Add test case for baseline_timepoints in derive_blfl function (#95)

* Modified test case * style file * Add examples to function * Empty commit, trigger CI jobs --------- Co-authored-by: Adam Forys <[email protected]>
pharmaverse · Sep 12, 2024 · 31aadcd · 31aadcd
1 parent 048aad5
commit 31aadcd
Show file tree

Hide file tree

Showing 4 changed files with 66 additions and 15 deletions.
diff --git a/R/derive_blfl.R b/R/derive_blfl.R
@@ -260,6 +260,7 @@ dtc_timepart <- function(dtc, partial_as_na = TRUE, ignore_seconds = TRUE) {
 #'
 #' sdtm_in
 #'
+#' # Example 1:
 #' observed_output <- derive_blfl(
 #'   sdtm_in = sdtm_in,
 #'   dm_domain = dm,
@@ -269,6 +270,27 @@ dtc_timepart <- function(dtc, partial_as_na = TRUE, ignore_seconds = TRUE) {
 #' )
 #' observed_output
 #'
+#' # Example 2:
+#' observed_output2 <- derive_blfl(
+#'   sdtm_in = sdtm_in,
+#'   dm_domain = dm,
+#'   tgt_var = "VSLOBXFL",
+#'   ref_var = "RFXSTDTC",
+#'   baseline_timepoints = c("PRE-DOSE")
+#' )
+#' observed_output2
+#'
+#' # Example 3: Output is the same as Example 2
+#' observed_output3 <- derive_blfl(
+#'   sdtm_in = sdtm_in,
+#'   dm_domain = dm,
+#'   tgt_var = "VSLOBXFL",
+#'   ref_var = "RFXSTDTC",
+#'   baseline_visits = c("SCREENING"),
+#'   baseline_timepoints = c("PRE-DOSE")
+#' )
+#' observed_output3
+#'
 derive_blfl <- function(sdtm_in,
                         dm_domain,
                         tgt_var,

diff --git a/man/derive_blfl.Rd b/man/derive_blfl.Rd
diff --git a/tests/testthat/_snaps/derive_blfl.md b/tests/testthat/_snaps/derive_blfl.md
@@ -16,7 +16,7 @@
         "names": {
           "type": "character",
           "attributes": {},
-          "value": ["DOMAIN", "oak_id", "raw_source", "patient_number", "USUBJID", "VSDTC", "VSTESTCD", "VSORRES", "VSSTAT", "VISIT", "VSLOBXFL"]
+          "value": ["DOMAIN", "oak_id", "raw_source", "patient_number", "USUBJID", "VSDTC", "VSTESTCD", "VSORRES", "VSSTAT", "VISIT", "VSTPT", "VSLOBXFL"]
         }
       },
       "value": [
@@ -73,7 +73,13 @@
         {
           "type": "character",
           "attributes": {},
-          "value": ["Y", null, null, null, "Y", null, "Y", null, "Y", "Y", null]
+          "value": ["PRE-DOSE", "30 DAY POST-DOSE", "28 DAY POST-DOSE", "30 DAY POST-DOSE", "28 DAY POST-DOSE", "28 DAY POST-DOSE",
+          "PRE-DOSE", "PRE-DOSE", "PRE-DOSE", "PRE-DOSE", "1 DAY POST-DOSE"]
+        },
+        {
+          "type": "character",
+          "attributes": {},
+          "value": ["Y", null, null, null, null, "Y", "Y", null, "Y", "Y", null]
         }
       ]
     }

diff --git a/tests/testthat/test-derive_blfl.R b/tests/testthat/test-derive_blfl.R
@@ -9,18 +9,18 @@ dm <- tibble::tribble(
 
