Closes #2037 deprecate dataset_expected_obs for dataset_ref in re…

…spective functions (#2039) feat: #2037 deprecate `dataset_expected_obs` for `dataset_ref` Co-authored-by: Zelos Zhu <[email protected]>
pharmaverse · Aug 2, 2023 · b6f39a5 · b6f39a5
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diff --git a/NEWS.md b/NEWS.md
@@ -40,6 +40,9 @@ the `filter_add` using the next phase of the deprecation process. (#1950)
 - The `na_val` argument in `derive_var_shift()` has been deprecated in favor of 
 `missing_value` using the first phase of the deprecation process. (#2014)
 
+- The `dataset_expected_obs` argument in `derive_expected_records()` and `derive_locf_records()`
+has been deprecated in favor of `dataset_ref`. (#2037)
+
 ## Documentation
 
 

diff --git a/R/derive_expected_records.R b/R/derive_expected_records.R
@@ -5,17 +5,19 @@
 #'
 #' @param dataset Input dataset
 #'
-#'   A data frame, the columns from `dataset_expected_obs` and specified by the
+#'   A data frame, the columns from `dataset_ref` and specified by the
 #'   `by_vars` parameter are expected.
 #'
-#' @param dataset_expected_obs Expected observations dataset
+#' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
+#'
+#' @param dataset_ref Expected observations dataset
 #'
 #'   Data frame with the expected observations, e.g., all the expected
 #'   combinations of `PARAMCD`, `PARAM`, `AVISIT`, `AVISITN`, ...
 #'
 #' @param by_vars Grouping variables
 #'
-#'   For each group defined by `by_vars` those observations from `dataset_expected_obs`
+#'   For each group defined by `by_vars` those observations from `dataset_ref`
 #'   are added to the output dataset which do not have a corresponding observation
 #'   in the input dataset.
 #'
@@ -31,7 +33,7 @@
 #'   "TDOSE", PARCAT1 = "OVERALL")`.
 #'
 #' @details For each group (the variables specified in the `by_vars` parameter),
-#' those records from `dataset_expected_obs` that are missing in the input
+#' those records from `dataset_ref` that are missing in the input
 #' dataset are added to the output dataset.
 #'
 #' @return The input dataset with the missed expected observations added for each
@@ -63,7 +65,7 @@
 #'
 #' derive_expected_records(
 #'   dataset = adqs,
-#'   dataset_expected_obs = parm_visit_ref,
+#'   dataset_ref = parm_visit_ref,
 #'   by_vars = exprs(USUBJID, PARAMCD),
 #'   set_values_to = exprs(DTYPE = "DERIVED")
 #' )
@@ -78,35 +80,46 @@
 #'
 #' derive_expected_records(
 #'   dataset = adqs,
-#'   dataset_expected_obs = parm_visit_ref,
+#'   dataset_ref = parm_visit_ref,
 #'   by_vars = exprs(USUBJID, PARAMCD),
 #'   set_values_to = exprs(DTYPE = "DERIVED")
 #' )
 #'
 derive_expected_records <- function(dataset,
                                     dataset_expected_obs,
+                                    dataset_ref,
                                     by_vars = NULL,
                                     set_values_to = NULL) {
+  if (!missing(dataset_expected_obs)) {
+    deprecate_warn(
+      "0.12.0",
+      "derive_expected_records(dataset_expected_obs = )",
+      "derive_expected_records(dataset_ref = )"
+    )
+    assert_data_frame(dataset_expected_obs)
+    dataset_ref <- dataset_expected_obs
+  }
+
   # Check input parameters
   assert_vars(by_vars, optional = TRUE)
-  assert_data_frame(dataset_expected_obs)
+  assert_data_frame(dataset_ref)
   assert_data_frame(
     dataset,
-    required_vars = expr_c(by_vars, chr2vars(colnames(dataset_expected_obs)))
+    required_vars = expr_c(by_vars, chr2vars(colnames(dataset_ref)))
   )
   assert_varval_list(set_values_to, optional = TRUE)
 
