Merge pull request #254 from pharmaverse/253-feature-request-deprecat…

…esupersede-derive_vars_crit 253 feature request deprecatesupersede derive vars crit
pharmaverse · Jan 28, 2025 · 187f152 · 187f152
2 parents 5bf3c69 + 959f2d2
commit 187f152
Show file tree

Hide file tree

Showing 8 changed files with 139 additions and 116 deletions.
diff --git a/.lycheeignore b/.lycheeignore
@@ -14,3 +14,4 @@ https://cran.r-project.org/package=admiralvaccine
 https://pharmaverse.github.io/admiralvaccine/reference
 https://pharmaverse.github.io/admiralvaccine/articles
 https://github.com/pharmaverse/admiralvaccine/blob/*
+https://www.fda.gov/media/112581/download
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: admiralvaccine
 Title: Vaccine Extension Package for ADaM in 'R' Asset Library
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: c(
     person("Sukalpo", "Saha", email = "[email protected]", role = c("aut", "cre")),
     person("Arjun", "Rubalingam", email = "[email protected]", role = "aut"),
@@ -83,8 +83,9 @@ Suggests:
     metatools
 VignetteBuilder: 
     knitr
+Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# admiralvaccine 0.4.0
+
+## Breaking Changes
+
+- Function `derive_vars_crit()` has been deprecated. Please use `admiral::derive_vars_crit_flag()` instead. (#253)
+
 # admiralvaccine 0.3.0
 
 ## Updates related to CBER requirements for eDiary data

diff --git a/R/derive_vars_crit.R b/R/derive_vars_crit.R
@@ -3,10 +3,10 @@
 #'
 #' @description
 #' Derive analysis criterion evaluation result variable, paired with character
-#' and numeric flags.
-#' This function allows also the derivation of a CRIT like variable with a
-#' different name (ex: `ANL01FL`), without generating additional numeric (ex: `ANL01FN`)
-#' and character label (ex: `ANL01`) variables.
+#'
+#' `r lifecycle::badge("deprecated")`
+#'
+#' This function is *deprecated*, please use `admiral::derive_vars_crit_flag()` instead.
 #'
 #' @param dataset Input dataset
 #'
@@ -94,6 +94,16 @@
 #' )
 #'
 derive_vars_crit <- function(dataset, prefix, crit_label, condition, criterion) {
+  deprecate_warn(
+    when = "0.4.0",
+    what = "derive_vars_crit()",
+    with = "admiral::derive_vars_crit_flag()",
+    details = c(
+      x = "This message will turn into a error at the beginning of 2026.",
+      i = "See admiral's deprecation guidance:
+      https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation"
+    )
+  )
   condition <- assert_filter_cond(enquo(condition))
   criterion <- assert_filter_cond(enquo(criterion))
 

diff --git a/inst/templates/ad_adis.R b/inst/templates/ad_adis.R
@@ -322,13 +322,19 @@ adis <- restrict_derivation(adis,
 
 
 # STEP 9 Derivation of CRITyFL and CRITyFN ----
-adis <- derive_vars_crit(
+adis <- restrict_derivation(
   dataset = adis,
-  prefix = "CRIT1",
-  crit_label = "Titer >= ISLLOQ",
-  condition = !is.na(AVAL) & !is.na(ISLLOQ),
-  criterion = AVAL >= ISLLOQ
-)
+  derivation = derive_vars_crit_flag,
+  args = params(
+    crit_nr = 1,
+    condition = AVAL >= ISLLOQ,
+    description = "Titer >= ISLLOQ",
+    values_yn = TRUE,
+    create_numeric_flag = TRUE
+  ),
+  filter = !is.na(AVAL)
+) %>%
+  arrange(STUDYID, USUBJID, DERIVED, ISSEQ)
 
 
 # STEP 10 Derivation of TRTP/A treatment variables ----

diff --git a/man/derive_vars_crit.Rd b/man/derive_vars_crit.Rd
diff --git a/tests/testthat/test-derive_vars_crit.R b/tests/testthat/test-derive_vars_crit.R
@@ -1,7 +1,6 @@
-## Test 1: Derive CRIT1 variables
+## Test 1: deprecation message if function is called
 
