tests: #2595 snapshots for inform messages for extreme_data fcns

pharmaverse · Dec 23, 2024 · 5419517 · 5419517
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diff --git a/NEWS.md b/NEWS.md
@@ -60,9 +60,10 @@ memory consumption. (#2590)
 ### Phase 1 (message)
 
   - `derive_param_extreme_record()` is deprecated and replaced by `derive_extreme_event()`
-  - `date_source()` is deprecated and replaced by `derive_vars_extreme_event()`
-
+  - `derive_var_dthcaus()` and `dthcaus_source()` are deprecated and replaced by `derive_vars_extreme_event()`
+  - `derive_var_extreme_dt()` is deprecated and replaced by `derive_vars_extreme_event()`
 
+
 ### Phase 2 (warning)
 
 ### Phase 3 (error)

diff --git a/R/derive_var_dthcaus.R b/R/derive_var_dthcaus.R
@@ -140,6 +140,16 @@ derive_var_dthcaus <- function(dataset,
                                ...,
                                source_datasets,
                                subject_keys = get_admiral_option("subject_keys")) {
+  deprecate_inform(
+    when = "1.2.0",
+    what = "derive_var_dthcaus()",
+    with = "derive_vars_extreme_event()",
+    details = c(
+      x = "This message will turn into a warning with release of 1.3.0",
+      i = "https://pharmaverse.github.io/admiral/reference/derive_vars_extreme_event.html"
+    )
+  )
+
   assert_vars(subject_keys)
   assert_data_frame(dataset, required_vars = subject_keys)
   assert_list_of(source_datasets, "data.frame")

diff --git a/R/derive_var_extreme_date.R b/R/derive_var_extreme_date.R
@@ -234,6 +234,17 @@ derive_var_extreme_dtm <- function(dataset,
                                    source_datasets,
                                    mode,
                                    subject_keys = get_admiral_option("subject_keys")) {
+
+  deprecate_inform(
+    when = "1.2.0",
+    what = "derive_var_extreme_dtm()",
+    with = "derive_vars_extreme_event()",
+    details = c(
+      x = "This message will turn into a warning with release of 1.3.0",
+      i = "https://pharmaverse.github.io/admiral/reference/derive_vars_extreme_event.html"
+    )
+  )
+
   assert_vars(subject_keys)
   assert_data_frame(dataset, required_vars = subject_keys)
   new_var <- assert_symbol(enexpr(new_var))
@@ -556,6 +567,18 @@ derive_var_extreme_dt <- function(dataset,
                                   source_datasets,
                                   mode,
                                   subject_keys = get_admiral_option("subject_keys")) {
+
+  deprecate_inform(
+    when = "1.2.0",
+    what = "derive_var_extreme_dt()",
+    with = "derive_vars_extreme_event()",
+    details = c(
+      x = "This message will turn into a warning with release of 1.3.0",
+      i = "https://pharmaverse.github.io/admiral/reference/derive_vars_extreme_event.html"
+    )
+  )
+
+
   new_var <- assert_symbol(enexpr(new_var))
 
   sources <- list(...)

diff --git a/tests/testthat/_snaps/derive_var_dthcaus.md b/tests/testthat/_snaps/derive_var_dthcaus.md
@@ -1,4 +1,4 @@
-# derive_var_dthcaus Test 2: Message sent to users
+# derive_var_dthcaus Test 1: Message sent to users
 
     Code
       src_ae <- dthcaus_source(dataset_name = "ae", filter = AEOUT == "FATAL", date = AEDTHDT,
@@ -20,6 +20,11 @@
     Code
       derive_var_dthcaus(adsl, source_datasets = list(ae = ae, ds = ds), src_ae,
       src_ds)
+    Message
+      `derive_var_dthcaus()` was deprecated in admiral 1.2.0.
+      i Please use `derive_vars_extreme_event()` instead.
+      x This message will turn into a warning with release of 1.3.0
+      i https://pharmaverse.github.io/admiral/reference/derive_vars_extreme_event.html
     Output
       # A tibble: 3 x 3
         STUDYID USUBJID DTHCAUS                            
@@ -28,7 +33,7 @@
       2 TEST01  PAT02   <NA>                               
       3 TEST01  PAT03   SUDDEN DEATH                       
 
