#246

removed metatools from imports but moved suggests
pharmaverse · Jul 31, 2024 · 3d4715a · 3d4715a
1 parent c2f817c
commit 3d4715a
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Showing 9 changed files with 20 additions and 159 deletions.
diff --git a/DESCRIPTION b/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),
@@ -81,7 +80,8 @@ Suggests:
     styler,
     testthat,
     tibble,
-    usethis
+    usethis,
+    metatools
 VignetteBuilder: 
     knitr
 Encoding: UTF-8

diff --git a/NAMESPACE b/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)

diff --git a/R/admiralvaccine.R b/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"
diff --git a/inst/templates/ad_adface.R b/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)
@@ -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")

diff --git a/inst/templates/ad_adis.R b/inst/templates/ad_adis.R
@@ -31,7 +31,7 @@ adsl <- convert_blanks_to_na(admiralvaccine_adsl)
 
 # STEP 1 - combine IS with SUPPIS.
 # Please, upload MOCK data
-is_suppis <- combine_supp(is, suppis)
+is_suppis <- metatools::combine_supp(is, suppis)
 
 
 # STEP 2 - Visits and timing variables derivation.

diff --git a/man/derive_vars_merged_vaccine.Rd b/man/derive_vars_merged_vaccine.Rd
diff --git a/tests/testthat/test-derive_vars_merged_vaccine.R b/tests/testthat/test-derive_vars_merged_vaccine.R
@@ -1,5 +1,3 @@
-## Test 1: Merging EXTRT variable from EX to FACE
-
 test_that("derive_vars_merged_vaccine Test 1: Merging EXTRT variable from EX to FACE", {
   face <- tibble::tribble(
     ~USUBJID, ~FACAT, ~FASCAT, ~FATESTCD, ~FAOBJ, ~FATEST, ~FALOC, ~FALAT, ~FATPTREF,
@@ -43,8 +41,6 @@ test_that("derive_vars_merged_vaccine Test 1: Merging EXTRT variable from EX to
   actual <- derive_vars_merged_vaccine(
     dataset = face,
     dataset_ex = ex,
-    dataset_supp = NULL,
-    dataset_suppex = NULL,
     by_vars_sys = exprs(USUBJID, FATPTREF = EXTPTREF),
     by_vars_adms = exprs(USUBJID, FATPTREF = EXTPTREF, FALOC = EXLOC, FALAT = EXLAT),
     ex_vars = exprs(EXTRT, EXDOSE)
@@ -55,123 +51,8 @@ test_that("derive_vars_merged_vaccine Test 1: Merging EXTRT variable from EX to
   ))
 })
 
