function `derive_param_exist_flag()` and
 `subject_keys` have been deprecated versions using the next phase of the deprecation process. (#1950)
 
+- The argument `wt` in the function `compute_egfr()` was deprecated in favor of `weight` using the first phase of the deprecation process. (#2020)
+
 - The `filter` argument in `derive_extreme_records()` was deprecated in favor of
 the `filter_add` using the next phase of the deprecation process. (#1950)
 
diff --git a/R/compute_kidney.R b/R/compute_kidney.R
index ab0a687859..6f7d1011b3 100644
--- a/R/compute_kidney.R
+++ b/R/compute_kidney.R
@@ -20,7 +20,7 @@
 #'
 #'   A numeric vector is expected.
 #'
-#' @param wt Weight (kg)
+#' @param weight Weight (kg)
 #'
 #'   A numeric vector is expected if `method = "CRCL"`
 #'
@@ -42,6 +42,8 @@
 #'
 #'   Expected Values: `"CRCL"`, `"CKD-EPI"`, `"MDRD"`
 #'
+#' @param wt *Deprecated*, please use `weight` instead.
+#'
 #' @details
 #'
 #' Calculates an estimate of Glomerular Filtration Rate (eGFR)
@@ -92,7 +94,7 @@
 #'
 #' @examples
 #' compute_egfr(
-#'   creat = 90, creatu = "umol/L", age = 53, wt = 85, sex = "M", method = "CRCL"
+#'   creat = 90, creatu = "umol/L", age = 53, weight = 85, sex = "M", method = "CRCL"
 #' )
 #'
 #' compute_egfr(
@@ -120,19 +122,28 @@
 #' base %>%
 #'   dplyr::mutate(
 #'     CRCL_CG = compute_egfr(
-#'       creat = CREATBL, creatu = CREATBLU, age = AGE, wt = WTBL, sex = SEX,
+#'       creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX,
 #'       method = "CRCL"
 #'     ),
 #'     EGFR_EPI = compute_egfr(
-#'       creat = CREATBL, creatu = CREATBLU, age = AGE, wt = WTBL, sex = SEX,
+#'       creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX,
 #'       method = "CKD-EPI"
 #'     ),
 #'     EGFR_MDRD = compute_egfr(
-#'       creat = CREATBL, creatu = CREATBLU, age = AGE, wt = WTBL, sex = SEX,
+#'       creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX,
 #'       race = RACE, method = "MDRD"
 #'     ),
 #'   )
-compute_egfr <- function(creat, creatu = "SI", age, wt, sex, race = NULL, method) {
+compute_egfr <- function(creat, creatu = "SI", age, weight, sex, race = NULL, method, wt) {
+
+  ### BEGIN DEPRECATION
+  if (!missing(wt)) {
+    deprecate_warn("0.12.0", "compute_egfr(old_param = 'wt')", "compute_egfr(new_param = 'weight')")
+    # old_param is given using exprs()
+    weight <- wt
+  }
+  ### END DEPRECATION
+
   assert_numeric_vector(creat)
   assert_character_vector(creatu, values = c(
     "SI", "CV", "mg/dL", "umol/L", NA_character_,
@@ -164,15 +175,15 @@ compute_egfr <- function(creat, creatu = "SI", age, wt, sex, race = NULL, method
       sex == "M" ~ 175 * (scr^-1.154) * (age^-0.203)
     )
   } else if (method == "CRCL") {
-    assert_numeric_vector(wt)
+    assert_numeric_vector(weight)
 
     egfr <- case_when(
       tolower(creatu) %in% c("cv", "mg/dl") & sex == "F" ~
-        ((140 - age) * wt * 0.85) / (creat * 72),
+        ((140 - age) * weight * 0.85) / (creat * 72),
       tolower(creatu) %in% c("cv", "mg/dl") & sex == "M" ~
-        ((140 - age) * wt) / (creat * 72),
-      sex == "F" ~ ((140 - age) * wt * 1.04) / creat,
-      sex == "M" ~ ((140 - age) * wt * 1.23) / creat
+        ((140 - age) * weight) / (creat * 72),
+      sex == "F" ~ ((140 - age) * weight * 1.04) / creat,
+      sex == "M" ~ ((140 - age) * weight * 1.23) / creat
     )
   } else if (method == "CKD-EPI") {
     kappa <- case_when(
diff --git a/tests/testthat/test-compute_kidney.R b/tests/testthat/test-compute_kidney.R
index 426fe80da2..f5e1dedc1f 100644
--- a/tests/testthat/test-compute_kidney.R
+++ b/tests/testthat/test-compute_kidney.R
@@ -27,7 +27,7 @@ test_that("compute_egfr Test 3: CRCL calculation", {
   # CRCL Cockcroft and Gault (1973) calculator at
   # https://www.kidney.org/professionals/kdoqi/gfr_calculatorCoc
   expect_equal(round(compute_egfr(
-    creat = 1.09, creatu = "mg/dL", age = 55, sex = "M", wt = 90, method = "CRCL"
+    creat = 1.09, creatu = "mg/dL", age = 55, sex = "M", weight = 90, method = "CRCL"
   ), 0L), 97)
 })
 
