Merge branch 'main' into patch

.Rprofile

@@ -1,8 +1,7 @@
 # Set renv profile base on R version.
 .get_dependencies <- function(project_dir) {
-
   admdev_loc <- find.package("admiraldev", lib.loc = .libPaths(), quiet = TRUE)
-  adm_dev_suggests <- if(length(admdev_loc) != 0) {
+  adm_dev_suggests <- if (length(admdev_loc) != 0) {
     renv:::renv_dependencies_discover_description(admdev_loc, fields = c("Depends", "Imports", "LinkingTo", "Suggests"))
   } else {
     data.frame(Packages = character(0))
@@ -19,7 +18,7 @@
       ))
     )
   )
-  packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", "pharmaversesdtm", getwd()))]
+  packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "pharmaversesdtm", getwd()))]
 }
 
 options(renv.snapshot.filter = .get_dependencies)

.devcontainer/4.1/devcontainer.json

@@ -31,7 +31,7 @@
 
 	"postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh",
 
-	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"",
+	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'",
 
 	"customizations": {
 		"vscode": {

.devcontainer/4.2/devcontainer.json

@@ -31,7 +31,7 @@
 
 	"postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh",
 
-	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"",
+	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'",
 
 	"customizations": {
 		"vscode": {

.devcontainer/devcontainer.json

@@ -31,7 +31,7 @@
 
 	"postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh",
 
-	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"",
+	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'",
 
 	"customizations": {
 		"vscode": {

.devcontainer/postCreateCommand.sh

@@ -1,5 +1,11 @@
 #!/bin/bash
 
+# move script rstudio into /usr/bin
+sudo cp "$(pwd)/.devcontainer/rstudio.sh" /usr/bin/rstudio
+sudo chmod +x /usr/bin/rstudio
+
+# Restore renv and install staged dependencies
 R -q -e 'renv::restore(lockfile = file.path("renv", "profiles", paste(R.version$major, substr(R.version$minor, 1, 1), sep = "."), "renv.lock")); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = ".", verbose = 1), verbose = 1);'
 
+# Define rstudio default working directory
 jq --arg folder "$(pwd)/" '. + { "initial_working_directory": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json

.devcontainer/rstudio.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+$BROWSER "https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}"
+
+exit 1

.github/pull_request_template.md

@@ -9,7 +9,7 @@ Please check off each taskbox as an acknowledgment that you completed the task o
 - [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the [categorization of functions](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html#categorization-of-functions) to tag appropriate keyword/family.
 - [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately
 - [ ] Address any updates needed for vignettes and/or templates
-- [ ] Update `NEWS.md` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers)
+- [ ] Update `NEWS.md` under the header `# admiral (development version)` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers)
 - [ ] Build admiral site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiral/cran-release/reference/index.html)" page. 
 - [ ] Address or fix all lintr warnings and errors - `lintr::lint_package()`
 - [ ] Run `R CMD check` locally and address all errors and warnings - `devtools::check()`

.github/workflows/common.yml

@@ -15,17 +15,13 @@ on:
       - "v*"
     branches:
       - main
-      - devel
       - patch
-      - pre-release
   # 'pull_request' events are triggered when PRs are
   # created against one of these target branches.
   pull_request:
     branches:
       - main
-      - devel
       - patch
-      - pre-release
   # 'release' events are triggered when...
   # you guessed it - when releases are made.
   release:
@@ -81,7 +77,7 @@ jobs:
       latest-tag-alt-name: cran-release
       multiversion-docs-landing-page: cran-release
       branches-or-tags-to-list: >-
-        ^cran-release$|^main$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)$
+        ^cran-release$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)$
   linter:
     name: Lint
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: admiral
 Type: Package
 Title: ADaM in R Asset Library
-Version: 0.12.3
+Version: 0.12.2.9001
 Authors@R: c(
     person("Ben", "Straub", email = "[email protected]", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),
@@ -37,7 +37,7 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Depends: R (>= 3.5)
+Depends: R (>= 4.0)
 Imports:
     admiraldev (>= 0.4.0),
     dplyr (>= 0.8.4),

