Merge branch 'main' into 2484-general-issue-chg-and-pchg-populated-fo…

…r-baseline-and-pre-baseline-records-in-the-templates
pharmaverse · Sep 3, 2024 · d4ec9ee · d4ec9ee
2 parents 6e1f83e + eea45a6
commit d4ec9ee
Show file tree

Hide file tree

Showing 27 changed files with 47 additions and 845 deletions.
diff --git a/.lycheeignore b/.lycheeignore
@@ -6,3 +6,4 @@ https://packagemanager.rstudio.com/cran/__linux__/focal/latest
 https://raw.githubusercontent.com/pharmaverse/admiral/main/inst/cheatsheet/cheatsheet_image.png
 https://rsc.niaid.nih.gov/clinical-research-sites/daids-adverse-event-grading-tables
 https://rsc.niaid.nih.gov/sites/default/files/daidsgradingcorrectedv21.pdf
+https://www.fda.gov/media/116737/download
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: admiral
 Title: ADaM in R Asset Library
-Version: 1.1.1.9006
+Version: 1.1.1.9007
 Authors@R: c(
     person("Ben", "Straub", , "[email protected]", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut",

diff --git a/NEWS.md b/NEWS.md
@@ -8,6 +8,28 @@
 ## Updates of Existing Functions
 
 ## Breaking Changes
+
+- The following function arguments are entering the next phase of the deprecation process: (#2487)
+
+### Phase 1 (warning)
+
+### Phase 2 (error)
+
+### Phase 3 (removed)
+  - `consolidate_metadata(check_keys)`
+  - Removed at v1.1.1 `compute_egfr(wt)`
+  - Removed at v1.1.1 `derive_expected_records(dataset_expected_obs)` 
+  - Removed at v1.1.1 `derive_locf_records(dataset_expected_obs)`
+  - `derive_extreme_event(ignore_event_order)`
+  - `derive_vars_merged(match_flag)`
+  - `derive_var_merged_summary(new_var, analysis_var, summary_fun)`
+  - Removed at v1.1.1 `derive_param_computed(analysis_value, analysis_var)`
+  - `derive_param_exposure(filter, analysis_var, summary_fun)`
+  - `derive_summary_records(filter)`
+  - Removed at v1.1.1 `derive_extreme_records(filter)`
+  - `derive_var_joined_exist_flag(first_cond, filter)`
+  - `event_joined(first_cond)`
+  - `filter_joined(first_cond, filter)`
 
 ## Documentation
 

diff --git a/R/consolidate_metadata.R b/R/consolidate_metadata.R
@@ -28,16 +28,6 @@
 #'
 #'   *Permitted Values*: `"none"`, `"message"`, `"warning"`, `"error"`
 #'
-#' @param check_keys Check keys?
-#'
-#'  `r lifecycle::badge("deprecated")` Please use `check_type` instead.
-#'
-#'   If `"warning"` or `"error"` is specified, a message is issued if the key
-#'   variables (`key_vars`) are not a unique key in all of the input datasets
-#'   (`datasets`).
-#'
-#'   *Permitted Values*: `"none"`, `"warning"`, `"error"`
-#'
 #' @param check_type Check uniqueness?
 #'
 #'   If `"warning"` or `"error"` is specified, a message is issued if the key
@@ -89,7 +79,6 @@ consolidate_metadata <- function(datasets,
                                  key_vars,
                                  source_var = SOURCE,
                                  check_vars = "warning",
-                                 check_keys,
                                  check_type = "error") {
   assert_list_of(datasets, cls = "data.frame", named = TRUE)
   assert_vars(key_vars)
@@ -100,20 +89,6 @@ consolidate_metadata <- function(datasets,
       values = c("none", "message", "warning", "error"),
       case_sensitive = FALSE
     )
-  if (!is_missing(check_keys)) {
-    deprecate_stop(
-      "1.1.0",
-      "consolidate_metadata(check_keys = )",
-      "consolidate_metadata(check_type = )"
-    )
-    check_type <-
-      assert_character_scalar(
-        check_keys,
-        values = c("none", "warning", "error"),
-        case_sensitive = FALSE,
-        optional = TRUE
-      )
-  }
   check_type <-
     assert_character_scalar(
       check_type,