@@ -38,7 +38,7 @@ test_that("compute_egfr Test 4: CRCL calculation", {
   # CRCL Cockcroft and Gault (1973) calculator at
   # https://www.kidney.org/professionals/kdoqi/gfr_calculatorCoc
   expect_equal(round(compute_egfr(
-    creat = 85, creatu = "umol/L", age = 65, sex = "F", wt = 60, method = "CRCL"
+    creat = 85, creatu = "umol/L", age = 65, sex = "F", weight = 60, method = "CRCL"
   ), 0L), 55)
 })
 
@@ -49,7 +49,7 @@ test_that("compute_egfr Test 5: EGFR MDRD calculation", {
   # MDRD GFR calculator at
   # https://www.mdcalc.com/calc/76/mdrd-gfr-equation
   expect_equal(round(compute_egfr(
-    creat = 1.09, creatu = "mg/dL", age = 55, sex = "M", wt = 90, race = "WHITE",
+    creat = 1.09, creatu = "mg/dL", age = 55, sex = "M", weight = 90, race = "WHITE",
     method = "MDRD"
   ), 1L), 70.2)
 })
@@ -87,7 +87,7 @@ test_that("compute_egfr Test 7: CKD-EPI calculated on input data", {
   egfr <- input %>%
     dplyr::mutate(
       EGFR = compute_egfr(
-        creat = CREATBL, creatu = CREATBLU, age = AGE, wt = WTBL, sex = SEX,
+        creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX,
         method = "CKD-EPI"
       ),
       EGFR = round(EGFR, 4L)
@@ -99,3 +99,13 @@ test_that("compute_egfr Test 7: CKD-EPI calculated on input data", {
     keys = c("USUBJID")
   )
 })
+
+## Test 8: Deprecate wt ----
+test_that("compute_egfr Test 8: 'wt' argument deprecation warning", {
+  # expect deprecation warning
+  expect_warning(
+    compute_egfr(
+      creat = 1.09, creatu = "mg/dL", age = 55, sex = "M", wt = 90, method = "CRCL"
+    )
+  )
+})
diff --git a/vignettes/pk_adnca.Rmd b/vignettes/pk_adnca.Rmd
index df24f633f8..b03675367e 100644
--- a/vignettes/pk_adnca.Rmd
+++ b/vignettes/pk_adnca.Rmd
@@ -1377,11 +1377,11 @@ covar_vslb <- covar %>%
     ),
     # Derive CRCLBL and EGFRBL using new function
     CRCLBL = compute_egfr(
-      creat = CREATBL, creatu = "SI", age = AGE, wt = WTBL, sex = SEX,
+      creat = CREATBL, creatu = "SI", age = AGE, weight = WTBL, sex = SEX,
       method = "CRCL"
     ),
     EGFRBL = compute_egfr(
-      creat = CREATBL, creatu = "SI", age = AGE, wt = WTBL, sex = SEX,
+      creat = CREATBL, creatu = "SI", age = AGE, weight = WTBL, sex = SEX,
       method = "CKD-EPI"
     )
   ) %>%

From 4bf63fdd535b1e56cd39dd37c6258ed24fc692af Mon Sep 17 00:00:00 2001
From: StefanThoma <40463122+StefanThoma@users.noreply.github.com>
Date: Thu, 3 Aug 2023 10:23:10 +0200
Subject: [PATCH 2/7] Chore #2020 go through checklist

