#216 admiral_0_11_update: remove library() calls from tests

pharmaverse · Jun 1, 2023 · 5579e71 · 5579e71
1 parent 54dfe65
commit 5579e71
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Showing 7 changed files with 65 additions and 75 deletions.
diff --git a/tests/testthat/test-check_crpr.R b/tests/testthat/test-check_crpr.R
@@ -1,9 +1,4 @@
-library(tibble)
-library(dplyr, warn.conflicts = FALSE)
-library(lubridate)
-library(admiraldev)
-
-adrs <- tribble(
+adrs <- tibble::tribble(
   ~USUBJID, ~ADTC,        ~AVALC,
   "1",      "2020-01-01", "PR",
   "1",      "2020-02-01", "CR",
@@ -15,7 +10,7 @@ adrs <- tribble(
   "2",      "2020-03-30", "PR"
 ) %>%
   mutate(
-    ADT = ymd(ADTC),
+    ADT = lubridate::ymd(ADTC),
     STUDYID = "XX1234"
   )
 
@@ -67,13 +62,13 @@ test_that("get_crpr_dataset() Test 2: dataset if returned", {
   )
 
   expect_dfs_equal(
-    base = tribble(
+    base = tibble::tribble(
       ~USUBJID, ~ADTC,        ~AVALC,
       "2",      "2020-02-16", "CR",
       "2",      "2020-03-30", "PR"
     ) %>%
       mutate(
-        ADT = ymd(ADTC),
+        ADT = lubridate::ymd(ADTC),
         STUDYID = "XX1234"
       ),
     compare = get_crpr_dataset(),

diff --git a/tests/testthat/test-derive_param_bor.R b/tests/testthat/test-derive_param_bor.R
@@ -29,7 +29,7 @@ adsl <- tibble::tribble(
   "8",      "2020-04-01",  "008",         "999"
 ) %>%
   mutate(
-    TRTSDT = ymd(TRTSDTC),
+    TRTSDT = lubridate::ymd(TRTSDTC),
     STUDYID = "XX1234"
   )
 
@@ -92,7 +92,7 @@ aval_fun_pass <- function(arg) {
 # excepcted dataframe, deviations from this are handeled in each individual test
 expected_01 <- bind_rows(
   adrs,
-  tribble(
+  tibble::tribble(
     ~USUBJID, ~ADTC, ~AVALC, ~AVAL, ~TRTSDTC, ~CHECKKEPTCOL,
     "1", "2020-02-01", "CR", 11, "2020-01-01", "001",
     "2", "2020-03-13", "CR", 11, "2019-12-12", "002",
@@ -104,8 +104,8 @@ expected_01 <- bind_rows(
     "8", "", "MISSING", 77, "2020-04-01", "008"
   ) %>%
     mutate(
-      ADT = ymd(ADTC),
-      TRTSDT = ymd(TRTSDTC),
+      ADT = lubridate::ymd(ADTC),
+      TRTSDT = lubridate::ymd(TRTSDTC),
       STUDYID = "XX1234",
       PARAMCD = "BOR",
       PARAM = "Best Overall Response"
@@ -178,9 +178,9 @@ test_that("derive_param_bor Test 1: No source_pd", {
   # set subject 7 to only have records before ADT
   adrs_01 <- adrs
   adrs_01$ADT[adrs_01$USUBJID == "7"][1:3] <- c(
-    ymd("2020-01-01"),
-    ymd("2020-01-02"),
-    ymd("2020-01-03")
+    lubridate::ymd("2020-01-01"),
+    lubridate::ymd("2020-01-02"),
+    lubridate::ymd("2020-01-03")
   )
 
   actual_02 <- derive_param_bor(
@@ -201,10 +201,10 @@ test_that("derive_param_bor Test 1: No source_pd", {
   # expected will be the same as previous test except ADT for subject 7
   expected_02 <- expected_01
   expected_02$ADT[expected_02$USUBJID == "7"][1:4] <- c(
-    ymd("2020-01-01"),
-    ymd("2020-01-02"),
-    ymd("2020-01-03"),
-    ymd("2020-01-02")
+    lubridate::ymd("2020-01-01"),
+    lubridate::ymd("2020-01-02"),
+    lubridate::ymd("2020-01-03"),
+    lubridate::ymd("2020-01-02")
   )
 
   expect_dfs_equal(
@@ -240,7 +240,7 @@ test_that("derive_param_bor Test 1: No source_pd", {
   # Expected Updated for Subject 7, response is now NE and 6 with a earlier ADT (first)
   expected_03 <- expected_02
   expected_03$AVALC[expected_03$USUBJID == "7"] <- "SD"
-  expected_03$ADT[expected_02$USUBJID == "7"][4] <- c(ymd("2020-01-01"))
+  expected_03$ADT[expected_02$USUBJID == "7"][4] <- c(lubridate::ymd("2020-01-01"))
   expected_03$AVALC[expected_02$USUBJID == "7"][4] <- "NE"
   expected_03$AVAL[expected_02$USUBJID == "7"][4] <- 66
 
