Aligned tables and changed the STUDYID, USUBJID to get_admiral_option…

…("subject_keys") for the bds_exposure vignette
pharmaverse · Oct 30, 2024 · c389dd9 · c389dd9
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diff --git a/NEWS.md b/NEWS.md
@@ -10,10 +10,8 @@
 - Replace use of `data("sdtm")` with `sdtm <- pharmaverse::sdtm` in templates and vignettes. (#2498)
 
 ## Updates of Existing Functions
-- `derive_vars_atc()` and `create_single_dose_dataset()` `by_vars` argument updated to use `get_admiral_option("subject_keys")` instead of  `USUBJID` or `STUDYID`.
-- test scripts, R, and markdown files for `create_single_dose_dataset` and `occds.Rmd` updated to include a `STUDYID` column because of `get_admiral_option("subject_keys")` update above. 
-- `derive_extreme_event()` was fixed such that `check_type = "none"` is accepted
-again. (#2462)
+
+
 
 ## Breaking Changes
 
@@ -50,6 +48,8 @@ again. (#2462)
 
 # admiral 1.1.1
 - `derive_locf_records()` documentation example was fixed to display LOCF records. (#2461)
+- `derive_vars_atc()` and `create_single_dose_dataset()` `by_vars` argument updated to use `get_admiral_option("subject_keys")` instead of  `USUBJID` or `STUDYID` in `bds_exposure.Rmd`.
+- test scripts, R, and markdown files for `create_single_dose_dataset` and `occds.Rmd` updated to include a `STUDYID` column because of `get_admiral_option("subject_keys")` update above. 
 
 # admiral 1.1.0
 
@@ -61,6 +61,8 @@ again. (#2462)
 - New `country_code_lookup()` metadata added to decode countries based on [ISO 3166 codes](https://www.iso.org/iso-3166-country-codes.html). (#2388)
 
 ## Updates of Existing Functions
+- `derive_extreme_event()` was fixed such that `check_type = "none"` is accepted
+again. (#2462)
 
 - `group_var` (optional) parameter is added to `derive_var_trtemfl()` to derive `TRTEMFL` for AE data if the data are collected as one episode of AE with multiple lines. (#2302)
 

diff --git a/tests/testthat/test-create_single_dose_dataset.R b/tests/testthat/test-create_single_dose_dataset.R
@@ -2,24 +2,24 @@
 ## Test 1: Works as expected for Q*/EVERY * cases ----
 test_that("create_single_dose_dataset Test 1: Works as expected for Q*/EVERY * cases", {
   input <- tibble::tribble(
-    ~STUDYID, ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~AENDT,
-    "STUDY01", "P01", "Q2D", ymd("2021-01-01"), ymd("2021-01-07"),
-    "STUDY01", "P01", "Q3D", ymd("2021-01-08"), ymd("2021-01-14"),
+    ~STUDYID, ~USUBJID, ~EXDOSFRQ,          ~ASTDT,           ~AENDT,
+    "STUDY01", "P01",     "Q2D",       ymd("2021-01-01"), ymd("2021-01-07"),
+    "STUDY01", "P01",     "Q3D",       ymd("2021-01-08"), ymd("2021-01-14"),
     "STUDY01", "P01", "EVERY 2 WEEKS", ymd("2021-01-15"), ymd("2021-01-29"),
-    "STUDY01", "P02", "ONCE", ymd("2021-02-02"), ymd("2021-02-02")
+    "STUDY01", "P02",     "ONCE",      ymd("2021-02-02"), ymd("2021-02-02")
   )
   expected_output <- tibble::tribble(
-    ~STUDYID, ~USUBJID, ~EXDOSFRQ, ~ASTDT, ~AENDT,
-    "STUDY01", "P01", "ONCE", ymd("2021-01-01"), ymd("2021-01-01"),
-    "STUDY01", "P01", "ONCE", ymd("2021-01-03"), ymd("2021-01-03"),
-    "STUDY01", "P01", "ONCE", ymd("2021-01-05"), ymd("2021-01-05"),
-    "STUDY01", "P01", "ONCE", ymd("2021-01-07"), ymd("2021-01-07"),
-    "STUDY01", "P01", "ONCE", ymd("2021-01-08"), ymd("2021-01-08"),
-    "STUDY01", "P01", "ONCE", ymd("2021-01-11"), ymd("2021-01-11"),
-    "STUDY01", "P01", "ONCE", ymd("2021-01-14"), ymd("2021-01-14"),
-    "STUDY01", "P01", "ONCE", ymd("2021-01-15"), ymd("2021-01-15"),
-    "STUDY01", "P01", "ONCE", ymd("2021-01-29"), ymd("2021-01-29"),
-    "STUDY01", "P02", "ONCE", ymd("2021-02-02"), ymd("2021-02-02")
+    ~STUDYID, ~USUBJID, ~EXDOSFRQ,    ~ASTDT,            ~AENDT,
+    "STUDY01", "P01",     "ONCE", ymd("2021-01-01"), ymd("2021-01-01"),
+    "STUDY01", "P01",     "ONCE", ymd("2021-01-03"), ymd("2021-01-03"),
+    "STUDY01", "P01",     "ONCE", ymd("2021-01-05"), ymd("2021-01-05"),
+    "STUDY01", "P01",     "ONCE", ymd("2021-01-07"), ymd("2021-01-07"),
+    "STUDY01", "P01",     "ONCE", ymd("2021-01-08"), ymd("2021-01-08"),
+    "STUDY01", "P01",     "ONCE", ymd("2021-01-11"), ymd("2021-01-11"),
+    "STUDY01", "P01",     "ONCE", ymd("2021-01-14"), ymd("2021-01-14"),
+    "STUDY01", "P01",     "ONCE", ymd("2021-01-15"), ymd("2021-01-15"),
+    "STUDY01", "P01",     "ONCE", ymd("2021-01-29"), ymd("2021-01-29"),
+    "STUDY01", "P02",     "ONCE", ymd("2021-02-02"), ymd("2021-02-02")
   )
 
   expect_dfs_equal(

diff --git a/vignettes/bds_exposure.Rmd b/vignettes/bds_exposure.Rmd
@@ -81,7 +81,7 @@ adex <- derive_vars_merged(
   ex,
   dataset_add = adsl,
   new_vars = adsl_vars,
-  by_vars = exprs(STUDYID, USUBJID)
+  by_vars = get_admiral_option("subject_keys")
 )
 ```
 
@@ -581,7 +581,7 @@ example call is:
 adex <- derive_var_obs_number(
   adex,
   new_var = ASEQ,
-  by_vars = exprs(STUDYID, USUBJID),
+  by_vars = get_admiral_option("subject_keys"),
   order = exprs(PARCAT1, ASTDT, VISIT, VISITNUM, EXSEQ, PARAMN),
   check_type = "error"
 )
@@ -602,7 +602,7 @@ If needed, the other `ADSL` variables can now be added:
 adex <- adex %>%
   derive_vars_merged(
     dataset_add = select(adsl, !!!negate_vars(adsl_vars)),
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 ```
 ## Add Labels and Attributes {#attributes}