-# derive_var_dthcaus Test 11: error if source dataset is not available
+# derive_var_dthcaus Test 12: error if source dataset is not available
 
     Code
       derive_var_dthcaus(adsl, source_datasets = list(ae = ae, dd = ds), src_ae,

diff --git a/tests/testthat/_snaps/derive_var_extreme_date.md b/tests/testthat/_snaps/derive_var_extreme_date.md
@@ -1,3 +1,40 @@
+# derive_var_extreme_dt Test 1: Message sent to users
+
+    Code
+      derive_var_extreme_dt(adsl, new_var = LSTALVDT, source_datasets = list(ae = ae,
+        adsl = adsl), ae_start, ae_end, adsl_trtdate, adsl_dthdate, mode = "last")
+    Message
+      `derive_var_extreme_dt()` was deprecated in admiral 1.2.0.
+      i Please use `derive_vars_extreme_event()` instead.
+      x This message will turn into a warning with release of 1.3.0
+      i https://pharmaverse.github.io/admiral/reference/derive_vars_extreme_event.html
+    Output
+      # A tibble: 3 x 6
+        STUDYID USUBJID TRTEDTM             DTHDTC  DTHDT      LSTALVDT  
+        <chr>   <chr>   <dttm>              <chr>   <date>     <date>    
+      1 STUDY01 1       2020-01-01 12:00:00 <NA>    NA         2020-02-01
+      2 STUDY01 2       NA                  2020-06 2020-06-01 NA        
+      3 STUDY01 3       2020-04-12 13:15:00 <NA>    NA         2020-04-12
+
+# derive_var_extreme_dtm Test 4: Message sent to users
+
+    Code
+      derive_var_extreme_dtm(adsl, new_var = LSTALVDTM, source_datasets = list(ae = ae,
+        adsl = adsl), ae_start, ae_end, adsl_trtdate, adsl_dthdate, mode = "last")
+    Message
+      `derive_var_extreme_dtm()` was deprecated in admiral 1.2.0.
+      i Please use `derive_vars_extreme_event()` instead.
+      x This message will turn into a warning with release of 1.3.0
+      i https://pharmaverse.github.io/admiral/reference/derive_vars_extreme_event.html
+    Output
+      # A tibble: 3 x 9
+        STUDYID USUBJID TRTEDTM             DTHDTC  DTHDT      LALVDOM LALVSEQ LALVVAR
+        <chr>   <chr>   <dttm>              <chr>   <date>     <chr>     <dbl> <chr>  
+      1 STUDY01 1       2020-01-01 12:00:00 <NA>    NA         AE            2 AEENDTC
+      2 STUDY01 2       NA                  2020-06 2020-06-01 <NA>         NA <NA>   
+      3 STUDY01 3       2020-04-12 13:15:00 <NA>    NA         ADSL         NA TRTEDTM
+      # i 1 more variable: LSTALVDTM <dttm>
+
 # derive_var_extreme_dtm Test 6: error if source dataset is not available
 
     Code

diff --git a/tests/testthat/test-derive_param_extreme_record.R b/tests/testthat/test-derive_param_extreme_record.R
@@ -129,7 +129,6 @@ test_that("derive_param_extreme_record Test 2: Analysis date are derived correct
     actual_output,
     keys = c("USUBJID", "PARAMCD", "PARAM", "ADT", "AVALC")
   )
-
 })
 
 ## Test 3: Error given when order variable is not inside source datasets ----

diff --git a/tests/testthat/test-derive_var_dthcaus.R b/tests/testthat/test-derive_var_dthcaus.R
@@ -1,4 +1,5 @@
-test_that("derive_var_dthcaus Test 2: Message sent to users", {
+## Test 1: Message sent to users ----
+test_that("derive_var_dthcaus Test 1: Message sent to users", {
   adsl <- tibble::tribble(
     ~STUDYID, ~USUBJID,
     "TEST01", "PAT01",
@@ -53,10 +54,10 @@ test_that("derive_var_dthcaus Test 2: Message sent to users", {
   })
 })
 
