Merge pull request #1956 from pharmaverse/1950_follow_deprecation_pro…

…cess@devel Closes #1950 following deprecation process, update Description versio…
pharmaverse · Jun 15, 2023 · c84c6c3 · c84c6c3
2 parents e952189 + ba9fd04
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: admiral
 Type: Package
 Title: ADaM in R Asset Library
-Version: 0.11.0
+Version: 0.12.0
 Authors@R: c(
     person("Ben", "Straub", email = "[email protected]", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -87,7 +87,6 @@ export(derive_var_base)
 export(derive_var_basetype)
 export(derive_var_chg)
 export(derive_var_confirmation_flag)
-export(derive_var_disposition_status)
 export(derive_var_dthcaus)
 export(derive_var_extreme_dt)
 export(derive_var_extreme_dtm)
@@ -107,10 +106,8 @@ export(derive_var_relative_flag)
 export(derive_var_shift)
 export(derive_var_trtdurd)
 export(derive_var_trtemfl)
-export(derive_var_worst_flag)
 export(derive_vars_aage)
 export(derive_vars_atc)
-export(derive_vars_disposition_reason)
 export(derive_vars_dt)
 export(derive_vars_dtm)
 export(derive_vars_dtm_to_dt)
@@ -139,8 +136,6 @@ export(filter_extreme)
 export(filter_joined)
 export(filter_not_exist)
 export(filter_relative)
-export(format_eoxxstt_default)
-export(format_reason_default)
 export(get_admiral_option)
 export(get_duplicates_dataset)
 export(get_many_to_one_dataset)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,43 @@
+# admiral 0.12.0
+
+## New Features
+
+
+## Updates of Existing Functions
+
+
+## Breaking Changes
+- The following functions, which were deprecated in previous `{admiral}` versions, have been removed: (#1950)
+
+  - `derive_var_disposition_status()`
+  - `derive_vars_disposition_reason()`
+  - `format_eoxxstt_default()`
+  - `format_reason_default()`
+  - `derive_var_worst_flag()`
+
+- The following functions have been deprecated from previous `{admiral}` versions using the next phase of the deprecation process: (#1950)
+
+  - `derive_param_extreme_event()`
+  - `derive_vars_last_dose()`
+  - `derive_var_last_dose_amt()`
+  - `derive_var_last_dose_date()`
+  - `derive_var_last_dose_grp()`
+  - `derive_var_basetype()`
+  - `derive_var_merged_cat()`
+  - `derive_var_merged_character()`
+
+- The arguments `dataset_adsl` in the function `derive_param_exist_flag()` and
+`subject_keys` have been deprecated versions using the next phase of the deprecation process. (#1950)
+
+- The `filter` argument in `derive_extreme_records()` was deprecated in favor of
+the `filter_add` using the next phase of the deprecation process. (#1950)
+
+## Documentation
+
+
+## Various
+
+
 # admiral 0.11.0
 
 ## New Features

diff --git a/R/derive_extreme_records.R b/R/derive_extreme_records.R
@@ -257,7 +257,7 @@ derive_extreme_records <- function(dataset = NULL,
                                    set_values_to,
                                    filter) {
   if (!missing(filter)) {
-    deprecate_warn(
+    deprecate_stop(
       "0.11.0",
       "derive_extreme_records(filter = )",
       "derive_extreme_records(filter_add = )"

