requested updates to documentation and test script for derive_param_tte

pharmaverse · Dec 16, 2024 · 47637a5 · 47637a5
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diff --git a/NEWS.md b/NEWS.md
@@ -12,9 +12,9 @@
 - Update `ADEG` template to flag `ABLFL` and `ANL01FL` based on `DTYPE == "AVERAGE"` records. (#2561)
 
 ## Updates of Existing Functions
-- added `message` as option for `check_type` argument in `filter_extreme`      function. (#2481)
+- added `message` as option for `check_type` argument in `filter_extreme()`      function. (#2481)
 
-- Users can now specify how duplicate records are handled in `derive_param_tte` using the `check_type` argument, with options including `"error"`, `"warning"`, `"message"`, or `"none"`, allowing for greater flexibility in managing duplicate data scenarios. (#2481)
+- Users can now specify how duplicate records are handled in `derive_param_tte()` using the `check_type` argument, with options including `"error"`, `"warning"`, `"message"`, or `"none"`, allowing for greater flexibility in managing duplicate data scenarios. (#2481)
 
 - `order` argument has been added to `event_source()` and `censor_source()` and  
   defaulted to `NULL` to allow specifying variables in addition to the date variable. This can be used to ensure the uniqueness of the select records if there is more than one record per date.  (#2481)  

diff --git a/R/derive_merged.R b/R/derive_merged.R
@@ -110,26 +110,20 @@
 #'   *Permitted Values*: named list of expressions, e.g.,
 #'   `exprs(BASEC = "MISSING", BASE = -1)`
 #'
-#'
-#'
 #'   If `"warning"` or `"error"` is specified, the specified message is issued
 #'   if the observations of the (restricted) additional dataset are not unique
 #'   with respect to the by variables and the order.
 #'
 #'   If the `order` argument is not specified, the `check_type` argument is ignored:
-#'    if the observations of the (restricted) additional dataset are not unique with respect
-#'    to the by variables, an error is issued.
+#'   if the observations of the (restricted) additional dataset are not unique with respect
+#'   to the by variables, an error is issued.
 #'
-#'   *Permitted Values*: `"none"`, `"warning"`, `"error"`
-#'
-#' @param check_type Check uniqueness?
+#'   *Permitted Values*: `"none"`,`"message"`, `"warning"`, `"error"`
 #'
 #'   If `"warning"`, `"message"`, or `"error"` is specified, the specified message is issued
 #'   if the observations of the input dataset are not unique with respect to the
 #'   by variables and the order.
 #'
-#'    Default: `"warning"`
-#'
 #' @param duplicate_msg Message of unique check
 #'
 #'   If the uniqueness check fails, the specified message is displayed.

diff --git a/R/derive_param_tte.R b/R/derive_param_tte.R
@@ -556,7 +556,7 @@ derive_param_tte <- function(dataset = NULL,
 #' @return A dataset with one observation per subject as described in the
 #'   "Details" section.
 #'
-#' @noRd
+#' @keywords internal
 #'
 #' @examples
 #' library(tibble)
@@ -647,7 +647,6 @@ filter_date_sources <- function(sources,
       {
         source_dataset %>%
           filter_if(sources[[i]]$filter) %>%
-          arrange(!!!sources[[i]]$order) %>% # Ensure order is applied
           filter_extreme(
             order = expr_c(exprs(!!source_date_var), sources[[i]]$order),
             by_vars = expr_c(subject_keys, by_vars),

diff --git a/man/derive_var_merged_summary.Rd b/man/derive_var_merged_summary.Rd
diff --git a/man/derive_vars_joined.Rd b/man/derive_vars_joined.Rd
diff --git a/man/derive_vars_merged.Rd b/man/derive_vars_merged.Rd
diff --git a/man/derive_vars_merged_lookup.Rd b/man/derive_vars_merged_lookup.Rd
diff --git a/man/filter_date_sources.Rd b/man/filter_date_sources.Rd
diff --git a/tests/testthat/test-derive_param_tte.R b/tests/testthat/test-derive_param_tte.R
@@ -932,51 +932,8 @@ test_that("derive_param_tte Test 13: error if dataset_name not in source_datsets
   )
 })
 