NAMESPACE

@@ -69,7 +69,6 @@ export(derive_param_computed)
 export(derive_param_doseint)
 export(derive_param_exist_flag)
 export(derive_param_exposure)
-export(derive_param_extreme_event)
 export(derive_param_extreme_record)
 export(derive_param_framingham)
 export(derive_param_map)
@@ -84,19 +83,12 @@ export(derive_var_anrind)
 export(derive_var_atoxgr)
 export(derive_var_atoxgr_dir)
 export(derive_var_base)
-export(derive_var_basetype)
 export(derive_var_chg)
-export(derive_var_confirmation_flag)
 export(derive_var_dthcaus)
 export(derive_var_extreme_dt)
 export(derive_var_extreme_dtm)
 export(derive_var_extreme_flag)
 export(derive_var_joined_exist_flag)
-export(derive_var_last_dose_amt)
-export(derive_var_last_dose_date)
-export(derive_var_last_dose_grp)
-export(derive_var_merged_cat)
-export(derive_var_merged_character)
 export(derive_var_merged_exist_flag)
 export(derive_var_merged_summary)
 export(derive_var_obs_number)
@@ -115,7 +107,6 @@ export(derive_vars_dtm_to_tm)
 export(derive_vars_duration)
 export(derive_vars_dy)
 export(derive_vars_joined)
-export(derive_vars_last_dose)
 export(derive_vars_merged)
 export(derive_vars_merged_lookup)
 export(derive_vars_period)

NEWS.md

@@ -1,3 +1,61 @@
+# admiral (development version)
+
+## New Features
+
+## Updates of Existing Functions
+
+- `derive_extreme_records()`, `derive_var_extreme_flag()`,`derive_vars_joined()` and `derive_vars_merged()` were enhanced with the arguments `true_value` and `false_value` to align with preexisting functions that had similar functionality (#2125)
+
+- `restrict_derivation()` now allows `{dplyr}` functions like `mutate` in the `derivation argument (#2143)
+
+- `derive_summary_records()`, `derive_var_merged_summary()`, and `get_summary_records()`
+were enhanced such that more than one summary variable can be derived, e.g.,
+`AVAL` as the sum and `ADT` as the maximum of the contributing records. (#1792)
+
+
+## Breaking Changes
+
+- In `derive_summary_records()` and `get_summary_records()` the arguments
+`analysis_var` and `summary_fun` were deprecated in favor of `set_values_to`.
+(#1792)
+
+- In `derive_var_merged_summary()` the arguments `new_var`, `analysis_var`, and
+`summary_fun` were deprecated in favor of `new_vars`. (#1792)
+
+- admiral now only supports R >= 4.0.0 
+
+- For the function `derive_vars_merged()`, the argument `match_flag` was renamed to `exist_flag` (#2125)
+
+- The default value for the `false_value` argument in `derive_extreme_records()` was changed to `NA_character_` (#2125)
+
+- The following functions, which were deprecated in previous `{admiral}` versions, have been removed: (#2098)
+  - `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()`
+  - `derive_var_confirmation_flag()`
+
+- The following function arguments are entering the next phase of the deprecation process: (#2098)
+
+  - `compute_egfr(wt)`
+  - `derive_extreme_records(filter)`
+  - `derive_param_computed(analysis_value, analysis_var)`
+  - `derive_var_shift(na_val)`
+  - `derive_expected_records(dataset_expected_obs)` 
+  - `derive_var_ontrtfl(span_period)` 
+
+## Documentation
+
+- A way to standardize roxygen labels and descriptions for function arguments was implemented and tested (#2034)
+
+- Link to published CDISC Population PK (ADPPK) implementation guide added. (#2161)
+
+## Various
+
 # admiral 0.12.3
 
 - Fixed a bug in `derive_var_dthcaus()` where if a subject has observations in

R/call_derivation.R

@@ -3,7 +3,7 @@
 #' Call a single derivation multiple times with some parameters/arguments being fixed across
 #' iterations and others varying.
 #'
-#' @param dataset The input dataset
+#' @param dataset  `r roxygen_param_dataset()`
 #' @param derivation The derivation function to call
 #'
 #'   A function that performs a specific derivation is expected. A derivation