---
 R/compute_kidney.R  |  1 -
 docs/pkgdown.yml    |  8 ++++----
 man/compute_egfr.Rd | 14 ++++++++------
 3 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/R/compute_kidney.R b/R/compute_kidney.R
index 6f7d1011b3..3d06062b56 100644
--- a/R/compute_kidney.R
+++ b/R/compute_kidney.R
@@ -135,7 +135,6 @@
 #'     ),
 #'   )
 compute_egfr <- function(creat, creatu = "SI", age, weight, sex, race = NULL, method, wt) {
-
   ### BEGIN DEPRECATION
   if (!missing(wt)) {
     deprecate_warn("0.12.0", "compute_egfr(old_param = 'wt')", "compute_egfr(new_param = 'weight')")
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 2e9fb51fe5..6620ae20d1 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 2.11.4
+pandoc: 3.1.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
@@ -19,8 +19,8 @@ articles:
   queries_dataset: queries_dataset.html
   questionnaires: questionnaires.html
   visits_periods: visits_periods.html
-last_built: 2023-07-19T10:42Z
+last_built: 2023-08-03T06:39Z
 urls:
-  reference: https://pharmaverse.github.io/admiral/cran-release/reference/
-  article: https://pharmaverse.github.io/admiral/cran-release/articles/
+  reference: https://pharmaverse.github.io/admiral/reference
+  article: https://pharmaverse.github.io/admiral/articles
 
diff --git a/man/compute_egfr.Rd b/man/compute_egfr.Rd
index db34c29df7..746f387d8f 100644
--- a/man/compute_egfr.Rd
+++ b/man/compute_egfr.Rd
@@ -4,7 +4,7 @@
 \alias{compute_egfr}
 \title{Compute Estimated Glomerular Filtration Rate (eGFR) for Kidney Function}
 \usage{
-compute_egfr(creat, creatu = "SI", age, wt, sex, race = NULL, method)
+compute_egfr(creat, creatu = "SI", age, weight, sex, race = NULL, method, wt)
 }
 \arguments{
 \item{creat}{Creatinine
@@ -23,7 +23,7 @@ Expected Values: \code{"SI"}, \code{"CV"}, \code{"umol/L"}, \code{"mg/dL"}}
 
 A numeric vector is expected.}
 
-\item{wt}{Weight (kg)
+\item{weight}{Weight (kg)
 
 A numeric vector is expected if \code{method = "CRCL"}}
 
@@ -44,6 +44,8 @@ Expected Values: \code{"BLACK OR AFRICAN AMERICAN"} and others}
 A character vector is expected.
 
 Expected Values: \code{"CRCL"}, \code{"CKD-EPI"}, \code{"MDRD"}}
+
+\item{wt}{\emph{Deprecated}, please use \code{weight} instead.}
 }
 \value{
 A numeric vector of egfr values
@@ -97,7 +99,7 @@ units = mL/min/1.73 m2
 }
 \examples{
 compute_egfr(
-  creat = 90, creatu = "umol/L", age = 53, wt = 85, sex = "M", method = "CRCL"
+  creat = 90, creatu = "umol/L", age = 53, weight = 85, sex = "M", method = "CRCL"
 )
 
 compute_egfr(
@@ -125,15 +127,15 @@ base <- tibble::tribble(
 base \%>\%
   dplyr::mutate(
     CRCL_CG = compute_egfr(
-      creat = CREATBL, creatu = CREATBLU, age = AGE, wt = WTBL, sex = SEX,
+      creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX,
       method = "CRCL"
     ),
     EGFR_EPI = compute_egfr(
-      creat = CREATBL, creatu = CREATBLU, age = AGE, wt = WTBL, sex = SEX,
+      creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX,
       method = "CKD-EPI"
     ),
     EGFR_MDRD = compute_egfr(
-      creat = CREATBL, creatu = CREATBLU, age = AGE, wt = WTBL, sex = SEX,
+      creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX,
       race = RACE, method = "MDRD"
     ),
   )

From abcaecf94b6fc03369061d3436d9d58ffa44edc9 Mon Sep 17 00:00:00 2001
From: StefanThoma <40463122+StefanThoma@users.noreply.github.com>
Date: Thu, 3 Aug 2023 14:43:07 +0200
Subject: [PATCH 3/7] update .lycheeignore

---
 .lycheeignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.lycheeignore b/.lycheeignore
index 5774d2a153..e0601dfa65 100644
--- a/.lycheeignore
+++ b/.lycheeignore
@@ -3,3 +3,5 @@ https://github.com/pharmaverse/admiral/blob/main/
 https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adxx.R
 irongut/CodeCoverageSummary@v1.2.0
 https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+https://pharmaverse.github.io/admiral/reference](https://pharmaverse.github.io/admiral/reference
+https://pharmaverse.github.io/admiral/articles](https://pharmaverse.github.io/admiral/articles