diff --git a/R/derive_merged.R b/R/derive_merged.R
@@ -456,67 +456,6 @@ derive_vars_merged <- function(dataset,
 #'
 #' @export
 #'
-#' @examples
-#' library(dplyr, warn.conflicts = FALSE)
-#'
-#' vs <- tribble(
-#'   ~STUDYID,  ~DOMAIN,  ~USUBJID,      ~VISIT, ~VSTESTCD, ~VSSTRESN, ~VSSEQ,       ~VSDTC,
-#'   "PILOT01",    "VS", "04-1127", "SCREENING",  "HEIGHT",     165.1,     43, "2013-09-16",
-#'   "PILOT01",    "VS", "04-1127", "SCREENING",  "WEIGHT",     42.87,    142, "2013-09-16",
-#'   "PILOT01",    "VS", "04-1127",  "BASELINE",  "WEIGHT",     41.05,    143, "2013-10-02",
-#'   "PILOT01",    "VS", "04-1127",    "WEEK 2",  "WEIGHT",     42.64,    144, "2013-10-16",
-#'   "PILOT01",    "VS", "04-1127",    "WEEK 4",  "WEIGHT",     41.73,    145, "2013-10-30",
-#'   "PILOT01",    "VS", "04-1127",   "WEEK 26",  "WEIGHT",     43.09,    152, "2014-03-31",
-#'   "PILOT01",    "VS", "06-1049", "SCREENING",  "HEIGHT",    167.64,     28, "2013-04-30",
-#'   "PILOT01",    "VS", "06-1049", "SCREENING",  "WEIGHT",     57.61,     92, "2013-04-30",
-#'   "PILOT01",    "VS", "06-1049",  "BASELINE",  "WEIGHT",     57.83,     93, "2013-05-14",
-#'   "PILOT01",    "VS", "06-1049",    "WEEK 2",  "WEIGHT",     58.29,     94, "2013-05-28",
-#'   "PILOT01",    "VS", "06-1049",    "WEEK 4",  "WEIGHT",     58.97,     95, "2013-06-11"
-#' )
-#'
-#' dm <- tribble(
-#'   ~STUDYID,  ~DOMAIN,  ~USUBJID, ~AGE,   ~AGEU,
-#'   "PILOT01",    "DM", "01-1057",   59, "YEARS",
-#'   "PILOT01",    "DM", "04-1127",   84, "YEARS",
-#'   "PILOT01",    "DM", "06-1049",   60, "YEARS"
-#' )
-#' wgt_cat <- function(wgt) {
-#'   case_when(
-#'     wgt < 50 ~ "low",
-#'     wgt > 90 ~ "high",
-#'     TRUE ~ "normal"
-#'   )
-#' }
-#'
-#' derive_var_merged_cat(
-#'   dm,
-#'   dataset_add = vs,
-#'   by_vars = exprs(STUDYID, USUBJID),
-#'   order = exprs(VSDTC, VSSEQ),
-#'   filter_add = VSTESTCD == "WEIGHT" & substr(VISIT, 1, 9) == "SCREENING",
-#'   new_var = WGTBLCAT,
-#'   source_var = VSSTRESN,
-#'   cat_fun = wgt_cat,
-#'   mode = "last"
-#' ) %>%
-#'   select(STUDYID, USUBJID, AGE, AGEU, WGTBLCAT)
-#'
-#'
-#'
-#' # defining a value for missing VS data
-#' derive_var_merged_cat(
-#'   dm,
-#'   dataset_add = vs,
-#'   by_vars = exprs(STUDYID, USUBJID),
-#'   order = exprs(VSDTC, VSSEQ),
-#'   filter_add = VSTESTCD == "WEIGHT" & substr(VISIT, 1, 9) == "SCREENING",
-#'   new_var = WGTBLCAT,
-#'   source_var = VSSTRESN,
-#'   cat_fun = wgt_cat,
-#'   mode = "last",
-#'   missing_value = "MISSING"
-#' ) %>%
-#'   select(STUDYID, USUBJID, AGE, AGEU, WGTBLCAT)
 derive_var_merged_cat <- function(dataset,
                                   dataset_add,
                                   by_vars,
@@ -527,22 +466,7 @@ derive_var_merged_cat <- function(dataset,
                                   filter_add = NULL,
                                   mode = NULL,
                                   missing_value = NA_character_) {
-  deprecate_warn("0.11.0", "derive_var_merged_cat()", "derive_vars_merged()")
-  new_var <- assert_symbol(enexpr(new_var))
-  source_var <- assert_symbol(enexpr(source_var))
-  filter_add <- assert_filter_cond(enexpr(filter_add), optional = TRUE)
-  assert_data_frame(dataset_add, required_vars = expr_c(by_vars, source_var))
-
-  derive_vars_merged(
-    dataset,
-    dataset_add = dataset_add,
-    filter_add = !!filter_add,
-    by_vars = by_vars,
-    order = order,
-    new_vars = exprs(!!new_var := {{ cat_fun }}(!!source_var)),
-    mode = mode,
-    missing_values = exprs(!!new_var := !!missing_value)
-  )
+  deprecate_stop("0.11.0", "derive_var_merged_cat()", "derive_vars_merged()")
 }
 
 #' Merge an Existence Flag
@@ -782,40 +706,7 @@ derive_var_merged_character <- function(dataset,
                                         filter_add = NULL,
                                         mode = NULL,
                                         missing_value = NA_character_) {
-  deprecate_warn("0.11.0", "derive_var_merged_character()", "derive_vars_merged()")
-
-  new_var <- assert_symbol(enexpr(new_var))
-  source_var <- assert_symbol(enexpr(source_var))
-  case <-
-    assert_character_scalar(
-      case,
-      values = c("lower", "upper", "title"),
-      case_sensitive = FALSE,
-      optional = TRUE
-    )
-  filter_add <- assert_filter_cond(enexpr(filter_add), optional = TRUE)
-  assert_data_frame(dataset_add, required_vars = expr_c(by_vars, source_var))
-  assert_character_scalar(missing_value)
-
-  if (is.null(case)) {
-    trans <- expr(!!source_var)
-  } else if (case == "lower") {
-    trans <- expr(str_to_lower(!!source_var))
-  } else if (case == "upper") {
-    trans <- expr(str_to_upper(!!source_var))
-  } else if (case == "title") {
-    trans <- expr(str_to_title(!!source_var))
-  }
-  derive_vars_merged(
-    dataset,
-    dataset_add = dataset_add,
-    by_vars = by_vars,
-    order = order,
-    new_vars = exprs(!!new_var := !!trans),
-    filter_add = !!filter_add,
-    mode = mode,
-    missing_values = exprs(!!new_var := !!missing_value)
-  )
+  deprecate_stop("0.11.0", "derive_var_merged_character()", "derive_vars_merged()")
 }
 
