Merge pull request #247 from pharmaverse/240-Documentation-and-Templates

Closes #240 documentation and templates
pharmaverse · Jul 31, 2024 · ab7dac5 · ab7dac5
2 parents 34fa7c0 + 712dbdb
commit ab7dac5
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Showing 8 changed files with 192 additions and 221 deletions.
diff --git a/inst/templates/ad_adce.R b/inst/templates/ad_adce.R
@@ -56,7 +56,7 @@ adce02 <- adce01 %>%
   derive_vars_merged(
     dataset_add = adsl,
     new_vars = adsl_vars,
-    by = exprs(STUDYID, USUBJID)
+    by = get_admiral_option("subject_keys")
   ) %>%
   ## Derive analysis start time
   ## Proposed imputations depending on situation: no needed -> highest imputation = “n”
@@ -84,7 +84,7 @@ adce03 <-
   derive_vars_joined(
     adce02,
     dataset_add = adperiods,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     filter_join = ASTDT >= APERSDT & ASTDT <= APEREDT,
     join_type = "all"
   ) %>%
@@ -121,7 +121,7 @@ adce05 <- adce04 %>%
   ## Derive ASEQ
   derive_var_obs_number(
     new_var = ASEQ,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(CEDECOD, CELAT, CETPTREF, APERIOD),
     check_type = "error"
   ) %>%
@@ -146,7 +146,7 @@ adsl_list <- adsl %>%
 adce <- adce05 %>%
   derive_vars_merged(
     dataset_add = adsl_list,
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 
 

diff --git a/inst/templates/ad_adface.R b/inst/templates/ad_adface.R
@@ -77,7 +77,7 @@ adface <- derive_vars_merged_vaccine(
   derive_vars_merged(
     dataset_add = adsl,
     new_vars = adsl_vars,
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   ) %>%
   # Step 4 - Deriving Fever OCCUR records from VS if FAOBJ = "FEVER" records not present in FACE
   derive_fever_records(
@@ -107,7 +107,7 @@ period_ref <- create_period_dataset(
 adface <- derive_vars_joined(
   adface,
   dataset_add = period_ref,
-  by_vars = exprs(STUDYID, USUBJID),
+  by_vars = get_admiral_option("subject_keys"),
   filter_join = ADT >= APERSDT & ADT <= APEREDT,
   join_type = "all"
 ) %>%
@@ -212,7 +212,7 @@ lookup_dataset <- tribble(
   "MAXDIAM", "MDISW", 29, "Maximum Diameter", "SWELLING",
   "MAXSEV", "MAXSPIS", 30, "Maximum Severity", "PAIN AT INJECTION SITE",
   "OCCUR", "OCCVOM", 31, "Occurrence Indicator", "VOMITING",
-  "DIAMETER", "DIASWEL", 32, "Diameter", "SWELLING",
+  "DIAMETER", "DIASWEL", 32, "Diameter", "SWELLING"
 )
 
 adface <- derive_vars_params(
@@ -241,7 +241,7 @@ adsl <- adsl %>%
 adface <- derive_vars_merged(
   dataset = adface,
   dataset_add = select(adsl, !!!negate_vars(adsl_vars)),
-  by_vars = exprs(STUDYID, USUBJID)
+  by_vars = get_admiral_option("subject_keys")
 ) %>%
   # Step 16 post processing
   post_process_reacto(