-# list_tte_source_objects ----
-## Test 14: error is issued if package does not exist ----
-test_that("list_tte_source_objects Test 14: error is issued if package does not exist", {
-  expect_snapshot(
-    list_tte_source_objects(package = "tte"),
-    error = TRUE
-  )
-})
-
-## Test 15: expected objects produced ----
-test_that("list_tte_source_objects Test 15: expected objects produced", {
-  expected_output <- tibble::tribble(
-    ~object,            ~dataset_name,                                              ~filter,
-    "ae_ser_event",            "adae",                 quote(TRTEMFL == "Y" & AESER == "Y"),
-    "ae_gr2_event",            "adae",                quote(TRTEMFL == "Y" & ATOXGR == "2"),
-    "ae_sev_event",            "adae",            quote(TRTEMFL == "Y" & AESEV == "SEVERE"),
-    "ae_gr4_event",            "adae",                quote(TRTEMFL == "Y" & ATOXGR == "4"),
-    "ae_gr3_event",            "adae",                quote(TRTEMFL == "Y" & ATOXGR == "3"),
-    "lastalive_censor",        "adsl",                                                 NULL,
-    "ae_event",                "adae",                                quote(TRTEMFL == "Y"),
-    "death_event",             "adsl",                                  quote(DTHFL == "Y"),
-    "ae_gr35_event",           "adae", quote(TRTEMFL == "Y" & ATOXGR %in% c("3", "4", "5")),
-    "ae_wd_event",             "adae",    quote(TRTEMFL == "Y" & AEACN == "DRUG WITHDRAWN"),
-    "ae_gr1_event",            "adae",                quote(TRTEMFL == "Y" & ATOXGR == "1"),
-    "ae_gr5_event",            "adae",                quote(TRTEMFL == "Y" & ATOXGR == "5")
-  ) %>%
-    mutate(
-      date = case_when(
-        object == "lastalive_censor" ~ "LSTALVDT",
-        object == "death_event" ~ "DTHDT",
-        TRUE ~ "ASTDT"
-      ),
-      censor = if_else(object == "lastalive_censor", 1, 0),
-      filter = as.character(filter),
-      censor = as.integer(censor)
-    )
-
-  observed_output <- list_tte_source_objects(package = "admiral") %>%
-    select(object, dataset_name, filter, date, censor)
-
-  expect_dfs_equal(expected_output, observed_output, keys = c("object"))
-})
-
-## Test 15: derive_param_tte detects duplicates when check_type = 'warning' ----
-test_that("derive_param_tte detects duplicates in the input datasets via pipeline functions", {
+## Test 14: derive_param_tte detects duplicates when check_type = 'warning' ----
+test_that("derive_param_tte Test 14: detects duplicates in input datasets via pipeline functions", {
   # Define ADSL dataset
   adsl <- tibble::tribble(
     ~USUBJID, ~TRTSDT,           ~TRTEDT,           ~EOSDT,
@@ -1033,8 +990,8 @@ test_that("derive_param_tte detects duplicates in the input datasets via pipelin
   )
 })
 
-## Test 16: derive_param_tte produces consistent results regardless of input sort order ----
-test_that("derive_param_tte produces consistent results regardless of input sort order", {
+## Test 15: derive_param_tte produces consistent results regardless of input sort order ----
+test_that("derive_param_tte Test 15: produces consistent results regardless of input sort order", {
   # Define ADSL dataset
   adsl <- tibble::tribble(
     ~USUBJID, ~TRTSDT,           ~TRTEDT,           ~EOSDT,
@@ -1100,3 +1057,46 @@ test_that("derive_param_tte produces consistent results regardless of input sort
 
   expect_equal(result_sorted, result_unsorted)
 })
+
+# list_tte_source_objects ----
+## Test 16: error is issued if package does not exist ----
+test_that("list_tte_source_objects Test 16: error is issued if package does not exist", {
+  expect_snapshot(
+    list_tte_source_objects(package = "tte"),
+    error = TRUE
+  )
+})
+
+## Test 17: expected objects produced ----
+test_that("list_tte_source_objects Test 17: expected objects produced", {
+  expected_output <- tibble::tribble(
+    ~object,            ~dataset_name,                                              ~filter,
+    "ae_ser_event",            "adae",                 quote(TRTEMFL == "Y" & AESER == "Y"),
+    "ae_gr2_event",            "adae",                quote(TRTEMFL == "Y" & ATOXGR == "2"),
+    "ae_sev_event",            "adae",            quote(TRTEMFL == "Y" & AESEV == "SEVERE"),
+    "ae_gr4_event",            "adae",                quote(TRTEMFL == "Y" & ATOXGR == "4"),
+    "ae_gr3_event",            "adae",                quote(TRTEMFL == "Y" & ATOXGR == "3"),
+    "lastalive_censor",        "adsl",                                                 NULL,
+    "ae_event",                "adae",                                quote(TRTEMFL == "Y"),
+    "death_event",             "adsl",                                  quote(DTHFL == "Y"),
+    "ae_gr35_event",           "adae", quote(TRTEMFL == "Y" & ATOXGR %in% c("3", "4", "5")),
+    "ae_wd_event",             "adae",    quote(TRTEMFL == "Y" & AEACN == "DRUG WITHDRAWN"),
+    "ae_gr1_event",            "adae",                quote(TRTEMFL == "Y" & ATOXGR == "1"),
+    "ae_gr5_event",            "adae",                quote(TRTEMFL == "Y" & ATOXGR == "5")
+  ) %>%
+    mutate(
+      date = case_when(
+        object == "lastalive_censor" ~ "LSTALVDT",
+        object == "death_event" ~ "DTHDT",
+        TRUE ~ "ASTDT"
+      ),
+      censor = if_else(object == "lastalive_censor", 1, 0),
+      filter = as.character(filter),
+      censor = as.integer(censor)
+    )
+
+  observed_output <- list_tte_source_objects(package = "admiral") %>%
+    select(object, dataset_name, filter, date, censor)
+
+  expect_dfs_equal(expected_output, observed_output, keys = c("object"))
+})