 sdtm_in <-
   tibble::tribble(
-    ~DOMAIN, ~oak_id, ~raw_source, ~patient_number, ~USUBJID, ~VSDTC, ~VSTESTCD, ~VSORRES, ~VSSTAT, ~VISIT,
-    "VS", 1L, "VTLS1", 375L, "test_study-375", "2020-09-01T13:31", "DIABP", "90", NA, "SCREENING",
-    "VS", 2L, "VTLS1", 375L, "test_study-375", "2020-10-01T11:20", "DIABP", "90", NA, "SCREENING",
-    "VS", 1L, "VTLS1", 375L, "test_study-375", "2020-09-28T10:10", "PULSE", "ND", NA, "SCREENING",
-    "VS", 2L, "VTLS1", 375L, "test_study-375", "2020-10-01T13:31", "PULSE", "85", NA, "SCREENING",
-    "VS", 1L, "VTLS2", 375L, "test_study-375", "2020-09-28T10:10", "SYSBP", "120", NA, "SCREENING",
-    "VS", 2L, "VTLS2", 375L, "test_study-375", "2020-09-28T10:05", "SYSBP", "120", NA, "SCREENING",
-    "VS", 1L, "VTLS1", 376L, "test_study-376", "2020-09-20", "DIABP", "75", NA, "SCREENING",
-    "VS", 1L, "VTLS1", 376L, "test_study-376", "2020-09-20", "PULSE", NA, "NOT DONE", "SCREENING", # nolint
-    "VS", 2L, "VTLS1", 376L, "test_study-376", "2020-09-20", "PULSE", "110", NA, "SCREENING",
-    "VS", 2L, "VTLS1", 378L, "test_study-378", "2020-01-20T10:00", "PULSE", "110", NA, "SCREENING",
-    "VS", 3L, "VTLS1", 378L, "test_study-378", "2020-01-21T11:00", "PULSE", "105", NA, "SCREENING"
+    ~DOMAIN, ~oak_id, ~raw_source, ~patient_number, ~USUBJID, ~VSDTC, ~VSTESTCD, ~VSORRES, ~VSSTAT, ~VISIT, ~VSTPT,
+    "VS", 1L, "VTLS1", 375L, "test_study-375", "2020-09-01T13:31", "DIABP", "90", NA, "SCREENING", "PRE-DOSE",
+    "VS", 2L, "VTLS1", 375L, "test_study-375", "2020-10-01T11:20", "DIABP", "90", NA, "SCREENING", "30 DAY POST-DOSE",
+    "VS", 1L, "VTLS1", 375L, "test_study-375", "2020-09-28T10:10", "PULSE", "ND", NA, "SCREENING", "28 DAY POST-DOSE",
+    "VS", 2L, "VTLS1", 375L, "test_study-375", "2020-10-01T13:31", "PULSE", "85", NA, "SCREENING", "30 DAY POST-DOSE",
+    "VS", 1L, "VTLS2", 375L, "test_study-375", "2020-09-28T10:10", "SYSBP", "120", NA, "SCREENING", "28 DAY POST-DOSE",
+    "VS", 2L, "VTLS2", 375L, "test_study-375", "2020-09-28T10:05", "SYSBP", "120", NA, "SCREENING", "28 DAY POST-DOSE",
+    "VS", 1L, "VTLS1", 376L, "test_study-376", "2020-09-20", "DIABP", "75", NA, "SCREENING", "PRE-DOSE",
+    "VS", 1L, "VTLS1", 376L, "test_study-376", "2020-09-20", "PULSE", NA, "NOT DONE", "SCREENING", "PRE-DOSE", # nolint
+    "VS", 2L, "VTLS1", 376L, "test_study-376", "2020-09-20", "PULSE", "110", NA, "SCREENING", "PRE-DOSE",
+    "VS", 2L, "VTLS1", 378L, "test_study-378", "2020-01-20T10:00", "PULSE", "110", NA, "SCREENING", "PRE-DOSE",
+    "VS", 3L, "VTLS1", 378L, "test_study-378", "2020-01-21T11:00", "PULSE", "105", NA, "SCREENING", "1 DAY POST-DOSE"
   )
 
 d <- list(sdtm_in = sdtm_in, dm = dm)
@@ -32,7 +32,8 @@ test_that("derive_blfl example works", {
     dm_domain = d$dm,
     tgt_var = "VSLOBXFL",
     ref_var = "RFXSTDTC",
-    baseline_visits = c("SCREENING")
+    baseline_visits = c("SCREENING"),
+    baseline_timepoints = c("PRE-DOSE")
   )
   observed_output