-test_that("derive_vars_crit Test 1: Derive CRIT1 variables", {
-  # input data
+test_that("derive_vars_crit() Test #: deprecation message if function is called", {
   input <- tibble::tribble(
     ~USUBJID, ~AVISITN, ~PARAMCD, ~AVAL, ~ISLLOQ,
     "999999-000001", 10, "J0033VN", 2, 4,
@@ -30,36 +29,26 @@ test_that("derive_vars_crit Test 1: Derive CRIT1 variables", {
         !is.na(AVAL) & !is.na(ISLLOQ) & AVAL < ISLLOQ ~ "N",
         TRUE ~ as.character(NA)
       ),
-      CRIT1FN = if_else(CRIT1FL == "Y", 1, 0),
-      CRIT1 = if_else(!is.na(CRIT1FL), "Titer >= ISLLOQ", as.character(NA))
+      CRIT1 = if_else(!is.na(CRIT1FL), "Titer >= ISLLOQ", as.character(NA)),
+      CRIT1FN = if_else(CRIT1FL == "Y", 1, 0)
     )
 
-
-  # actual dataset
-  actual <- derive_vars_crit(
-    dataset = input,
-    prefix = "CRIT1",
-    crit_label = "Titer >= ISLLOQ",
-    condition = !is.na(AVAL) & !is.na(ISLLOQ),
-    criterion = AVAL >= ISLLOQ
-  )
-
-  expect_dfs_equal(actual,
-    expected,
-    keys = c(
-      "USUBJID", "AVISITN", "PARAMCD", "AVAL", "ISLLOQ", "CRIT1FL",
-      "CRIT1FN", "CRIT1"
-    )
+  expect_warning(
+    derive_vars_crit(
+      dataset = input,
+      prefix = "CRIT1",
+      crit_label = "Titer >= ISLLOQ",
+      condition = !is.na(AVAL) & !is.na(ISLLOQ),
+      criterion = AVAL >= ISLLOQ
+    ),
+    class = "lifecycle_warning_deprecated"
   )
 })
 
 
+## Test 2: Derive CRIT1 variables
 
-
-## Test 2: Derive CRIT1 variables when AVAL is missing
-
-test_that("derive_vars_crit Test 2: Derive CRIT1 variables
-                    when AVAL is missing", {
+test_that("derive_vars_crit Test 2: Derive CRIT1 variables", {
   # input data
   input <- tibble::tribble(
     ~USUBJID, ~AVISITN, ~PARAMCD, ~AVAL, ~ISLLOQ,
@@ -71,14 +60,14 @@ test_that("derive_vars_crit Test 2: Derive CRIT1 variables
     "999999-000001", 30, "I0019NT", 567, 6,
     "999999-000001", 30, "M0019LN", 659, 4,
     "999999-000001", 30, "R0003MA", 250, 6,
-    "999999-000002", 10, "J0033VN", NA, 4,
-    "999999-000002", 10, "I0019NT", NA, 6,
-    "999999-000002", 10, "M0019LN", NA, 4,
-    "999999-000002", 10, "R0003MA", NA, 6,
-    "999999-000002", 30, "J0033VN", NA, 4,
-    "999999-000002", 30, "I0019NT", NA, 6,
-    "999999-000002", 30, "M0019LN", NA, 4,
-    "999999-000002", 30, "R0003MA", NA, 6
+    "999999-000002", 10, "J0033VN", 2, 4,
+    "999999-000002", 10, "I0019NT", 7, 6,
+    "999999-000002", 10, "M0019LN", 5, 4,
+    "999999-000002", 10, "R0003MA", 3, 6,
+    "999999-000002", 30, "J0033VN", 55, 4,
+    "999999-000002", 30, "I0019NT", 89, 6,
+    "999999-000002", 30, "M0019LN", 990, 4,
+    "999999-000002", 30, "R0003MA", 340, 6
   )
 
