Merge branch 'main' into 2495-restricted_imputed_dtc_dt

.Rbuildignore

@@ -31,3 +31,5 @@
 ^\.devcontainer$
 ^vignettes/articles$
 ^inst/cheatsheet$
+^data-raw$
+^doc$

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check for Snapshot Testing
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/verdepcheck.yml

@@ -0,0 +1,23 @@
+---
+name: Dependency Conformance Test
+
+on:
+  workflow_dispatch:
+
+jobs:
+  dependency-test:
+    strategy:
+      fail-fast: false
+      matrix:
+        test-strategy: ["min_cohort", "min_isolated", "release", "max"]
+    uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@main
+    name: Dependency Conformance Test - ${{ matrix.test-strategy }}
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+      GCHAT_WEBHOOK: ${{ secrets.GCHAT_WEBHOOK }}
+    with:
+      strategy: ${{ matrix.test-strategy }}
+      additional-env-vars: |
+        PKG_SYSREQS_DRY_RUN=true
+      extra-deps: |
+        lme4 (>= 1.1-35)

.gitignore

@@ -54,3 +54,5 @@ admiral*.tgz
 ._.DS_Store
 
 .Rprofile
+/doc/
+/Meta/

.lycheeignore

@@ -6,3 +6,5 @@ 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
+

DESCRIPTION

@@ -1,24 +1,28 @@
 Type: Package
 Package: admiral
 Title: ADaM in R Asset Library
-Version: 1.1.1.9004
+Version: 1.1.1.9012
 Authors@R: c(
     person("Ben", "Straub", , "[email protected]", role = c("aut", "cre")),
-    person("Stefan", "Bundfuss", role = "aut"),
+    person("Stefan", "Bundfuss", role = "aut",
+           comment = c(ORCID = "0009-0005-0027-1198")),
     person("Jeffrey", "Dickinson", role = "aut"),
     person("Ross", "Farrugia", role = "aut"),
     person("Fanny", "Gautier", role = "aut"),
     person("G", "Gayatri", role = "aut"),
     person("Asha", "Chakma", role = "aut"),
     person("Dinakar", "Kulkarni", role = "aut"),
-    person("Edoardo", "Mancini", role = "aut"),
+    person("Edoardo", "Mancini", role = "aut",
+           comment = c(ORCID = "0009-0006-4899-8641")),
     person("Sadchla", "Mascary", role = "aut"),
     person("Gordon", "Miller", role = "aut"),
     person("Lina", "Patil", role = "aut"),
     person("Sophie", "Shapcott", role = "aut"),
     person("Eric", "Simms", role = "aut"),
-    person("Daniel", "Sjoberg", role = "aut"),
-    person("Stefan", "Thoma", role = "aut"),
+    person("Daniel", "Sjoberg", role = "aut",
+           comment = c(ORCID = "0000-0003-0862-2018")),
+    person("Stefan", "Thoma", role = "aut",
+           comment = c(ORCID = "0000-0002-5553-9252")),
     person("Phillip", "Webster", role = "aut"),
     person("Kangjie", "Zhang", role = "aut"),
     person("Zelos", "Zhu", role = "aut"),

NAMESPACE

@@ -100,6 +100,7 @@ export(derive_var_trtdurd)
 export(derive_var_trtemfl)
 export(derive_vars_aage)
 export(derive_vars_atc)
+export(derive_vars_cat)
 export(derive_vars_computed)
 export(derive_vars_crit_flag)
 export(derive_vars_dt)

NEWS.md

@@ -2,12 +2,38 @@
 
 ## New Features
 
+- New function `derive_vars_cat()` for deriving pairs of variables or more, e.g. 
+`AVALCATx` & `AVALCAxN`. (#2480)
 - New function `derive_vars_crit_flag()` for deriving criterion flag variables
 (`CRITy`, `CRITyFL`, `CRITyFLN`). (#2468)
 
+- Replace use of `data("sdtm")` with `sdtm <- pharmaverse::sdtm` in templates and vignettes. (#2498)
+
 ## 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
 
@@ -16,6 +42,8 @@
 <details>
 <summary>Developer Notes</summary>
 
+- Adopted `data-raw/data` R Package Convention (#2427)
+
 </details>
 
 # admiral 1.1.1

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,

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(

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,