diff --git a/R/derive_extreme_event.R b/R/derive_extreme_event.R
@@ -51,22 +51,6 @@
 #'   A named list of datasets is expected. The `dataset_name` field of `event()`
 #'   and `event_joined()` refers to the dataset provided in the list.
 #'
-#' @param ignore_event_order Ignore event order
-#'
-#'   `r lifecycle::badge("deprecated")`
-#'
-#'   This argument is *deprecated*. If event order should be ignored, please
-#'   specify neither `ignore_event_order` nor `tmp_event_nr_var`. If the event
-#'   order should be considered, don't specify `ignore_event_order` but specify
-#'   `tmp_event_nr_var` and and the specified variable to `order`.
-#'
-#'   If the argument is set to `TRUE`, all events defined by `events` are
-#'   considered equivalent. If there is more than one observation per by group
-#'   the first or last (with respect to `mode` and `order`) is select without
-#'   taking the order of the events into account.
-#'
-#'   *Permitted Values:* `TRUE`, `FALSE`
-#'
 #' @param keep_source_vars Variables to keep from the source dataset
 #'
 #'  For each event the specified variables are kept from the selected
@@ -353,7 +337,6 @@ derive_extreme_event <- function(dataset = NULL,
                                  order,
                                  mode,
                                  source_datasets = NULL,
-                                 ignore_event_order = NULL,
                                  check_type = "warning",
                                  set_values_to = NULL,
                                  keep_source_vars = exprs(everything())) {
@@ -382,27 +365,6 @@ derive_extreme_event <- function(dataset = NULL,
     )
   )
 
-  if (!is.null(ignore_event_order)) {
-    if (ignore_event_order) {
-      deprecate_details <- paste(
-        "The event order is ignored by default.",
-        "Please remove `ignore_event_order = TRUE` from the call.",
-        sep = "\n"
-      )
-    } else {
-      deprecate_details <- c(
-        "Please remove `ignore_event_order = FALSE` from the call.",
-        "Specify `tmp_event_nr_var`.",
-        "Add the specified variable to `order`."
-      )
-    }
-    deprecate_stop(
-      "1.1.0",
-      "derive_extreme_event(ignore_event_order=)",
-      "derive_extreme_event(tmp_event_nr_var=)",
-      details = deprecate_details
-    )
-  }
   tmp_event_nr_var <- assert_symbol(enexpr(tmp_event_nr_var), optional = TRUE)
   check_type <-
     assert_character_scalar(

diff --git a/R/derive_merged.R b/R/derive_merged.R
@@ -77,17 +77,6 @@
 #'
 #'   *Permitted Values*: `"first"`, `"last"`, `NULL`
 #'
-#' @param match_flag Match flag
-#'
-#'  `r lifecycle::badge("deprecated")` Please use `exist_flag` instead.
-#'
-#'   If the argument is specified (e.g., `match_flag = FLAG`), the specified
-#'   variable (e.g., `FLAG`) is added to the input dataset. This variable will
-#'   be `TRUE` for all selected records from `dataset_add` which are merged into
-#'   the input dataset, and `NA` otherwise.
-#'
-#'   *Permitted Values*: Variable name
-#'
 #' @param exist_flag Exist flag
 #'
 #'   If the argument is specified (e.g., `exist_flag = FLAG`), the specified
@@ -321,7 +310,6 @@ derive_vars_merged <- function(dataset,
                                new_vars = NULL,
                                filter_add = NULL,
                                mode = NULL,
-                               match_flag,
                                exist_flag = NULL,
                                true_value = "Y",
                                false_value = NA_character_,
@@ -344,14 +332,7 @@ derive_vars_merged <- function(dataset,
       extract_vars(new_vars)
     )
   )
-  if (!is_missing(enexpr(match_flag))) {
-    deprecate_stop(
-      "1.1.0",
-      "derive_vars_merged(match_flag =)",
-      "derive_vars_merged(exist_flag =)"
-    )
-    exist_flag <- assert_symbol(enexpr(match_flag), optional = TRUE)
-  }
+
   exist_flag <- assert_symbol(enexpr(exist_flag), optional = TRUE)
   assert_atomic_vector(true_value, optional = TRUE)
   assert_atomic_vector(false_value, optional = TRUE)
@@ -814,13 +795,6 @@ get_not_mapped <- function() {
 #'   The variables specified by the `by_vars` and the variables used on the left
 #'   hand sides of the `new_vars` arguments are expected.
 #'
-#' @param new_var Variable to add
-#'
-#'  `r lifecycle::badge("deprecated")` Please use `new_vars` instead.
-#'
-#'   The specified variable is added to the input dataset (`dataset`) and set to
-#'   the summarized values.
-#'
 #' @param by_vars Grouping variables
 #'
 #'   The expressions on the left hand sides of `new_vars` are evaluated by the
@@ -855,21 +829,6 @@ get_not_mapped <- function() {
 #'
 #'   *Permitted Values*: a condition
 #'
-#' @param analysis_var Analysis variable
-#'
-#'  `r lifecycle::badge("deprecated")` Please use `new_vars` instead.
-#'
-#'   The values of the specified variable are summarized by the function
-#'   specified for `summary_fun`.
-#'
-#' @param summary_fun Summary function
-#'
-#'  `r lifecycle::badge("deprecated")` Please use `new_vars` instead.
-#'
-#'   The specified function that takes as input `analysis_var` and performs the
-#'   calculation. This can include built-in functions as well as user defined
-#'   functions, for example `mean` or `function(x) mean(x, na.rm = TRUE)`.
-#'
 #' @inheritParams derive_vars_merged
 #'
 #' @details
@@ -959,11 +918,8 @@ derive_var_merged_summary <- function(dataset,
                                       dataset_add,
                                       by_vars,
                                       new_vars = NULL,
-                                      new_var,
                                       filter_add = NULL,
-                                      missing_values = NULL,
-                                      analysis_var,
-                                      summary_fun) {
+                                      missing_values = NULL) {
   assert_vars(by_vars)
   by_vars_left <- replace_values_by_names(by_vars)
   by_vars_right <- chr2vars(paste(vars2chr(by_vars)))
@@ -980,18 +936,6 @@ derive_var_merged_summary <- function(dataset,
     required_vars = expr_c(by_vars_right, extract_vars(new_vars))
   )
 