   # expected dataset
@@ -89,18 +78,21 @@ test_that("derive_vars_crit Test 2: Derive CRIT1 variables
         !is.na(AVAL) & !is.na(ISLLOQ) & AVAL < ISLLOQ ~ "N",
         TRUE ~ as.character(NA)
       ),
-      CRIT1FN = if_else(CRIT1FL == "Y", 1, 0),
-      CRIT1 = if_else(!is.na(CRIT1FL), "Titer >= ISLLOQ", as.character(NA))
+      CRIT1 = if_else(!is.na(CRIT1FL), "Titer >= ISLLOQ", as.character(NA)),
+      CRIT1FN = if_else(CRIT1FL == "Y", 1, 0)
     )
 
 
   # actual dataset
-  actual <- derive_vars_crit(
-    dataset = input,
-    prefix = "CRIT1",
-    crit_label = "Titer >= ISLLOQ",
-    condition = !is.na(AVAL) & !is.na(ISLLOQ),
-    criterion = AVAL >= ISLLOQ
+  actual <- admiraldev::suppress_warning(
+    derive_vars_crit(
+      dataset = input,
+      prefix = "CRIT1",
+      crit_label = "Titer >= ISLLOQ",
+      condition = !is.na(AVAL) & !is.na(ISLLOQ),
+      criterion = AVAL >= ISLLOQ
+    ),
+    regexpr = "was deprecated"
   )
 
   expect_dfs_equal(actual,
@@ -112,64 +104,67 @@ test_that("derive_vars_crit Test 2: Derive CRIT1 variables
   )
 })
 
+## Test 3: Derive CRIT1 variables when AVAL is missing
 
-
-
-## Test 3: Try to apply different vars name and missing ISLLOQ or AVAL
-
-test_that("derive_vars_crit Test 3: Try to apply different vars name and
-                    missing ISLLOQ or AVAL", {
+test_that("derive_vars_crit Test 3: Derive CRIT1 variables when AVAL is missing", {
   # input data
   input <- tibble::tribble(
     ~USUBJID, ~AVISITN, ~PARAMCD, ~AVAL, ~ISLLOQ,
-    "999999-000001", 10, "J0033VN", NA, NA,
-    "999999-000001", 10, "I0019NT", NA, 6,
-    "999999-000001", 10, "M0019LN", NA, 4,
-    "999999-000001", 10, "R0003MA", NA, 6,
-    "999999-000001", 30, "J0033VN", NA, NA,
-    "999999-000001", 30, "I0019NT", NA, 6,
-    "999999-000001", 30, "M0019LN", NA, 4,
-    "999999-000001", 30, "R0003MA", NA, 6,
-    "999999-000002", 10, "J0033VN", 2, NA,
-    "999999-000002", 10, "I0019NT", 7, 6,
-    "999999-000002", 10, "M0019LN", 5, 4,
-    "999999-000002", 10, "R0003MA", 3, 6,
-    "999999-000002", 30, "J0033VN", 55, NA,
-    "999999-000002", 30, "I0019NT", 89, 6,
-    "999999-000002", 30, "M0019LN", 990, 4,
-    "999999-000002", 30, "R0003MA", 340, 6
+    "999999-000001", 10, "J0033VN", 2, 4,
+    "999999-000001", 10, "I0019NT", 3, 6,
+    "999999-000001", 10, "M0019LN", 4, 4,
+    "999999-000001", 10, "R0003MA", 3, 6,
+    "999999-000001", 30, "J0033VN", 60, 4,
+    "999999-000001", 30, "I0019NT", 567, 6,
+    "999999-000001", 30, "M0019LN", 659, 4,
+    "999999-000001", 30, "R0003MA", 250, 6,
+    "999999-000002", 10, "J0033VN", NA, 4,
+    "999999-000002", 10, "I0019NT", NA, 6,
+    "999999-000002", 10, "M0019LN", NA, 4,
+    "999999-000002", 10, "R0003MA", NA, 6,
+    "999999-000002", 30, "J0033VN", NA, 4,
+    "999999-000002", 30, "I0019NT", NA, 6,
+    "999999-000002", 30, "M0019LN", NA, 4,
+    "999999-000002", 30, "R0003MA", NA, 6
   )
 
