#2481: cosmetics

pharmaverse · Jan 13, 2025 · 961bdbe · 961bdbe
1 parent 9980980
commit 961bdbe
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Showing 5 changed files with 38 additions and 37 deletions.
diff --git a/R/derive_param_tte.R b/R/derive_param_tte.R
@@ -67,7 +67,7 @@
 #'   by variables and the date and order specified in the `event_source()` and
 #'   `censor_source()` objects.
 #'
-#'  *Permitted Values*: `"none"`, `"message"`, `"warning"`, `"error"`
+#'   *Permitted Values*: `"none"`, `"message"`, `"warning"`, `"error"`
 #'
 #' @details The following steps are performed to create the observations of the
 #'   new parameter:
@@ -271,10 +271,10 @@
 #'   mutate(STUDYID = "AB42")
 #'
 #' ae <- tribble(
-#'   ~USUBJID, ~AESTDTC, ~AESEQ, ~AEDECOD,
-#'   "01", "2021-01-03T10:56", 1, "Flu",
-#'   "01", "2021-03-04", 2, "Cough",
-#'   "01", "2021", 3, "Flu"
+#'   ~USUBJID, ~AESTDTC,           ~AESEQ, ~AEDECOD,
+#'   "01",     "2021-01-03T10:56",      1, "Flu",
+#'   "01",     "2021-03-04",            2, "Cough",
+#'   "01",     "2021",                  3, "Flu"
 #' ) %>%
 #'   mutate(STUDYID = "AB42")
 #'
@@ -325,16 +325,16 @@
 #'
 #' # Resolve tie when serious AE share a date by sorting with order argument
 #' adsl <- tribble(
-#'   ~USUBJID,    ~TRTSDT,           ~EOSDT,
-#'   "01",        ymd("2020-12-06"), ymd("2021-03-06"),
-#'   "02",        ymd("2021-01-16"), ymd("2021-02-03")
+#'   ~USUBJID, ~TRTSDT,           ~EOSDT,
+#'   "01",     ymd("2020-12-06"), ymd("2021-03-06"),
+#'   "02",     ymd("2021-01-16"), ymd("2021-02-03")
 #' ) %>% mutate(STUDYID = "AB42")
 #'
 #' ae <- tribble(
-#'   ~USUBJID, ~AESTDTC, ~AESEQ, ~AESER, ~AEDECOD,
-#'   "01", "2021-01-03", 1, "Y", "Flu",
-#'   "01", "2021-01-03", 2, "Y", "Cough",
-#'   "01", "2021-01-20", 3, "N", "Headache",
+#'   ~USUBJID, ~AESTDTC,     ~AESEQ, ~AESER, ~AEDECOD,
+#'   "01",     "2021-01-03",      1, "Y",    "Flu",
+#'   "01",     "2021-01-03",      2, "Y",    "Cough",
+#'   "01",     "2021-01-20",      3, "N",    "Headache"
 #' ) %>% mutate(
 #'   AESTDT = ymd(AESTDTC),
 #'   STUDYID = "AB42"
@@ -565,16 +565,15 @@ derive_param_tte <- function(dataset = NULL,
 #'   respect to the date is included in the output dataset. If `"last"` is
 #'   specified, the last observation is included in the output dataset.
 #'
-#'   Permitted Values:  `"first"`, `"last"`
+#'   *Permitted Values*:  `"first"`, `"last"`
 #'
 #' @param check_type Check uniqueness
 #'
 #'   If `"warning"`, `"message"`, or `"error"` is specified, the specified message is issued
 #'   if the observations of the source datasets are not unique with respect to the
 #'   by variables and the date and order specified in the `tte_source()` objects.
 #'
-#'  Default: `"none"`
-#'  Permitted Values: `"none"`, `"warning"`, `"error"`, `"message"`
+#'   *Permitted Values*: `"none"`, `"warning"`, `"error"`, `"message"`
 #'
 #' @details The following steps are performed to create the output dataset:
 #'
@@ -701,9 +700,12 @@ filter_date_sources <- function(sources,
       duplicate_records = function(cnd) {
         cnd_funs <- list(message = cli_inform, warning = cli_warn, error = cli_abort)
         cnd_funs[[check_type]](
-          paste(
-            "Dataset {.val {sources[[i]]$dataset_name}} contains duplicate records with respect to",
-            "{.var {cnd$by_vars}}"
+          c(
+            paste(
+              "Dataset {.val {sources[[i]]$dataset_name}} contains duplicate records with respect to",
+              "{.var {cnd$by_vars}}"
+            ),
+            i = "Run {.run admiral::get_duplicates_dataset()} to access the duplicate records"
           ),
           class = class(cnd))
         cnd_muffle(cnd)

diff --git a/man/derive_param_tte.Rd b/man/derive_param_tte.Rd
diff --git a/man/filter_date_sources.Rd b/man/filter_date_sources.Rd
diff --git a/tests/testthat/_snaps/derive_param_tte.md b/tests/testthat/_snaps/derive_param_tte.md
@@ -70,6 +70,7 @@
     Condition
       Warning:
       Dataset "ae" contains duplicate records with respect to `STUDYID`, `USUBJID`, and `AESTDT`
+      i Run `admiral::get_duplicates_dataset()` to access the duplicate records
     Output
       # A tibble: 2 x 10
         USUBJID STUDYID EVENTDESC  SRCDOM SRCVAR  SRCSEQ  CNSR ADT        STARTDT   

diff --git a/tests/testthat/test-derive_param_tte.R b/tests/testthat/test-derive_param_tte.R
@@ -932,7 +932,7 @@ test_that("derive_param_tte Test 13: error if dataset_name not in source_datsets
   )
 })
 
-## Test 14: derive_param_tte detects duplicates when check_type = 'warning' ----
+## Test 14: detects duplicates in input datasets via pipeline functions ----
 test_that("derive_param_tte Test 14: detects duplicates in input datasets via pipeline functions", {
   # Define ADSL dataset
   adsl <- tibble::tribble(
@@ -989,9 +989,8 @@ test_that("derive_param_tte Test 14: detects duplicates in input datasets via pi
   )
 })
 
-## Test 15: derive_param_tte resolves ties using order argument when input is sorted descending
-test_that("derive_param_tte Test 15: derive_param_tte resolves ties using order argument when
-input is sorted descending", {
+## Test 15: using order for resolving ties ----
+test_that("derive_param_tte Test 15: using order for resolving ties", {
   adsl <- tibble::tribble(
     ~USUBJID, ~TRTSDT,           ~EOSDT,
     "01",     ymd("2020-12-06"), ymd("2021-03-06"),
@@ -1049,7 +1048,7 @@ input is sorted descending", {
   is chosen on tie.")
 })
 
-## Test 16: derive_param_tte produces consistent results regardless of input sort order ----
+## Test 16: produces consistent results regardless of input sort order ----
 test_that("derive_param_tte Test 16: produces consistent results regardless of input sort order", {
   # Define ADSL dataset
   adsl <- tibble::tribble(