tests: #2595 snapshots for get_summary_records; quiet messages for ot…

…her tests
pharmaverse · Dec 23, 2024 · f66b567 · f66b567
1 parent 5419517
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diff --git a/NEWS.md b/NEWS.md
@@ -60,8 +60,11 @@ memory consumption. (#2590)
 ### Phase 1 (message)
 
   - `derive_param_extreme_record()` is deprecated and replaced by `derive_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()`
+  - `derive_var_dthcaus()` is deprecated and replaced by `derive_vars_extreme_event()`
+  - `date_source()` is deprecated and replaced by `derive_vars_extreme_event()`
+  - `dthcaus_source()` is deprecated and replaced by `derive_vars_extreme_event()`
+  - `derive_var_extreme_dt()` and `derive_var_extreme_dtm` are deprecated and replaced by `derive_vars_extreme_event()`
+  - `get_summary_records()` is deprecated. Please use the `dataset_add` argument in `derive_summary_records()`.
 
 
 ### Phase 2 (warning)

diff --git a/R/derive_var_extreme_date.R b/R/derive_var_extreme_date.R
@@ -234,7 +234,6 @@ 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()",
@@ -567,7 +566,6 @@ 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()",

diff --git a/R/get_summary_records.R b/R/get_summary_records.R
@@ -148,6 +148,16 @@ get_summary_records <- function(dataset,
                                 by_vars,
                                 filter = NULL,
                                 set_values_to = NULL) {
+  deprecate_inform(
+    when = "1.2.0",
+    what = "get_summary_records()",
+    with = "derive_summary_records()",
+    details = c(
+      x = "This message will turn into a warning with release of 1.3.0",
+      i = "https://pharmaverse.github.io/admiral/reference/derive_summary_records.html"
+    )
+  )
+
   assert_vars(by_vars)
   filter <- assert_filter_cond(enexpr(filter), optional = TRUE)
   assert_data_frame(

diff --git a/tests/testthat/_snaps/get_summary_records.md b/tests/testthat/_snaps/get_summary_records.md
@@ -0,0 +1,12 @@
+# get_summary_records Test 1: Summarize average of triplicate ECG interval values
+
+    Code
+      df <- input %>% get_summary_records(by_vars = exprs(USUBJID, PARAM, AVISIT),
+      set_values_to = exprs(AVAL = mean(AVAL, na.rm = TRUE), DTYPE = "AVERAGE")) %>%
+        dplyr::mutate(AVAL = round(AVAL))
+    Message
+      `get_summary_records()` was deprecated in admiral 1.2.0.
+      i Please use `derive_summary_records()` instead.
+      x This message will turn into a warning with release of 1.3.0
+      i https://pharmaverse.github.io/admiral/reference/derive_summary_records.html
+
diff --git a/tests/testthat/test-derive_var_extreme_date.R b/tests/testthat/test-derive_var_extreme_date.R
@@ -25,7 +25,6 @@ ae <- tibble::tribble(
 # derive_var_extreme_dt ----
 ## Test 1: Message sent to users ----
 test_that("derive_var_extreme_dt Test 1: Message sent to users", {
-
   ae_start <- date_source(
     dataset_name = "ae",
     date = AESTDTM
@@ -54,8 +53,8 @@ test_that("derive_var_extreme_dt Test 1: Message sent to users", {
       source_datasets = list(ae = ae, adsl = adsl),
       ae_start, ae_end, adsl_trtdate, adsl_dthdate,
       mode = "last"
+    )
   )
-)
 })
 
 # derive_var_extreme_dt ----
@@ -168,7 +167,6 @@ test_that("derive_var_extreme_dt Test 4: `NA` dates are excluded", {
 # derive_var_extreme_dtm ----
 ## Test 5: Message sent to users ----
 test_that("derive_var_extreme_dtm Test 5: Message sent to users", {
-
   ae_start <- date_source(
     dataset_name = "ae",
     date = convert_dtc_to_dtm(AESTDTC),
@@ -210,16 +208,15 @@ test_that("derive_var_extreme_dtm Test 5: Message sent to users", {
     )
   )
 
-expect_snapshot(
-  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"
+  expect_snapshot(
+    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"
+    )
   )
-)
-
 })
 
 # derive_var_extreme_dtm ----

diff --git a/tests/testthat/test-get_summary_records.R b/tests/testthat/test-get_summary_records.R
@@ -22,6 +22,46 @@ test_that("get_summary_records Test 1: Summarize average of triplicate ECG inter
     "XYZ-1002", 9,      "QTcF Int. (msec)", "Visit 3",  "2016-03-24T10:56", 402,   "Active 20mg"
   )
 