   # expected dataset
   expected <- input %>%
     mutate(
-      ANL01FL = case_when(
+      CRIT1FL = case_when(
         !is.na(AVAL) & !is.na(ISLLOQ) & AVAL >= ISLLOQ ~ "Y",
         !is.na(AVAL) & !is.na(ISLLOQ) & AVAL < ISLLOQ ~ "N",
         TRUE ~ as.character(NA)
-      )
+      ),
+      CRIT1 = if_else(!is.na(CRIT1FL), "Titer >= ISLLOQ", as.character(NA)),
+      CRIT1FN = if_else(CRIT1FL == "Y", 1, 0)
     )
 
-
   # actual dataset
-  actual <- derive_vars_crit(
-    dataset = input,
-    prefix = "ANL01",
-    crit_label = "Titer >= ISLLOQ",
-    condition = !is.na(AVAL) & !is.na(ISLLOQ),
-    criterion = AVAL >= ISLLOQ
+  actual <- admiraldev::suppress_warning(
+    derive_vars_crit(
+      dataset = input,
+      prefix = "CRIT1",
+      crit_label = "Titer >= ISLLOQ",
+      condition = !is.na(AVAL) & !is.na(ISLLOQ),
+      criterion = AVAL >= ISLLOQ
+    ),
+    regexpr = "was deprecated"
   )
 
   expect_dfs_equal(actual,
     expected,
-    keys = c("USUBJID", "AVISITN", "PARAMCD", "AVAL", "ISLLOQ", "ANL01FL")
+    keys = c(
+      "USUBJID", "AVISITN", "PARAMCD", "AVAL", "ISLLOQ", "CRIT1FL",
+      "CRIT1FN", "CRIT1"
+    )
   )
 })
 
 ## Test 4: Complicated selections and missing values for AVAL and ISLLOQ
 
-test_that("derive_vars_crit Test 4: Complicated selections and missing values
-                    for AVAL and ISLLOQ", {
+test_that("derive_vars_crit Test 4: Complicated selections and missing values for AVAL and
+          ISLLOQ", {
   # input data
   input <- tibble::tribble(
     ~USUBJID, ~AVISITN, ~PARAMCD, ~AVAL, ~ISLLOQ, ~BASE,
@@ -194,23 +189,23 @@ test_that("derive_vars_crit Test 4: Complicated selections and missing values
   # expected dataset
   expected <- input %>%
     mutate(
-      CRIT1FL = case_when(
-        !is.na(AVAL) & !is.na(ISLLOQ) & is.na(BASE) & AVAL >= ISLLOQ & AVAL >= 2 * BASE ~ "Y",
-        !is.na(AVAL) & !is.na(ISLLOQ) & is.na(BASE) & AVAL < ISLLOQ & AVAL >= 2 * BASE ~ "N",
-        TRUE ~ as.character(NA)
+      CRIT1FL = if_else(
+        AVAL >= ISLLOQ & AVAL >= 2 * BASE, "Y", "N"
       ),
-      CRIT1FN = if_else(CRIT1FL == "Y", 1, 0),
-      CRIT1 = if_else(!is.na(CRIT1FL), "Titer >= ISLLOQ", as.character(NA))
+      CRIT1 = if_else(!is.na(CRIT1FL), "Titer >= ISLLOQ and Titer >= 2*BASE", as.character(NA)),
+      CRIT1FN = if_else(CRIT1FL == "Y", 1, 0)
     )
 
-
   # actual dataset
-  actual <- derive_vars_crit(
-    dataset = input,
-    prefix = "CRIT1",
-    crit_label = "Titer >= ISLLOQ and Titer >= 2*BASE",
-    condition = !is.na(AVAL) & !is.na(ISLLOQ) & is.na(BASE),
-    criterion = AVAL >= ISLLOQ & AVAL >= 2 * BASE
+  actual <- admiraldev::suppress_warning(
+    derive_vars_crit(
+      dataset = input,
+      prefix = "CRIT1",
+      crit_label = "Titer >= ISLLOQ and Titer >= 2*BASE",
+      condition = !is.na(AVAL),
+      criterion = AVAL >= ISLLOQ & AVAL >= 2 * BASE
+    ),
+    regexpr = "was deprecated"
   )
 
   expect_dfs_equal(actual,