 

diff --git a/R/derive_param_exist_flag.R b/R/derive_param_exist_flag.R
@@ -184,21 +184,17 @@ derive_param_exist_flag <- function(dataset = NULL,
                                     subject_keys) {
   ### BEGIN DEPRECATION
   if (!missing(dataset_adsl)) {
-    deprecate_warn(
+    deprecate_stop(
       "0.11.0", "derive_param_exist_flag(dataset_adsl = )",
       "derive_param_exit_flag(dataset_ref = )"
     )
-    # assign deprecated argument to new variable
-    dataset_ref <- dataset_adsl
   }
 
   if (!missing(subject_keys)) {
-    deprecate_warn(
+    deprecate_stop(
       "0.11.0", "derive_param_exist_flag(subject_keys = )",
       "derive_param_exit_flag(by_vars = )"
     )
-    # assign deprecated argument to new variable
-    by_vars <- subject_keys
   }
   ### END DEPRECATION
 
@@ -223,12 +219,11 @@ derive_param_exist_flag <- function(dataset = NULL,
 
   if (!missing(aval_fun)) {
     assert_function(aval_fun)
-    deprecate_warn(
+    deprecate_stop(
       "0.11.0",
       "derive_param_exist_flag(aval_fun = )",
       "derive_param_exist_flag(set_values_to = )"
     )
-    set_values_to <- exprs(!!!set_values_to, AVAL = aval_fun(AVALC))
   }
 
   # Create new observations

diff --git a/R/derive_param_extreme_event.R b/R/derive_param_extreme_event.R
@@ -124,47 +124,5 @@ derive_param_extreme_event <- function(dataset = NULL,
                                        subject_keys = get_admiral_option("subject_keys"),
                                        set_values_to,
                                        check_type = "warning") {
-  deprecate_warn("0.11.0", "derive_param_extreme_event()", "derive_extreme_records()")
-
-  # Check input arguments
-  filter_source <- assert_filter_cond(enexpr(filter_source))
-  assert_vars(subject_keys)
-  assert_expr_list(order, optional = TRUE)
-  assert_data_frame(dataset_source,
-    required_vars = exprs(!!!subject_keys, !!!extract_vars(order))
-  )
-  new_var <- assert_symbol(enexpr(new_var), optional = TRUE)
-  assert_same_type(true_value, false_value)
-  assert_data_frame(dataset, optional = TRUE)
-  assert_data_frame(dataset_adsl, required_vars = subject_keys)
-  check_type <-
-    assert_character_scalar(
-      check_type,
-      values = c("none", "warning", "error"),
-      case_sensitive = FALSE
-    )
-  mode <- assert_character_scalar(
-    mode,
-    values = c("first", "last"),
-    case_sensitive = FALSE
-  )
-  assert_varval_list(set_values_to, required_elements = "PARAMCD")
-  if (!is.null(set_values_to$PARAMCD) && !is.null(dataset)) {
-    assert_param_does_not_exist(dataset, set_values_to$PARAMCD)
-  }
-
-  derive_extreme_records(
-    dataset,
-    dataset_add = dataset_source,
-    dataset_ref = dataset_adsl,
-    by_vars = subject_keys,
-    order = order,
-    mode = mode,
-    filter_add = !!filter_source,
-    check_type = check_type,
-    exist_flag = !!new_var,
-    true_value = true_value,
-    false_value = false_value,
-    set_values_to = set_values_to
-  )
+  deprecate_stop("0.11.0", "derive_param_extreme_event()", "derive_extreme_records()")
 }
diff --git a/R/derive_var_basetype.R b/R/derive_var_basetype.R
@@ -42,10 +42,5 @@
 #'
 #' @export
 derive_var_basetype <- function(dataset, basetypes) {
-  deprecate_warn("0.11.0", "derive_var_basetype()", "derive_basetype_records()")
-
-  derive_basetype_records(
-    dataset = dataset,
-    basetypes = basetypes
-  )
+  deprecate_stop("0.11.0", "derive_var_basetype()", "derive_basetype_records()")
 }