   # Derive expected records
-  ## ids: Variables from by_vars but not in dataset_expected_obs
+  ## ids: Variables from by_vars but not in dataset_ref
   ids <- dataset %>%
-    select(!!!setdiff(by_vars, chr2vars(colnames(dataset_expected_obs)))) %>%
+    select(!!!setdiff(by_vars, chr2vars(colnames(dataset_ref)))) %>%
     distinct()
 
   if (ncol(ids) > 0) {
     exp_obsv <- ids %>%
-      crossing(dataset_expected_obs)
+      crossing(dataset_ref)
   } else {
-    exp_obsv <- dataset_expected_obs
+    exp_obsv <- dataset_ref
   } # tmp workaround, update after using tidyr 1.2.0
 
   exp_obs_vars <- exp_obsv %>%

diff --git a/R/derive_locf_records.R b/R/derive_locf_records.R
@@ -8,14 +8,17 @@
 #'   The columns specified by the `by_vars`, `analysis_var`, `order`,
 #'   `keep_vars` parameters are expected.
 #'
-#' @param dataset_expected_obs Expected observations dataset
+#' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
+#'
+#' @param dataset_ref Expected observations dataset
 #'
 #'   Data frame with all the combinations of `PARAMCD`, `PARAM`, `AVISIT`,
 #'   `AVISITN`, ... which are expected in the dataset is expected.
 #'
+#'
 #' @param by_vars Grouping variables
 #'
-#'   For each group defined by `by_vars` those observations from `dataset_expected_obs`
+#'   For each group defined by `by_vars` those observations from `dataset_ref`
 #'   are added to the output dataset which do not have a corresponding observation
 #'   in the input dataset or for which `analysis_var` is `NA` for the corresponding observation
 #'   in the input dataset.
@@ -40,7 +43,7 @@
 #' @author G Gayatri
 #'
 #' @details For each group (with respect to the variables specified for the
-#' by_vars parameter) those observations from dataset_expected_obs are added to
+#' by_vars parameter) those observations from `dataset_ref` are added to
 #' the output dataset
 #' - which do not have a corresponding observation in the input dataset or
 #' - for which `analysis_var` is NA for the corresponding observation in the input dataset.
@@ -101,19 +104,30 @@
 #' )
 #'
 #' derive_locf_records(
-#'   data = advs,
-#'   dataset_expected_obs = advs_expected_obsv,
+#'   dataset = advs,
+#'   dataset_ref = advs_expected_obsv,
 #'   by_vars = exprs(STUDYID, USUBJID, PARAMCD),
 #'   order = exprs(AVISITN, AVISIT),
 #'   keep_vars = exprs(PARAMN)
 #' )
 #'
 derive_locf_records <- function(dataset,
                                 dataset_expected_obs,
+                                dataset_ref,
                                 by_vars,
                                 analysis_var = AVAL,
                                 order,
                                 keep_vars = NULL) {
+  if (!missing(dataset_expected_obs)) {
+    deprecate_warn(
+      "0.12.0",
+      "derive_locf_records(dataset_expected_obs = )",
+      "derive_locf_records(dataset_ref = )"
+    )
+    assert_data_frame(dataset_expected_obs)
+    dataset_ref <- dataset_expected_obs
+  }
+
   #### Input Checking ####
   analysis_var <- assert_symbol(enexpr(analysis_var))
 
@@ -123,27 +137,27 @@ derive_locf_records <- function(dataset,
   assert_expr_list(order)
 
   # Check by_vars and order variables in input datasets
-  assert_data_frame(dataset_expected_obs)
+  assert_data_frame(dataset_ref)
   assert_data_frame(
     dataset,
     required_vars = expr_c(
       by_vars, analysis_var, extract_vars(order), keep_vars,
-      chr2vars(colnames(dataset_expected_obs))
+      chr2vars(colnames(dataset_ref))
     )
   )
 
 
-  #### Prepping 'dataset_expected_obs' ####
+  #### Prepping 'dataset_ref' ####
 
 
   # Get the IDs from input dataset for which the expected observations are to be added
 
   ids <- dataset %>%
-    select(!!!setdiff(by_vars, chr2vars(colnames(dataset_expected_obs)))) %>%
+    select(!!!setdiff(by_vars, chr2vars(colnames(dataset_ref)))) %>%
     distinct()
 
   exp_obsv <- ids %>%
-    crossing(dataset_expected_obs)
+    crossing(dataset_ref)
 
