Updating create_dcut() to allow for NA as a datacut date

.lintr

@@ -2,7 +2,6 @@ linters: linters_with_defaults(
     line_length_linter(100),
     object_usage_linter=NULL,
     infix_spaces_linter=NULL,
-    indentation_linter=NULL,
     cyclocomp_linter(complexity_limit = 22)
   )
 exclusions: list(

NEWS.md

@@ -4,9 +4,9 @@
 - Added a "Report a bug" link to `{datacutr}` website (#182)
 
 ## Updates of Existing Functions
-- Update to `impute_dcutdtc()`, `date_cut()` and `special_dm_cut()` functions to allow for 
-datacut date to be null. In this case, all records for this patient 
-will be kept/left unchanged.
+- Update to `impute_dcutdtc()`, `create_dcut()`, `date_cut()` and `special_dm_cut()` functions
+to allow for datacut date to be null. In this case, all records for this patient will be 
+kept/left unchanged.
 - Warning added to `process_cut` if expected dataset `dm` is missing
 
 ## Breaking Changes

R/create_dcut.R

@@ -10,7 +10,7 @@
 #' @param ds_date_var Character date/time variable in the DS SDTMv to be compared against the
 #' datacut date
 #' @param filter Condition to filter patients in DS, should give 1 row per patient
-#' @param cut_date Datacut date/time, e.g. "2022-10-22"
+#' @param cut_date Datacut date/time, e.g. "2022-10-22", or NA if no date cut is to be applied
 #' @param cut_description Datacut date/time description, e.g. "Clinical Cut Off Date"
 #'
 #' @author Alana Harris
@@ -74,13 +74,18 @@ create_dcut <- function(dataset_ds,
     mutate(DCUTDTC = cut_date) %>%
     mutate(DCUTDESC = cut_description) %>%
     impute_dcutdtc(dsin = ., varin = DCUTDTC, varout = DCUTDTM) %>%
-    filter(., DCUTDTM >= DCUT_TEMP_DATE) %>%
+    filter(., (!is.na(DCUTDTM) & DCUTDTM >= DCUT_TEMP_DATE) | is.na(DCUTDTM)) %>%
     filter_if(filter) %>%
     subset(select = c(USUBJID, DCUTDTC, DCUTDTM, DCUTDESC))
 
   assert_that(
     (length(get_duplicates(dataset$USUBJID)) == 0),
     msg = "Duplicate patients in the final returned dataset, please update."
   )
+
+  # Print message if cut date is null
+  ifelse(any(is.na(mutate(dataset, DCUTDTM))) == TRUE,
+    print("At least 1 patient with missing datacut date."), NA
+  )
   dataset
 }

tests/testthat/test-create_dcut.R

@@ -28,3 +28,25 @@ test_that("One observation in DCUT", {
     expected_dcut
   )
 })
+
+# Test 2 - Cut date as NA
+expected_dcutna <- tibble::tribble(
+  ~USUBJID, ~DCUTDTC, ~DCUTDTM, ~DCUTDESC,
+  "subject1", NA, NA, "Patients with Informed Consent",
+  "subject2", NA, NA, "Patients with Informed Consent",
+  "subject3", NA, NA, "Patients with Informed Consent",
+  "subject4", NA, NA, "Patients with Informed Consent"
+)
+
+test_that("One observation in DCUT", {
+  expect_equal(
+    create_dcut(
+      dataset_ds = input_ds,
+      ds_date_var = DSSTDTC,
+      filter = DSDECOD == "INFORMED CONSENT",
+      cut_date = NA,
+      cut_description = "Patients with Informed Consent"
+    ),
+    expected_dcutna
+  )
+})