-  if (!missing(new_var) || !missing(analysis_var) || !missing(summary_fun)) {
-    deprecate_stop(
-      "1.1.0",
-      I("derive_var_merged_summary(new_var = , anaylsis_var = , summary_fun = )"),
-      "derive_var_merged_summary(new_vars = )"
-    )
-    new_var <- assert_symbol(enexpr(new_var))
-    analysis_var <- assert_symbol(enexpr(analysis_var))
-    assert_s3_class(summary_fun, "function")
-    new_vars <- exprs(!!new_var := {{ summary_fun }}(!!analysis_var), !!!new_vars)
-  }
-
   # Summarise the analysis value and merge to the original dataset
   derive_vars_merged(
     dataset,

diff --git a/R/derive_param_exposure.R b/R/derive_param_exposure.R
@@ -13,23 +13,6 @@
 #'   Observations from the specified dataset are going to be used to calculate and added
 #'   as new records to the input dataset (`dataset`).
 #'
-#'
-#' @param filter
-#'
-#'  `r lifecycle::badge("deprecated")` Please use `filter_add` instead.
-#'
-#'   Filter condition as logical expression to apply during
-#'   summary calculation. By default, filtering expressions are computed within
-#'   `by_vars` as this will help when an aggregating, lagging, or ranking
-#'   function is involved.
-#'
-#'   For example,
-#'
-#'   + `filter = (AVAL > mean(AVAL, na.rm = TRUE))` will filter all `AVAL`
-#'   values greater than mean of `AVAL` with in `by_vars`.
-#'   + `filter = (dplyr::n() > 2)` will filter n count of `by_vars` greater
-#'   than 2.
-#'
 #' @param filter_add Filter condition as logical expression to apply during
 #'   summary calculation. By default, filtering expressions are computed within
 #'   `by_vars` as this will help when an aggregating, lagging, or ranking
@@ -49,13 +32,6 @@
 #'
 #'   *Permitted Values:* A character of `PARAMCD` value
 #'
-#' @param analysis_var Analysis variable.
-#'
-#' @param summary_fun Function that takes as an input the `analysis_var` and
-#'   performs the calculation.
-#'   This can include built-in functions as well as user defined functions,
-#'   for example `mean` or `function(x) mean(x, na.rm = TRUE)`.
-#'
 #' @param by_vars Grouping variables
 #'
 #'   For each group defined by `by_vars` an observation is added to the output
@@ -164,19 +140,9 @@ derive_param_exposure <- function(dataset = NULL,
                                   dataset_add,
                                   by_vars,
                                   input_code,
-                                  analysis_var,
-                                  summary_fun,
-                                  filter = NULL,
                                   filter_add = NULL,
                                   set_values_to = NULL) {
   by_vars <- assert_vars(by_vars)
-  if (!missing(analysis_var) || !missing(summary_fun)) {
-    deprecate_stop(
-      "1.1.0",
-      I("derive_param_exposure(anaylsis_var = , summary_fun = )"),
-      "derive_param_exposure(set_values_to = )"
-    )
-  }
 