-## Test 1: error on invalid mode ----
-test_that("dthcaus_source Test 1: error on invalid mode", {
+## Test 2: error on invalid mode ----
+test_that("derive_var_dthcaus Test 2: error on invalid mode", {
   # Suppress lifecycle messages within the test environment
-  original_verbosity <- options(lifecycle_verbosity = "quiet")
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
 
   expect_error(dthcaus_source(
     dataset_name = "ae",
@@ -65,16 +66,13 @@ test_that("dthcaus_source Test 1: error on invalid mode", {
     mode = "blah",
     dthcaus = AEDECOD
   ))
-
-  # Ensure to reset options after tests
-  on.exit(options(original_verbosity))
 })
 
 # derive_var_dthcaus ----
-## Test 2: DTHCAUS is added from AE and DS ----
-test_that("derive_var_dthcaus Test 2: DTHCAUS is added from AE and DS", {
+## Test 3: DTHCAUS is added from AE and DS ----
+test_that("derive_var_dthcaus Test 3: DTHCAUS is added from AE and DS", {
   # Suppress lifecycle messages within the test environment
-  original_verbosity <- options(lifecycle_verbosity = "quiet")
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
 
   adsl <- tibble::tribble(
     ~STUDYID, ~USUBJID,
@@ -135,15 +133,12 @@ test_that("derive_var_dthcaus Test 2: DTHCAUS is added from AE and DS", {
   )
 
   expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
-
-  # Ensure to reset options after tests
-  on.exit(options(original_verbosity))
 })
 
-## Test 3: `dthcaus` handles symbols and string literals correctly ----
-test_that("derive_var_dthcaus Test 3: `dthcaus` handles symbols and string literals correctly", {
+## Test 4: `dthcaus` handles symbols and string literals correctly ----
+test_that("derive_var_dthcaus Test 4: `dthcaus` handles symbols and string literals correctly", {
   # Suppress lifecycle messages within the test environment
-  original_verbosity <- options(lifecycle_verbosity = "quiet")
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
 
   adsl <- tibble::tribble(
     ~STUDYID, ~USUBJID,
@@ -202,15 +197,12 @@ test_that("derive_var_dthcaus Test 3: `dthcaus` handles symbols and string liter
   )
 
   expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
-
-  # Ensure to reset options after tests
-  on.exit(options(original_verbosity))
 })
 
-## Test 4: traceability variables are added from AE and DS ----
-test_that("derive_var_dthcaus Test 4: traceability variables are added from AE and DS", {
+## Test 5: traceability variables are added from AE and DS ----
+test_that("derive_var_dthcaus Test 5: traceability variables are added from AE and DS", {
   # Suppress lifecycle messages within the test environment
-  original_verbosity <- options(lifecycle_verbosity = "quiet")
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
 
   adsl <- tibble::tribble(
     ~STUDYID, ~USUBJID,
@@ -276,15 +268,12 @@ test_that("derive_var_dthcaus Test 4: traceability variables are added from AE a
   )
 
   expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
-
-  # Ensure to reset options after tests
-  on.exit(options(original_verbosity))
 })
 
-## Test 5: DTHCAUS/traceabiity are added from 2 input datasets ----
-test_that("derive_var_dthcaus Test 5: DTHCAUS/traceabiity are added from 2 input datasets", {
+## Test 6: DTHCAUS/traceabiity are added from 2 input datasets ----
+test_that("derive_var_dthcaus Test 6: DTHCAUS/traceabiity are added from 2 input datasets", {
   # Suppress lifecycle messages within the test environment
-  original_verbosity <- options(lifecycle_verbosity = "quiet")
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
 
   adsl <- tibble::tribble(
     ~STUDYID, ~USUBJID,
@@ -351,15 +340,12 @@ test_that("derive_var_dthcaus Test 5: DTHCAUS/traceabiity are added from 2 input
   )
 
   expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
-
-  # Ensure to reset options after tests
-  on.exit(options(original_verbosity))
 })
 
-## Test 6: DTHCAUS is added from AE and DS if filter is not specified ----
-test_that("derive_var_dthcaus Test 6: DTHCAUS is added from AE and DS if filter is not specified", {
+## Test 7: DTHCAUS is added from AE and DS if filter is not specified ----
+test_that("derive_var_dthcaus Test 7: DTHCAUS is added from AE and DS if filter is not specified", {
   # Suppress lifecycle messages within the test environment
-  original_verbosity <- options(lifecycle_verbosity = "quiet")
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
 
