#1984 allowing missing trt end date

pharmaverse · Jul 25, 2023 · c707bbb · c707bbb
1 parent 939fbd9
commit c707bbb
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Showing 3 changed files with 59 additions and 2 deletions.
diff --git a/R/derive_var_ontrtfl.R b/R/derive_var_ontrtfl.R
@@ -236,9 +236,9 @@ derive_var_ontrtfl <- function(dataset,
   } else {
     # Scenario 2: Treatment end date is passed, window added above
     if (ignore_time_for_ref_end_date) {
-      end_cond <- expr(date(!!start_date) <= date(!!ref_end_date) + days(!!ref_end_window))
+      end_cond <- expr((date(!!start_date) <= date(!!ref_end_date) + days(!!ref_end_window)) | is.na(!!ref_end_date))
     } else {
-      end_cond <- expr(!!start_date <= !!ref_end_date + days(!!ref_end_window))
+      end_cond <- expr((!!start_date <= !!ref_end_date + days(!!ref_end_window)) | is.na(!!ref_end_date))
     }
     dataset <- mutate(
       dataset,

diff --git a/tests/testthat/_snaps/derive_var_ontrtfl.md b/tests/testthat/_snaps/derive_var_ontrtfl.md
@@ -0,0 +1,22 @@
+# derive_var_ontrtfl Test 15: if trt end date is missing, the obs may still be flagged
+
+    Code
+      derive_var_ontrtfl(adcm, start_date = ASTDT, end_date = AENDT, ref_start_date = TRTSDT,
+        ref_end_date = TRTEDT, span_period = "Y")
+    Output
+        USUBJID      ASTDT     TRTSDT TRTEDT      AENDT ONTRTFL
+      1     P01 2018-03-15 2019-01-01     NA 2022-12-01       Y
+      2     P02 2020-04-30 2019-01-01     NA 2022-03-15       Y
+      3     P03 2020-04-30 2019-01-01     NA       <NA>       Y
+
+---
+
+    Code
+      derive_var_ontrtfl(adcm, start_date = ASTDT, end_date = AENDT, ref_start_date = TRTSDT,
+        ref_end_date = TRTEDT)
+    Output
+        USUBJID      ASTDT     TRTSDT TRTEDT      AENDT ONTRTFL
+      1     P01 2018-03-15 2019-01-01     NA 2022-12-01    <NA>
+      2     P02 2020-04-30 2019-01-01     NA 2022-03-15       Y
+      3     P03 2020-04-30 2019-01-01     NA       <NA>       Y
+
diff --git a/tests/testthat/test-derive_var_ontrtfl.R b/tests/testthat/test-derive_var_ontrtfl.R
@@ -402,3 +402,38 @@ test_that("derive_var_ontrtfl Test 14: start_date < ref_start_date and end_date
     keys = c("STUDYID", "USUBJID", "ASTDT")
   )
 })
+
+
+## Test 15: if trt end date is missing, the obs may still be flagged ----
+test_that("derive_var_ontrtfl Test 15: if trt end date is missing, the obs may still be flagged", { # nolint
+  adcm <- tibble::tribble(
+    ~USUBJID, ~ASTDT,            ~TRTSDT,           ~TRTEDT,    ~AENDT,
+    "P01",    ymd("2018-03-15"), ymd("2019-01-01"), NA,      ymd("2022-12-01"),
+    "P02",    ymd("2020-04-30"), ymd("2019-01-01"), NA,      ymd("2022-03-15"),
+    "P03",    ymd("2020-04-30"), ymd("2019-01-01"), NA,      NA,
+  ) %>%
+    as.data.frame()
+
+  # all flags should be "Y" because span_period flag is "Y"
+  expect_snapshot(
+    derive_var_ontrtfl(
+      adcm,
+      start_date = ASTDT,
+      end_date = AENDT,
+      ref_start_date = TRTSDT,
+      ref_end_date = TRTEDT,
+      span_period = "Y"
+    )
+  )
+
+  # first obs started before treatment, and it should NOT be flagged
+  expect_snapshot(
+    derive_var_ontrtfl(
+      adcm,
+      start_date = ASTDT,
+      end_date = AENDT,
+      ref_start_date = TRTSDT,
+      ref_end_date = TRTEDT
+    )
+  )
+})