@@ -305,7 +305,7 @@ test_that("derive_param_bor Test 2: With source_pd", {
   expected_pd_01$AVAL[expected_pd_01$USUBJID == 2 &
     expected_pd_01$PARAMCD == "BOR"] <- 22
   expected_pd_01$ADT[expected_pd_01$USUBJID == 2 &
-    expected_pd_01$PARAMCD == "BOR"] <- ymd("2020-02-01")
+    expected_pd_01$PARAMCD == "BOR"] <- lubridate::ymd("2020-02-01")
 
 
   # This is now MISSING as PD removed all records
@@ -396,7 +396,7 @@ test_that("derive_param_bor Test 4: Deprecation warning for aval_fun", {
   expected_pd_01$AVAL[expected_pd_01$USUBJID == 2 &
     expected_pd_01$PARAMCD == "BOR"] <- 22
   expected_pd_01$ADT[expected_pd_01$USUBJID == 2 &
-    expected_pd_01$PARAMCD == "BOR"] <- ymd("2020-02-01")
+    expected_pd_01$PARAMCD == "BOR"] <- lubridate::ymd("2020-02-01")
 
 
   # This is now MISSING as PD removed all records

diff --git a/tests/testthat/test-derive_param_clinbenefit.R b/tests/testthat/test-derive_param_clinbenefit.R
@@ -10,8 +10,8 @@ adsl <- tibble::tribble(
 ) %>%
   mutate(
     STUDYID = "AB42",
-    TRTSDT = as_date(TRTSDT),
-    EOSDT = as_date(EOSDT),
+    TRTSDT = lubridate::as_date(TRTSDT),
+    EOSDT = lubridate::as_date(EOSDT),
   )
 
 adrs <- tibble::tribble(
@@ -44,7 +44,7 @@ adrs <- tibble::tribble(
 ) %>%
   mutate(
     STUDYID = "AB42",
-    ADT = as_date(ADT),
+    ADT = lubridate::as_date(ADT),
     ANL01FL = "Y"
   ) %>%
   derive_vars_merged(
@@ -79,7 +79,7 @@ test_that("derive_param_clinbenefit Test 1: ignore NON-CR/NON-PD", {
   ) %>%
     mutate(
       STUDYID = "AB42",
-      ADT = as_date(ADT),
+      ADT = lubridate::as_date(ADT),
       ANL01FL = "Y"
     ) %>%
     left_join(adsl, by = c("STUDYID", "USUBJID")) %>%
@@ -111,7 +111,7 @@ test_that("derive_param_clinbenefit Test 1: ignore NON-CR/NON-PD", {
 
 ## Test 2: No source_pd ----
 test_that("derive_param_clinbenefit Test 2: No source_pd", {
-  input_cbr <- tribble(
+  input_cbr <- tibble::tribble(
     ~USUBJID, ~PARAMCD, ~AVALC, ~AVAL, ~ADT,
     "01",     "CBR",    "Y",    1,     "2021-03-07",
     "02",     "CBR",    "Y",    1,     "2021-03-07",
@@ -123,7 +123,7 @@ test_that("derive_param_clinbenefit Test 2: No source_pd", {
   ) %>%
     mutate(
       STUDYID = "AB42",
-      ADT = as_date(ADT),
+      ADT = lubridate::as_date(ADT),
       ANL01FL = "Y"
     ) %>%
     left_join(adsl, by = c("STUDYID", "USUBJID")) %>%
@@ -155,7 +155,7 @@ test_that("derive_param_clinbenefit Test 2: No source_pd", {
 