   # test based on covr report - the case for unspecified filter has not been tested
 
@@ -425,15 +411,12 @@ test_that("derive_var_dthcaus Test 6: DTHCAUS is added from AE and DS if filter
   )
 
   expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
-
-  # Ensure to reset options after tests
-  on.exit(options(original_verbosity))
 })
 
-## Test 7: error on a dthcaus_source object with invalid order ----
-test_that("derive_var_dthcaus Test 7: error on a dthcaus_source object with invalid order", {
+## Test 8: error on a dthcaus_source object with invalid order ----
+test_that("derive_var_dthcaus Test 8: error on a dthcaus_source object with invalid order", {
   # Suppress lifecycle messages within the test environment
-  original_verbosity <- options(lifecycle_verbosity = "quiet")
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
 
   expect_error(dthcaus_source(
     dataset_name = "ae",
@@ -443,15 +426,12 @@ test_that("derive_var_dthcaus Test 7: error on a dthcaus_source object with inva
     mode = "first",
     dthcaus = AEDECOD
   ))
-
-  # Ensure to reset options after tests
-  on.exit(options(original_verbosity))
 })
 
-## Test 8: `dataset` is sorted using the `order` parameter ----
-test_that("derive_var_dthcaus Test 8: `dataset` is sorted using the `order` parameter", {
+## Test 9: `dataset` is sorted using the `order` parameter ----
+test_that("derive_var_dthcaus Test 9: `dataset` is sorted using the `order` parameter", {
   # Suppress lifecycle messages within the test environment
-  original_verbosity <- options(lifecycle_verbosity = "quiet")
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
 
   adsl <- tibble::tribble(
     ~STUDYID, ~USUBJID,
@@ -511,15 +491,12 @@ test_that("derive_var_dthcaus Test 8: `dataset` is sorted using the `order` para
   )
 
   expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
-
-  # Ensure to reset options after tests
-  on.exit(options(original_verbosity))
 })
 
-## Test 9: multiple observations from different sources ----
-test_that("derive_var_dthcaus Test 9: multiple observations from different sources", {
+## Test 10: multiple observations from different sources ----
+test_that("derive_var_dthcaus Test 10: multiple observations from different sources", {
   # Suppress lifecycle messages within the test environment
-  original_verbosity <- options(lifecycle_verbosity = "quiet")
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
 
   expected <- tibble::tribble(
     ~STUDYID, ~USUBJID, ~DTHCAUS,
@@ -573,15 +550,12 @@ test_that("derive_var_dthcaus Test 9: multiple observations from different sourc
     compare = actual,
     keys = c("USUBJID")
   )
-
-  # Ensure to reset options after tests
-  on.exit(options(original_verbosity))
 })
 
-## Test 10: multiple observations with same date ----
-test_that("derive_var_dthcaus Test 10: multiple observations with same date", {
+## Test 11: multiple observations with same date ----
+test_that("derive_var_dthcaus Test 11: multiple observations with same date", {
   # Suppress lifecycle messages within the test environment
-  original_verbosity <- options(lifecycle_verbosity = "quiet")
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
 
   expected <- tibble::tribble(
     ~STUDYID, ~USUBJID, ~DTHCAUS,
@@ -635,15 +609,12 @@ test_that("derive_var_dthcaus Test 10: multiple observations with same date", {
     compare = actual,
     keys = c("USUBJID")
   )
-
-  # Ensure to reset options after tests
-  on.exit(options(original_verbosity))
 })
 
-## Test 11: error if source dataset is not available ----
-test_that("derive_var_dthcaus Test 11: error if source dataset is not available", {
+## Test 12: error if source dataset is not available ----
+test_that("derive_var_dthcaus Test 12: error if source dataset is not available", {
   # Suppress lifecycle messages within the test environment
-  original_verbosity <- options(lifecycle_verbosity = "quiet")
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
 
   adsl <- tibble::tribble(
     ~STUDYID, ~USUBJID,
@@ -698,7 +669,4 @@ test_that("derive_var_dthcaus Test 11: error if source dataset is not available"
     ),
     error = TRUE
   )
-
-  # Ensure to reset options after tests
-  on.exit(options(original_verbosity))
 })
-Original file line number
+Diff line change
@@ Expand Up @@
         actual_output,
         keys = c("USUBJID", "PARAMCD", "PARAM", "ADT", "AVALC")
       )
     })
     ## Test 3: Error given when order variable is not inside source datasets ----
@@ Expand Down @@