Closes #2014 derive_var_shift change na_val@devel (#2032)

* #2014 `na_val` deprecated and `missing_value` inserted into `derive_var_shift`.

* #2014 - Update `NEWS.md`.

* #2014 - update tests and write deprecation parameter test

* #2014 - run required tasks for PR

---------

Co-authored-by: Ben Straub <ben.x.straub@gsk.com>

.Rprofile

@@ -1,7 +1,7 @@
 # Set renv profile base on R version.
 renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")
 if (file.exists("./renv/profile")) {
-   message("Using renv profile from `renv/profile` file.")
+  message("Using renv profile from `renv/profile` file.")
 } else if (renv_profile %in% c("4.1", "4.2", "4.3")) {
   message("Set renv profile to `", renv_profile, "`")
   Sys.setenv("RENV_PROFILE" = renv_profile)
@@ -11,6 +11,6 @@ if (file.exists("./renv/profile")) {
 
 if ((Sys.getenv("GITHUB_ACTIONS") != "") || (Sys.getenv("DOCKER_CONTAINER_CONTEXT") != "")) {
   options(repos = c(CRAN = "https://cran.rstudio.com"))
-  Sys.setenv(RENV_AUTOLOADER_ENABLED=FALSE)
+  Sys.setenv(RENV_AUTOLOADER_ENABLED = FALSE)
 }
 source("renv/activate.R")

NEWS.md

@@ -34,6 +34,9 @@
 - The `filter` argument in `derive_extreme_records()` was deprecated in favor of
 the `filter_add` using the next phase of the deprecation process. (#1950)
 
+- The `na_val` argument in `derive_var_shift()` has been deprecated in favor of 
+`missing_value` using the first phase of the deprecation process. (#2014)
+
 ## Documentation
 
 

R/derive_var_shift.R

@@ -14,7 +14,9 @@
 #'
 #' @param to_var Variable containing value to shift to.
 #'
-#' @param na_val Character string to replace missing values in `from_var` or `to_var`.
+#' @param na_val *Deprecated*, please use `missing_value` instead.
+#'
+#' @param missing_value Character string to replace missing values in `from_var` or `to_var`.
 #'
 #'  Default: "NULL"
 #'
@@ -24,7 +26,7 @@
 #'
 #' @details `new_var` is derived by concatenating the values of `from_var` to values of `to_var`
 #' (e.g. "NORMAL to HIGH"). When `from_var` or `to_var` has missing value, the
-#' missing value is replaced by `na_val` (e.g. "NORMAL to NULL").
+#' missing value is replaced by `missing_value` (e.g. "NORMAL to NULL").
 #'
 #'
 #' @return The input dataset with the character shift variable added
@@ -71,20 +73,28 @@ derive_var_shift <- function(dataset,
                              new_var,
                              from_var,
                              to_var,
-                             na_val = "NULL",
+                             na_val,
+                             missing_value = "NULL",
                              sep_val = " to ") {
+  ### BEGIN DEPRECATION
+  if (!missing(na_val)) {
+    deprecate_warn("0.12.0", "derive_var_shift(na_val = )", "derive_var_shift(missing_value = )")
+    missing_value <- na_val
+  }
+  ### END DEPRECATION
+
   new_var <- assert_symbol(enexpr(new_var))
   from_var <- assert_symbol(enexpr(from_var))
   to_var <- assert_symbol(enexpr(to_var))
-  na_val <- assert_character_scalar(na_val)
+  missing_value <- assert_character_scalar(missing_value)
   sep_val <- assert_character_scalar(sep_val)
   assert_data_frame(dataset, required_vars = exprs(!!from_var, !!to_var))
 
   # Derive shift variable. If from_var or to_var has missing value then set to na_val.
   dataset %>%
     mutate(
-      temp_from_var = if_else(is.na(!!from_var), !!na_val, as.character(!!from_var)),
-      temp_to_var = if_else(is.na(!!to_var), !!na_val, as.character(!!to_var))
+      temp_from_var = if_else(is.na(!!from_var), !!missing_value, as.character(!!from_var)),
+      temp_to_var = if_else(is.na(!!to_var), !!missing_value, as.character(!!to_var))
     ) %>%
     mutate(
       !!new_var := paste(temp_from_var, temp_to_var, sep = !!sep_val)

tests/testthat/test-derive_var_shift.R

@@ -1,4 +1,7 @@
-test_that("Shift based on character variables", {
+# derive_var_shift ----
+
+## Test 1: Shift based on character variables ----
+test_that("derive_var_shift Test 1: Shift based on character variables", {
   input <- tibble::tribble(
     ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND,
     "P01", "ALB", 33, "Y", "LOW", "LOW",
@@ -28,7 +31,8 @@ test_that("Shift based on character variables", {
 })
 
 
-test_that("Shift based on character variables with missing values", {
+## Test 2: Shift based on character variables with missing values ----
+test_that("derive_var_shift Test 2: Shift based on character variables with missing values", {
   input <- tibble::tribble(
     ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND,
     "P01", "ALB", 33, "Y", "LOW", "LOW",
@@ -60,7 +64,8 @@ test_that("Shift based on character variables with missing values", {
 })
 
 
-test_that("Shift based on numeric variables with missing values", {
+## Test 3: Shift based on numeric variables with missing values ----
+test_that("derive_var_shift Test 3: Shift based on numeric variables with missing values", {
   input <- tibble::tribble(
     ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BASE,
     "P01", "ALB", 33.1, "Y", 33.1,
@@ -91,7 +96,8 @@ test_that("Shift based on numeric variables with missing values", {
   )
 })
 
-test_that("Shift with user-specified na_val and sep_val", {
+## Test 4: Shift with user-specified missing_value and sep_val ----
+test_that("derive_var_shift Test 4: Shift with user-specified missing_value and sep_val", {
   input <- tibble::tribble(
     ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND,
     "P01", "ALB", 33, "Y", "LOW", "LOW",
@@ -117,9 +123,34 @@ test_that("Shift with user-specified na_val and sep_val", {
       new_var = SHIFT1,
       from_var = BNRIND,
       to_var = ANRIND,
-      na_val = "MISSING",
+      missing_value = "MISSING",
       sep_val = " - "
     ),
     expected_output
   )
 })
+
+## Test 5: Test deprecation warning of na_val argument ----
+test_that("derive_var_shift Test 5: Test deprecation warning of na_val argument", {
+  input <- tibble::tribble(
+    ~USUBJID, ~PARAMCD, ~AVAL, ~ABLFL, ~BNRIND, ~ANRIND,
+    "P01", "ALB", 33, "Y", "LOW", "LOW",
+    "P01", "ALB", 38, NA, "LOW", "NORMAL",
+    "P01", "ALB", NA, NA, "LOW", NA,
+    "P02", "ALB", NA, "Y", NA, NA,
+    "P02", "ALB", 49, NA, NA, "HIGH",
+    "P02", "SODIUM", 147, "Y", "HIGH", "HIGH"
+  )
+
+  expect_warning(
+    derive_var_shift(
+      input,
+      new_var = SHIFT1,
+      from_var = BNRIND,
+      to_var = ANRIND,
+      na_val = "MISSING",
+      sep_val = " - "
+    ),
+    class = "lifecycle_warning_deprecated"
+  )
+})