#246

removed supp dataset args
pharmaverse · Jul 31, 2024 · f429c66 · f429c66
1 parent 3d4715a
commit f429c66
Showing 1 changed file with 7 additions and 40 deletions.
diff --git a/R/derive_vars_merged_vaccine.R b/R/derive_vars_merged_vaccine.R
@@ -4,27 +4,15 @@
 #' The variables to be added to the output dataset will be based on input variables
 #' passed on `ex_vars` argument.
 #'
-#' @param dataset Input dataset
+#' @param dataset Input dataset which should have been combined with the supplementary(if exists).
 #'
 #'   The variables specified by the `by_vars` argument inside the
 #'    `derive_vars_merged`are expected.
 #'
-#' @param dataset_ex EX dataset to merge with the input dataset.
+#' @param dataset_ex `ex` dataset(combined with `suppex`) to merge with the input dataset.
 #'
 #'   The variables specified by the `ex_vars` argument are expected.
 #'
-#' @param dataset_supp Supplementary input dataset
-#'
-#'    By default `dataset_supp` will be `NULL`, user has to provide
-#'    supplementary dataset to merge it back with original input dataset
-#'    if they have supplementary dataset in their case.
-#'
-#' @param dataset_suppex Supplementary EX dataset
-#'
-#'    By default `dataset_suppex` will be `NULL`, user has to provide
-#'    supplementary dataset to merge it back with original `EX` dataset
-#'    if they have supplementary dataset in their case.
-#'
 #' @param by_vars_sys Grouping variables for systemic events.
 #'
 #' @param by_vars_adms Grouping variables for administration site events.
@@ -45,8 +33,7 @@
 #' Only the variables passed to the `ex_vars` will be added in the output dataset
 #'
 #' If the input dataset has multiple vaccination for a subject at same visit
-#' then this function will not merge ex dataset and will return only the input
-#' dataset merged with its supplementary dataset.
+#' then this function will not merge ex dataset and will return the `dataset`.
 #'
 #' @author Vikram S
 #'
@@ -66,8 +53,6 @@
 #' derive_vars_merged_vaccine(
 #'   dataset = face_vaccine,
 #'   dataset_ex = ex_vaccine,
-#'   dataset_supp = NULL,
-#'   dataset_suppex = NULL,
 #'   by_vars_sys = exprs(USUBJID, FATPTREF = EXLNKGRP),
 #'   by_vars_adms = exprs(USUBJID, FATPTREF = EXLNKGRP, FALOC = EXLOC, FALAT = EXLAT),
 #'   ex_vars = exprs(EXTRT, EXDOSE, EXDOSU, EXSTDTC, EXENDTC)
@@ -78,38 +63,21 @@
 #' derive_vars_merged_vaccine(
 #'   dataset = face_vaccine,
 #'   dataset_ex = ex_vaccine,
-#'   dataset_supp = suppface_vaccine,
-#'   dataset_suppex = suppex_vaccine,
 #'   by_vars_sys = exprs(USUBJID, FATPTREF = EXLNKGRP),
 #'   by_vars_adms = exprs(USUBJID, FATPTREF = EXLNKGRP, FALOC = EXLOC, FALAT = EXLAT),
 #'   ex_vars = exprs(EXTRT, EXDOSE, EXDOSU, EXSTDTC, EXENDTC)
-#' ) %>%
-#'   filter(CLTYP == "DAIRY") %>%
-#'   select(USUBJID, FATPTREF, CLTYP, EXTRT, EXDOSE, EXDOSU, EXSTDTC, EXENDTC)
+#' )
+#'
 derive_vars_merged_vaccine <- function(dataset,
                                        dataset_ex,
                                        by_vars_sys,
                                        by_vars_adms,
-                                       dataset_supp = NULL,
-                                       dataset_suppex = NULL,
                                        ex_vars) {
   assert_data_frame(dataset)
   assert_vars(by_vars_sys)
   assert_vars(by_vars_adms)
   assert_vars(ex_vars)
-  assert_data_frame(dataset_supp, optional = TRUE)
   assert_data_frame(dataset_ex)
-  assert_data_frame(dataset_suppex, optional = TRUE)
-
-  # combine face and suppface dataset
-  if (!is.null(dataset_supp)) {
-    dataset <- combine_supp(dataset, dataset_supp)
-  }
-
-  # combine face and suppex dataset
-  if (!is.null(dataset_suppex)) {
-    dataset_ex <- combine_supp(dataset_ex, dataset_suppex)
-  }
 
   if ("VISIT" %in% names(dataset_ex)) {
     ex_distinct <- dataset_ex %>% distinct(USUBJID, VISIT, .keep_all = TRUE)
@@ -119,8 +87,7 @@ derive_vars_merged_vaccine <- function(dataset,
 
   if (nrow(dataset_ex) != nrow(ex_distinct)) {
     warning("Subjects have multiple vaccinations at same visit")
-
-    dataset <- dataset
+    return(dataset)
   } else {
     # Filter records for  ADMINISTRATION SITE events and merge it with EX dataset
     dataset_adminstration <- dataset %>%
@@ -145,6 +112,6 @@ derive_vars_merged_vaccine <- function(dataset,
     )
 
     # bind face1 and face2 datasets
-    bind_rows(face1, face2)
+    return(bind_rows(face1, face2))
   }
 }