diff --git a/R/derive_vars_merged_vaccine.R b/R/derive_vars_merged_vaccine.R index cf666435..2d43f239 100644 --- 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)) } }