Merge branch 'main' into 239-general-issue-remove-styler-dependency

DESCRIPTION

@@ -58,7 +58,6 @@ Imports:
     lifecycle (>= 0.1.0),
     lubridate (>= 1.7.4),
     magrittr (>= 1.5),
-    metatools,
     purrr (>= 0.3.3),
     rlang (>= 0.4.4),
     stringr (>= 1.4.0),
@@ -80,7 +79,8 @@ Suggests:
     spelling,
     testthat,
     tibble,
-    usethis
+    usethis,
+    metatools
 VignetteBuilder: 
     knitr
 Encoding: UTF-8

NAMESPACE

@@ -87,7 +87,6 @@ importFrom(lubridate,years)
 importFrom(lubridate,ymd)
 importFrom(lubridate,ymd_hms)
 importFrom(magrittr,"%>%")
-importFrom(metatools,combine_supp)
 importFrom(purrr,compose)
 importFrom(purrr,every)
 importFrom(purrr,flatten)

NEWS.md

@@ -1,4 +1,12 @@
-# admiralvaccine (development version)
+# admiralvaccine 0.3.0
+
+## Breaking Changes
+
+- Removed `dataset_supp` and `dataset_suppex` arguments from `derive_vars_merged_vaccine()` as we are not combining the parental with supplementary inside the function, but can be optionally combined in the ADCE, ADFACE and ADIS templates using `combine_supp()` function from {metatools}. (#246)
+
+## Updates to Templates
+
+- Supplementary domains are now optionally combined with parental domain within the template. (#246)
 
 # admiralvaccine 0.2.0
 

R/admiralvaccine.R

@@ -32,5 +32,4 @@
 #' @importFrom admiraldev assert_logical_scalar assert_character_vector assert_vars
 #'             assert_data_frame assert_character_scalar assert_numeric_vector assert_filter_cond
 #'             assert_symbol assert_expr_list expect_dfs_equal
-#' @importFrom metatools combine_supp
 "_PACKAGE"

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))
   }
 }

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")
   )
 
 

inst/templates/ad_adface.R

@@ -58,13 +58,17 @@ face <- face %>%
 
 adsl_vars <- exprs(RFSTDTC, RFENDTC)
 
+# Combine the parental datasets with their respective supp datasets (only if exist)
+# User can use `combine_supp()` from {metatools} to combine the parental with supp dataset.
+
+face <- metatools::combine_supp(face, suppface)
+ex <- metatools::combine_supp(ex, suppex)
+
 # Step 2 - Merging supplementary datasets and FACE with EX
 
 adface <- derive_vars_merged_vaccine(
   dataset = face,
   dataset_ex = ex,
-  dataset_supp = suppface,
-  dataset_suppex = suppex,
   by_vars_sys = exprs(USUBJID, FATPTREF = EXLNKGRP),
   by_vars_adms = exprs(USUBJID, FATPTREF = EXLNKGRP, FALOC = EXLOC, FALAT = EXLAT),
   ex_vars = exprs(EXTRT, EXDOSE, EXSEQ, EXSTDTC, EXENDTC, VISIT, VISITNUM)
@@ -73,7 +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(
@@ -103,7 +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"
 ) %>%
@@ -208,7 +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(
@@ -237,7 +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(
@@ -261,13 +265,11 @@ keep_vars <- c(
   "APEREDT", "APERETM", "APEREDTM", "APERDY", "FAORRES"
 )
 
-adface <- adface %>% select(
+admiralvaccine_adface <- adface %>% select(
   any_of(keep_vars), starts_with("TRT0"), starts_with("VAX"),
   starts_with("EVE"), starts_with("ANL")
 )
 
-admiralvaccine_adface <- adface
-
 # Save output ----
 
 dir <- tools::R_user_dir("admiralvaccine_templates_data", which = "cache")