From 9c3e9f7b26b9feeffc1e8eeee52644996465d6df Mon Sep 17 00:00:00 2001
From: StefanThoma <40463122+StefanThoma@users.noreply.github.com>
Date: Thu, 3 Aug 2023 14:43:07 +0200
Subject: [PATCH 4/7] update .lycheeignore

---
 .lycheeignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.lycheeignore b/.lycheeignore
index 5774d2a153..f9def1165e 100644
--- a/.lycheeignore
+++ b/.lycheeignore
@@ -3,3 +3,5 @@ https://github.com/pharmaverse/admiral/blob/main/
 https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adxx.R
 irongut/CodeCoverageSummary@v1.2.0
 https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+https://pharmaverse.github.io/admiral/reference
+https://pharmaverse.github.io/admiral/articles

From 73c144458584a6ab7b051bd6e5a89f8e91ebb8fc Mon Sep 17 00:00:00 2001
From: StefanThoma <40463122+StefanThoma@users.noreply.github.com>
Date: Fri, 4 Aug 2023 14:53:21 +0200
Subject: [PATCH 5/7] adjusted templates

---
 inst/templates/ad_adppk.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/inst/templates/ad_adppk.R b/inst/templates/ad_adppk.R
index ea4ceb122b..7d69820370 100644
--- a/inst/templates/ad_adppk.R
+++ b/inst/templates/ad_adppk.R
@@ -448,11 +448,11 @@ covar_vslb <- covar %>%
       method = "Mosteller"
     ),
     CRCLBL = compute_egfr(
-      creat = CREATBL, creatu = "SI", age = AGE, wt = WTBL, sex = SEX,
+      creat = CREATBL, creatu = "SI", age = AGE, weight = WTBL, sex = SEX,
       method = "CRCL"
     ),
     EGFRBL = compute_egfr(
-      creat = CREATBL, creatu = "SI", age = AGE, wt = WTBL, sex = SEX,
+      creat = CREATBL, creatu = "SI", age = AGE, weight = WTBL, sex = SEX,
       method = "CKD-EPI"
     )
   ) %>%

From dd93e3f68dea5f353a67a2f052d8e65a1a683820 Mon Sep 17 00:00:00 2001
From: StefanThoma <40463122+StefanThoma@users.noreply.github.com>
Date: Wed, 9 Aug 2023 15:37:57 +0200
Subject: [PATCH 6/7] chore: removed links from .lycheeignore

---
 .lycheeignore    | 2 --
 docs/pkgdown.yml | 6 +++---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/.lycheeignore b/.lycheeignore
index f9def1165e..5774d2a153 100644
--- a/.lycheeignore
+++ b/.lycheeignore
@@ -3,5 +3,3 @@ https://github.com/pharmaverse/admiral/blob/main/
 https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adxx.R
 irongut/CodeCoverageSummary@v1.2.0
 https://packagemanager.rstudio.com/cran/__linux__/focal/latest
-https://pharmaverse.github.io/admiral/reference
-https://pharmaverse.github.io/admiral/articles
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 6620ae20d1..3a4645246c 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -19,8 +19,8 @@ articles:
   queries_dataset: queries_dataset.html
   questionnaires: questionnaires.html
   visits_periods: visits_periods.html
-last_built: 2023-08-03T06:39Z
+last_built: 2023-08-07T09:14Z
 urls:
-  reference: https://pharmaverse.github.io/admiral/reference
-  article: https://pharmaverse.github.io/admiral/articles
+  reference: https://pharmaverse.github.io/admiral/cran-release/reference/
+  article: https://pharmaverse.github.io/admiral/cran-release/articles/
 

From 0ed1371ba4d51ccd9fe55a975054872dd38c493d Mon Sep 17 00:00:00 2001
From: Ben Straub <ben.x.straub@gsk.com>
Date: Thu, 10 Aug 2023 16:30:10 -0400
Subject: [PATCH 7/7] chore: #2020 removing file

---
 .gitignore | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 6887dd7f14..aedad7715d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -40,7 +40,6 @@ vignettes/*.pdf
 
 # website documents
 /docs/*
-!/docs/pkgdown.yml
 doc
 Meta
 admiral.Rcheck/