 
 

diff --git a/man/derive_expected_records.Rd b/man/derive_expected_records.Rd
diff --git a/man/derive_locf_records.Rd b/man/derive_locf_records.Rd
diff --git a/tests/testthat/test-derive_expected_records.R b/tests/testthat/test-derive_expected_records.R
@@ -30,7 +30,7 @@ test_that("derive_expected_records Test 1: missing values in `by_vars`", {
 
   actual_output <- derive_expected_records(
     dataset = input,
-    dataset_expected_obs = expected_obsv,
+    dataset_ref = expected_obsv,
     by_vars = exprs(USUBJID),
     set_values_to = exprs(DTYPE = "DERIVED")
   )
@@ -71,7 +71,7 @@ test_that("derive_expected_records Test 2: `by_vars` = NULL", {
 
   actual_output <- derive_expected_records(
     dataset = input,
-    dataset_expected_obs = expected_obsv,
+    dataset_ref = expected_obsv,
     by_vars = NULL,
     set_values_to = exprs(DTYPE = "DERIVED")
   )
@@ -114,7 +114,7 @@ test_that("derive_expected_records Test 3: visit variables are parameter indepen
 
   actual_output <- derive_expected_records(
     dataset = input,
-    dataset_expected_obs = expected_obsv,
+    dataset_ref = expected_obsv,
     by_vars = exprs(USUBJID, PARAMCD),
     set_values_to = exprs(DTYPE = "DERIVED")
   )
@@ -157,7 +157,7 @@ test_that("derive_expected_records Test 4: visit variables are parameter depende
 
   actual_output <- derive_expected_records(
     dataset = input,
-    dataset_expected_obs = expected_obsv,
+    dataset_ref = expected_obsv,
     by_vars = exprs(USUBJID),
     set_values_to = exprs(DTYPE = "DERIVED")
   )

diff --git a/tests/testthat/test-derive_locf_records.R b/tests/testthat/test-derive_locf_records.R
@@ -32,7 +32,7 @@ test_that("derive_locf_records Test 1: visits are missing", {
 
   actual_output <- derive_locf_records(
     input,
-    dataset_expected_obs = advs_expected_obsv,
+    dataset_ref = advs_expected_obsv,
     by_vars = exprs(STUDYID, USUBJID, PARAM, PARAMCD),
     order = exprs(AVISITN, AVISIT)
   )
@@ -82,7 +82,7 @@ test_that("derive_locf_records Test 2: some visits have missing AVAL", {
 
   actual_output <- derive_locf_records(
     input,
-    dataset_expected_obs = advs_expected_obsv,
+    dataset_ref = advs_expected_obsv,
     by_vars = exprs(STUDYID, USUBJID, PARAM, PARAMCD),
     order = exprs(AVISITN, AVISIT)
   )
@@ -142,7 +142,7 @@ test_that("derive_locf_records Test 3: visits are missing - and DTYPE already ex
 
   actual_output <- derive_locf_records(
     input,
-    dataset_expected_obs = advs_expected_obsv,
+    dataset_ref = advs_expected_obsv,
     by_vars = exprs(STUDYID, USUBJID, PARAM, PARAMCD),
     order = exprs(AVISITN, AVISIT)
   )
@@ -190,7 +190,7 @@ test_that("derive_locf_records Test 4: visit variables are parameter independent
 
   actual_output <- derive_locf_records(
     input,
-    dataset_expected_obs = advs_expected_obsv,
+    dataset_ref = advs_expected_obsv,
     by_vars = exprs(STUDYID, USUBJID, PARAM, PARAMCD),
     order = exprs(AVISITN, AVISIT)
   )
@@ -246,7 +246,7 @@ test_that("derive_locf_records Test 5: visit variables are parameter dependent",
 
   actual_output <- derive_locf_records(
     input,
-    dataset_expected_obs = advs_expected_obsv,
+    dataset_ref = advs_expected_obsv,
     by_vars = exprs(STUDYID, USUBJID, PARAM, PARAMCD),
     order = exprs(AVISITN, AVISIT)
   )
@@ -290,7 +290,7 @@ test_that("derive_locf_records Test 6: populate VISITNUM for LOCF records", {
 
   actual_output <- derive_locf_records(
     input,
-    dataset_expected_obs = advs_expected_obsv,
+    dataset_ref = advs_expected_obsv,
     by_vars = exprs(STUDYID, USUBJID, PARAM, PARAMCD),
     analysis_var = AVALC,
     order = exprs(AVISITN, AVISIT),