   dtm <- c("ASTDTM", "AENDTM") %in% colnames(dataset)
   dt <- c("ASTDT", "AENDT") %in% colnames(dataset)
@@ -203,14 +169,6 @@ derive_param_exposure <- function(dataset = NULL,
     required_vars = expr_c(by_vars, exprs(PARAMCD), dates)
   )
 
-  if (!missing(filter)) {
-    deprecate_stop(
-      "1.1.0",
-      I("derive_param_exposure(filter = )"),
-      "derive_param_exposure(filter_add = )"
-    )
-    filter_add <- assert_filter_cond(enexpr(filter), optional = TRUE)
-  }
   filter_add <- assert_filter_cond(enexpr(filter_add), optional = TRUE)
   assert_varval_list(set_values_to, required_elements = "PARAMCD")
   assert_param_does_not_exist(dataset, set_values_to$PARAMCD)

diff --git a/R/derive_summary_records.R b/R/derive_summary_records.R
@@ -33,22 +33,6 @@
 #'
 #'   `r roxygen_param_by_vars()`
 #'
-#' @param filter
-#'
-#'  `r lifecycle::badge("deprecated")` Please use `filter_add` instead.
-#'
-#'   Filter condition as logical expression to apply during
-#'   summary calculation. By default, filtering expressions are computed within
-#'   `by_vars` as this will help when an aggregating, lagging, or ranking
-#'   function is involved.
-#'
-#'   For example,
-#'
-#'   + `filter = (AVAL > mean(AVAL, na.rm = TRUE))` will filter all `AVAL`
-#'   values greater than mean of `AVAL` with in `by_vars`.
-#'   + `filter = (dplyr::n() > 2)` will filter n count of `by_vars` greater
-#'   than 2.
-#'
 #' @param filter_add Filter condition as logical expression to apply during
 #'   summary calculation. By default, filtering expressions are computed within
 #'   `by_vars` as this will help when an aggregating, lagging, or ranking
@@ -89,8 +73,6 @@
 #'   *Permitted Values*: named list of expressions, e.g.,
 #'   `exprs(AVAL = -9999)`
 #'
-#' @inheritParams get_summary_records
-#'
 #' @return A data frame with derived records appended to original dataset.
 #'
 #' @family der_prm_bds_findings
@@ -191,10 +173,7 @@ derive_summary_records <- function(dataset = NULL,
                                    dataset_add,
                                    dataset_ref = NULL,
                                    by_vars,
-                                   filter = NULL,
                                    filter_add = NULL,
-                                   analysis_var,
-                                   summary_fun,
                                    set_values_to,
                                    missing_values = NULL) {
   assert_vars(by_vars)
@@ -209,25 +188,6 @@ derive_summary_records <- function(dataset = NULL,
   assert_varval_list(set_values_to)
   assert_expr_list(missing_values, named = TRUE, optional = TRUE)
 
-  if (!missing(analysis_var) || !missing(summary_fun)) {
-    deprecate_stop(
-      "1.1.0",
-      I("derive_summary_records(anaylsis_var = , summary_fun = )"),
-      "derive_summary_records(set_values_to = )"
-    )
-    analysis_var <- assert_symbol(enexpr(analysis_var))
-    assert_s3_class(summary_fun, "function")
-    set_values_to <- exprs(!!analysis_var := {{ summary_fun }}(!!analysis_var), !!!set_values_to)
-  }
-
-  if (!missing(filter)) {
-    deprecate_stop(
-      "1.1.0",
-      I("derive_summary_records(filter = )"),
-      "derive_summary_records(filter_add = )"
-    )
-    filter_add <- assert_filter_cond(enexpr(filter), optional = TRUE)
-  }
   filter_add <- assert_filter_cond(enexpr(filter_add), optional = TRUE)
 
   summary_records <- dataset_add %>%