-## Test 2: Check if supp datasets merged properly if they exist
-
-test_that("derive_vars_merged_vaccine Test 2: Check if supp datasets merged
-          properly if they exist", {
-  face <- tibble::tribble(
-    ~STUDYID, ~DOMAIN, ~USUBJID, ~FACAT, ~FASCAT, ~FATESTCD, ~FAOBJ, ~FATEST, ~FALOC, ~FALAT,
-    ~FATPTREF, ~FASEQ,
-    "ABC", "FACE", "ABC101", "REACTO", "ADMINISTRATION SITE", "SEV", "Redness", "Severity", "ARM",
-    "RIGHT", "VAC 1", 1,
-    "ABC", "FACE", "ABC101", "REACTO", "ADMINISTRATION SITE", "DIAMETER", "Redness", "Diameter",
-    "ARM", "LEFT", "VAC 1", 2,
-    "ABC", "FACE", "ABC101", "REACTO", "ADMINISTRATION SITE", "DIAM", "Redness", "Diameter",
-    NA, NA, "VAC 2", 3,
-    "ABC", "FACE", "ABC101", "REACTO", "SYSTEMIC", "OCCUR", "Fatigue", "Occurrence",
-    "LEG", "LEFT", "VAC 3", 5,
-    "ABC", "FACE", "ABC101", "REACTO", "ADMINISTRATION SITE", "OCCUR", "Erythema",
-    "Occurrence", "LEG", "LEFT", "VAC 3", 6,
-    "ABC", "FACE", "ABC101", "REACTO", "ADMINISTRATION SITE", "SEV", "Swelling",
-    "Severity", NA, NA, "VAC 4", 7,
-    "ABC", "FACE", "ABC101", "REACTO", "ADMINISTRATION SITE", "OCCUR", "Swelling",
-    "Occurrence", NA, NA, "VAC 4", 8,
-    "ABC", "FACE", "ABC102", "REACTO", "ADMINISTRATION SITE", "OCCUR", "Swelling",
-    "Occurrence", NA, NA, "VAC 1", 1
-  )
-
-  ex <- tibble::tribble(
-    ~STUDYID, ~DOMAIN, ~USUBJID, ~EXSTDTC, ~VISITNUM, ~EXTRT, ~EXTPTREF, ~VISIT, ~EXLOC, ~EXLAT,
-    ~EXDOSE, ~EXSEQ,
-    "ABC", "EX", "ABC101", "2015-01-10", 1, "DRUG A", "VAC 1", "VISIT 1", "ARM", "RIGHT", 20, 1,
-    "ABC", "EX", "ABC101", "2015-01-11", 2, "DRUG A", "VAC 2", "VISIT 2", NA, NA, 30, 2,
-    "ABC", "EX", "ABC101", "2015-01-12", 3, "DRUG B", "VAC 3", "VISIT 3", "LEG", "LEFT", 25, 3,
-    "ABC", "EX", "ABC101", "2015-01-13", 4, "DRUG C", "VAC 4", "VISIT 4", NA, NA, 30, 4,
-    "ABC", "EX", "ABC102", "2015-01-13", 1, "DRUG B", "VAC 1", "VISIT 5", NA, NA, 10, 1
-  )
-
-  suppface <- tibble::tribble(
-    ~STUDYID, ~USUBJID, ~RDOMAIN, ~IDVAR, ~IDVARVAL, ~QNAM, ~QVAL, ~QLABEL, ~QORIG,
-    "ABC", "ABC101", "FACE", "FASEQ", 1, "CLTYP", "DAIRY", "Collection Type",
-    "Predecessor",
-    "ABC", "ABC101", "FACE", "FASEQ", 2, "CLTYP", "CRF", "Collection Type",
-    "Predecessor"
-  )
-
-  suppex <- tibble::tribble(
-    ~STUDYID, ~USUBJID, ~RDOMAIN, ~IDVAR, ~IDVARVAL, ~QNAM, ~QVAL, ~QLABEL, ~QORIG,
-    "ABC", "ABC101", "EX", "EXSEQ", 1, "EXTDV", "N", "Temporary Delay of Vaccination",
-    "ASSIGNED",
-    "ABC", "ABC101", "EX", "EXSEQ", 2, "EXTDV", "Y", "Temporary Delay of Vaccination",
-    "ASSIGNED"
-  )
-
-  temp <- suppface %>%
-    pivot_wider(
-      id_cols = c(USUBJID, IDVAR, IDVARVAL),
-      names_from = QNAM,
-      values_from = QVAL
-    ) %>%
-    mutate(FASEQ = IDVARVAL) %>%
-    select(-c(IDVAR, IDVARVAL))
-  facef <- left_join(face, temp, by = c("USUBJID", "FASEQ"), keep = FALSE)
-  face1 <- facef %>%
-    mutate(LOC = FALOC, LAT = FALAT, TPTREF = FATPTREF)
-
-  tempex <- suppex %>%
-    pivot_wider(
-      id_cols = c(USUBJID, IDVAR, IDVARVAL),
-      names_from = QNAM,
-      values_from = QVAL
-    ) %>%
-    mutate(EXSEQ = IDVARVAL) %>%
-    select(-c(IDVAR, IDVARVAL))
-  exf <- left_join(ex, tempex, by = c("USUBJID", "EXSEQ"), keep = FALSE)
-
-  ex1 <- exf %>%
-    mutate(LOC = EXLOC, LAT = EXLAT, TPTREF = EXTPTREF) %>%
-    select(-c(
-      "VISITNUM", "VISIT", "EXLOC", "EXLAT", "EXSTDTC",
-      "EXTPTREF", "STUDYID", "DOMAIN", "EXSEQ"
-    ))
-
-  admin <- face1 %>%
-    filter(FASCAT == "ADMINISTRATION SITE")
-  expected1 <- left_join(admin,
-    ex1,
-    by = c("USUBJID", "LOC", "LAT", "TPTREF"), keep = FALSE
-  ) %>%
-    select(-c("LOC", "LAT", "TPTREF"))
-
-  sys <- face1 %>% filter(FASCAT == "SYSTEMIC")
-  expected2 <- left_join(sys,
-    ex1,
-    by = c("USUBJID", "TPTREF"), keep = FALSE
-  ) %>%
-    select(-c("TPTREF", "LOC.x", "LOC.y", "LAT.x", "LAT.y"))
-
-  expected <- bind_rows(expected1, expected2)
-
-
-  actual <- derive_vars_merged_vaccine(
-    dataset = face,
-    dataset_ex = ex,
-    dataset_supp = suppface,
-    dataset_suppex = suppex,
-    by_vars_sys = exprs(USUBJID, FATPTREF = EXTPTREF),
-    by_vars_adms = exprs(USUBJID, FATPTREF = EXTPTREF, FALOC = EXLOC, FALAT = EXLAT),
-    ex_vars = exprs(EXTRT, EXDOSE, EXTDV)
-  )
-  expect_dfs_equal(actual, expected, keys = c(
-    "USUBJID", "FAOBJ", "FATESTCD", "FATPTREF",
-    "FALOC", "FALAT"
-  ))
-})
-
-
-## Test 3: Check if warning is raised when there are multiple vaccination in same visit
 