 ## Test 3: Deprecation warning for aval_fun ----
 test_that("derive_param_clinbenefit Test 3: Deprecation warning for aval_fun", {
-  input_cbr <- tribble(
+  input_cbr <- tibble::tribble(
     ~USUBJID, ~PARAMCD, ~AVALC, ~AVAL, ~ADT,
     "01",     "CBR",    "Y",    1,     "2021-03-07",
     "02",     "CBR",    "Y",    1,     "2021-03-07",
@@ -167,7 +167,7 @@ test_that("derive_param_clinbenefit Test 3: Deprecation warning for aval_fun", {
   ) %>%
     mutate(
       STUDYID = "AB42",
-      ADT = as_date(ADT),
+      ADT = lubridate::as_date(ADT),
       ANL01FL = "Y"
     ) %>%
     left_join(adsl, by = c("STUDYID", "USUBJID")) %>%

diff --git a/tests/testthat/test-derive_param_confirmed_bor.R b/tests/testthat/test-derive_param_confirmed_bor.R
@@ -48,7 +48,7 @@ adrs <- tibble::tribble(
   "9",      "2020-03-06", "SD"
 ) %>%
   mutate(PARAMCD = "OVR") %>%
-  bind_rows(tribble(
+  bind_rows(tibble::tribble(
     ~USUBJID, ~ADTC,        ~AVALC,
     "9",      "2020-02-16", "Y"
   ) %>%
@@ -94,7 +94,7 @@ test_that("derive_param_confirmed_bor Test 1: default confirmed BOR", {
 
   expected <- bind_rows(
     adrs,
-    tribble(
+    tibble::tribble(
       ~USUBJID, ~ADTC,         ~AVALC,          ~AVAL,
       "1",      "2020-02-01",  "CR",            1,
       "2",      "2020-02-01",  "SD",            3,
@@ -280,7 +280,7 @@ test_that("derive_param_confirmed_bor Test 4: No source_pd", {
       "9",      "2020-03-06",  "SD",            3 # expected is now SD
     ) %>%
       mutate(
-        ADT = ymd(ADTC),
+        ADT = lubridate::ymd(ADTC),
         STUDYID = "XX1234",
         PARAMCD = "CBOR",
         PARAM = "Best Confirmed Overall Response by Investigator"
@@ -339,7 +339,7 @@ test_that("derive_param_confirmed_bor Test 5: Deprecation warning for aval_fun",
       "9",      "2020-03-06",  "SD",            3 # expected is now SD
     ) %>%
       mutate(
-        ADT = ymd(ADTC),
+        ADT = lubridate::ymd(ADTC),
         STUDYID = "XX1234",
         PARAMCD = "CBOR",
         PARAM = "Best Confirmed Overall Response by Investigator"

diff --git a/tests/testthat/test-derive_param_confirmed_resp.R b/tests/testthat/test-derive_param_confirmed_resp.R
@@ -251,7 +251,7 @@ test_that("derive_param_confirmed_resp Test 4: No source_pd", {
 
   expected_no_source_pd <- bind_rows(
     adrs,
-    tribble(
+    tibble::tribble(
       ~USUBJID, ~ADTC,         ~AVALC, ~AVAL,
       "1",      "2020-02-16",  "Y",    1,
       "2",      NA_character_, "N",    0,
@@ -264,7 +264,7 @@ test_that("derive_param_confirmed_resp Test 4: No source_pd", {
       "9",      NA_character_, "N",    0
     ) %>%
       mutate(
-        ADT = ymd(ADTC),
+        ADT = lubridate::ymd(ADTC),
         STUDYID = "XX1234",
         PARAMCD = "CRSP",
         PARAM = "Confirmed Response by Investigator"
@@ -278,7 +278,8 @@ test_that("derive_param_confirmed_resp Test 4: No source_pd", {
   )
 })
 
-test_that("derive_param_confirmed_resp Test 4: Deprecation warning for aval_fun", {
+## Test 5: Deprecation warning for aval_fun ----
+test_that("derive_param_confirmed_resp Test 5: Deprecation warning for aval_fun", {
   adrs <- tibble::tribble(
     ~USUBJID, ~ADTC,        ~AVALC,
     "1",      "2020-01-01", "SD",
@@ -316,7 +317,7 @@ test_that("derive_param_confirmed_resp Test 4: Deprecation warning for aval_fun"
 
   expected_no_source_pd <- bind_rows(
     adrs,
-    tribble(
+    tibble::tribble(
       ~USUBJID, ~ADTC,         ~AVALC, ~AVAL,
       "1",      "2020-02-16",  "Y",    1,
       "2",      NA_character_, "N",    0,
@@ -329,7 +330,7 @@ test_that("derive_param_confirmed_resp Test 4: Deprecation warning for aval_fun"
       "9",      NA_character_, "N",    0
     ) %>%
       mutate(
-        ADT = ymd(ADTC),
+        ADT = lubridate::ymd(ADTC),
         STUDYID = "XX1234",
         PARAMCD = "CRSP",
         PARAM = "Confirmed Response by Investigator"