+  expect_snapshot(
+  df <- input %>%
+    get_summary_records(
+      by_vars = exprs(USUBJID, PARAM, AVISIT),
+      set_values_to = exprs(
+        AVAL = mean(AVAL, na.rm = TRUE),
+        DTYPE = "AVERAGE"
+      )
+    ) %>%
+    dplyr::mutate(AVAL = round(AVAL))
+  )
+})
+
+## Test 1: Summarize the average of the triplicate ECG interval values (AVAL) ----
+test_that("get_summary_records Test 1: Summarize average of triplicate ECG interval values", {
+  # Suppress lifecycle messages within the test environment
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
+
+  input <- tibble::tribble(
+    ~USUBJID,   ~EGSEQ, ~PARAM,             ~AVISIT,    ~EGDTC,             ~AVAL, ~TRTA,
+    "XYZ-1001", 1,      "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385,   NA_character_,
+    "XYZ-1001", 2,      "QTcF Int. (msec)", "Baseline", "2016-02-24T07:52", 399,   NA_character_,
+    "XYZ-1001", 3,      "QTcF Int. (msec)", "Baseline", "2016-02-24T07:56", 396,   NA_character_,
+    "XYZ-1001", 4,      "QTcF Int. (msec)", "Visit 2",  "2016-03-08T09:45", 384,   "Placebo",
+    "XYZ-1001", 5,      "QTcF Int. (msec)", "Visit 2",  "2016-03-08T09:48", 393,   "Placebo",
+    "XYZ-1001", 6,      "QTcF Int. (msec)", "Visit 2",  "2016-03-08T09:51", 388,   "Placebo",
+    "XYZ-1001", 7,      "QTcF Int. (msec)", "Visit 3",  "2016-03-22T10:45", 385,   "Placebo",
+    "XYZ-1001", 8,      "QTcF Int. (msec)", "Visit 3",  "2016-03-22T10:48", 394,   "Placebo",
+    "XYZ-1001", 9,      "QTcF Int. (msec)", "Visit 3",  "2016-03-22T10:51", 402,   "Placebo",
+    "XYZ-1002", 1,      "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 399,   NA_character_,
+    "XYZ-1002", 2,      "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 410,   NA_character_,
+    "XYZ-1002", 3,      "QTcF Int. (msec)", "Baseline", "2016-02-22T08:01", 392,   NA_character_,
+    "XYZ-1002", 4,      "QTcF Int. (msec)", "Visit 2",  "2016-03-06T09:50", 401,   "Active 20mg",
+    "XYZ-1002", 5,      "QTcF Int. (msec)", "Visit 2",  "2016-03-06T09:53", 407,   "Active 20mg",
+    "XYZ-1002", 6,      "QTcF Int. (msec)", "Visit 2",  "2016-03-06T09:56", 400,   "Active 20mg",
+    "XYZ-1002", 7,      "QTcF Int. (msec)", "Visit 3",  "2016-03-24T10:50", 412,   "Active 20mg",
+    "XYZ-1002", 8,      "QTcF Int. (msec)", "Visit 3",  "2016-03-24T10:53", 414,   "Active 20mg",
+    "XYZ-1002", 9,      "QTcF Int. (msec)", "Visit 3",  "2016-03-24T10:56", 402,   "Active 20mg"
+  )
+
   actual_output <- input %>%
     get_summary_records(
       by_vars = exprs(USUBJID, PARAM, AVISIT),
@@ -51,6 +91,9 @@ test_that("get_summary_records Test 1: Summarize average of triplicate ECG inter
 
 ## Test 2: Derive more than one summary variable ----
 test_that("get_summary_records Test 2: Derive more than one summary variable", {
+  # Suppress lifecycle messages within the test environment
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
+
   input <- tibble::tribble(
     ~USUBJID,   ~EGSEQ, ~PARAM,             ~AVISIT,    ~EGDTC,             ~AVAL, ~TRTA,
     "XYZ-1001", 1,      "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385,   NA_character_,
@@ -110,6 +153,9 @@ test_that("get_summary_records Test 2: Derive more than one summary variable", {
 
 ## Test 3: Compute avg AVAL only if >2 records within by group ----
 test_that("get_summary_records Test 3: Compute avg AVAL only if >2 records within by group", {
+  # Suppress lifecycle messages within the test environment
+  withr::local_options(list(lifecycle_verbosity = "quiet"))
+
   input <- tibble::tribble(
     ~USUBJID,   ~EGSEQ, ~PARAM,             ~AVISIT,    ~EGDTC,             ~AVAL, ~TRTA,
     "XYZ-1001", 1,      "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385,   NA_character_,