-test_that("derive_vars_merged_vaccine Test 3: Check if warning is raised when
+test_that("derive_vars_merged_vaccine Test 2: Check if warning is raised when
           there are multiple vaccination in same ", {
   face <- tibble::tribble(
     ~STUDYID, ~DOMAIN, ~USUBJID, ~FACAT, ~FASCAT, ~FATESTCD, ~FAOBJ, ~FATEST, ~FALOC, ~FALAT,
@@ -207,8 +88,6 @@ test_that("derive_vars_merged_vaccine Test 3: Check if warning is raised when
     derive_vars_merged_vaccine(
       dataset = face,
       dataset_ex = ex,
-      dataset_supp = NULL,
-      dataset_suppex = NULL,
       by_vars_sys = exprs(USUBJID, FATPTREF = EXTPTREF),
       by_vars_adms = exprs(USUBJID, FATPTREF = EXTPTREF, FALOC = EXLOC, FALAT = EXLAT),
       ex_vars = exprs(EXTRT, EXDOSE)

diff --git a/vignettes/adface.Rmd b/vignettes/adface.Rmd
@@ -84,12 +84,15 @@ adsl <- convert_blanks_to_na(admiralvaccine_adsl)
 ## Pre-processing of Input Dataset {#input}
 
 This step involves company-specific pre-processing of required input dataset for
-further analysis. In this step, we will filter records that has only reactogenicity events.
+further analysis. In this step, we will filter records that has only reactogenicity events and
+combine the `face` and `ex` with their supplementary datasets `suppface` and `suppex` respectively.
 
 ```{r eval=TRUE}
 face <- face %>%
   filter(FACAT == "REACTOGENICITY" & grepl("ADMIN|SYS", FASCAT)) %>%
-  mutate(FAOBJ = str_to_upper(FAOBJ))
+  mutate(FAOBJ = str_to_upper(FAOBJ)) %>%
+  metatools::combine_supp(suppface)
+ex <- metatools::combine_supp(ex, suppex)
 ```
 
 ```{r, echo=FALSE}
@@ -109,8 +112,6 @@ The function `derive_vars_merged_vaccine()` is used to merge `face` with `ex` do
 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)

diff --git a/vignettes/adis.Rmd b/vignettes/adis.Rmd
@@ -102,7 +102,7 @@ adsl <- convert_blanks_to_na(admiralvaccine_adsl)
 ## Combine IS with SUPPIS {#combine_supp}
 Combine `IS` with its supplemental domain `SUPPIS`.
 ```{r eval=TRUE}
-is_suppis <- combine_supp(is, suppis)
+is_suppis <- metatools::combine_supp(is, suppis)
 ```