R/compute_kidney.R

@@ -137,9 +137,7 @@
 compute_egfr <- function(creat, creatu = "SI", age, weight, sex, race = NULL, method, wt) {
   ### BEGIN DEPRECATION
   if (!missing(wt)) {
-    deprecate_warn("0.12.0", "compute_egfr(old_param = 'wt')", "compute_egfr(new_param = 'weight')")
-    # old_param is given using exprs()
-    weight <- wt
+    deprecate_stop("0.12.0", "compute_egfr(old_param = 'wt')", "compute_egfr(new_param = 'weight')")
   }
   ### END DEPRECATION
 

R/create_single_dose_dataset.R

@@ -185,10 +185,8 @@ dose_freq_lookup <- tribble(
 #' necessary when e.g. calculating last dose before an adverse event in `ADAE`
 #' or deriving a total dose parameter in `ADEX` when `EXDOSFRQ != ONCE`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The columns specified by `dose_freq`, `start_date` and the `end_date`
-#'   parameters are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dose_freq", "start_date", "end_date"))`
 #'
 #' @param dose_freq The dose frequency
 #'

R/derive_adeg_params.R

@@ -6,10 +6,9 @@
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` and the `unit_var` parameter,
-#'   `PARAMCD`, and `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars", "get_unit_expr"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`
@@ -257,10 +256,9 @@ compute_qtc <- function(qt, rr, method) {
 #' The analysis value of the new parameter is derived as
 #' \deqn{\frac{60000}{HR}}{60000 / HR}
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and `AVAL`
-#'   are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`

R/derive_advs_params.R

@@ -5,10 +5,9 @@
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`
@@ -226,10 +225,9 @@ compute_map <- function(diabp, sysbp, hr = NULL) {
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`
@@ -549,10 +547,9 @@ compute_bsa <- function(height = height,
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`

R/derive_basetype_records.R

@@ -12,9 +12,8 @@
 #' Adds the `BASETYPE` variable to a dataset and duplicates records based upon
 #' the provided conditions.
 #'
-#' @param dataset Input dataset
-#'
-#'   The columns specified in the expressions inside `basetypes` are required.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("basetypes"))`
 #'
 #' @param basetypes A *named* list of expressions created using the
 #' `rlang::exprs()` function

R/derive_date_vars.R

@@ -1252,9 +1252,8 @@ compute_tmf <- function(dtc,
 #' impute, we only enable to impute up to a highest level, i.e. you couldn't
 #' choose to say impute months, but not days.
 #'
-#' @param dataset Input dataset.
-#'
-#'   The date character vector (`dtc`) must be present.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dtc"))`
 #'
 #' @param new_vars_prefix Prefix used for the output variable(s).
 #'
@@ -1461,9 +1460,8 @@ derive_vars_dt <- function(dataset, # nolint: cyclocomp_linter
 #' impute, we only enable to impute up to a highest level, i.e. you couldn't
 #' choose to say impute months, but not days.
 #'
-#' @param dataset Input dataset
-#'
-#'   The date character vector (`dtc`) must be present.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dtc"))`
 #'
 #' @param new_vars_prefix Prefix used for the output variable(s).
 #'

R/derive_expected_records.R

@@ -3,10 +3,8 @@
 #' Add expected records as new observations for each 'by group' when the dataset
 #' contains missing observations.
 #'
-#' @param dataset Input dataset
-#'
-#'   A data frame, the columns from `dataset_ref` and specified by the
-#'   `by_vars` parameter are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dataset_ref", "by_vars"))`
 #'
 #' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
 #'
@@ -91,7 +89,7 @@ derive_expected_records <- function(dataset,
                                     by_vars = NULL,
                                     set_values_to = NULL) {
   if (!missing(dataset_expected_obs)) {
-    deprecate_warn(
+    deprecate_stop(
       "0.12.0",
       "derive_expected_records(dataset_expected_obs = )",
       "derive_expected_records(dataset_ref = )"