Merge branch '2143_restrict_derivation_lighten_assertion' of https://…

…github.com/pharmaverse/admiral into 2143_restrict_derivation_lighten_assertion
pharmaverse · Oct 10, 2023 · b5d91e3 · b5d91e3
2 parents 54dca70 + 159a6be
commit b5d91e3
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Showing 141 changed files with 978 additions and 912 deletions.
diff --git a/.Rprofile b/.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)

diff --git a/.devcontainer/4.1/devcontainer.json b/.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": {

diff --git a/.devcontainer/4.2/devcontainer.json b/.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": {

diff --git a/.devcontainer/devcontainer.json b/.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": {

diff --git a/.devcontainer/postCreateCommand.sh b/.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": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json
diff --git a/.devcontainer/rstudio.sh b/.devcontainer/rstudio.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+$BROWSER "https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}"
+
+exit 1
diff --git a/.github/workflows/common.yml b/.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

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: admiral
 Type: Package
 Title: ADaM in R Asset Library
-Version: 0.12.2.9000
+Version: 0.12.2.9001
 Authors@R: c(
     person("Ben", "Straub", email = "[email protected]", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),

diff --git a/NEWS.md b/NEWS.md
@@ -6,8 +6,20 @@
 
 - `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 
 
 - The following functions, which were deprecated in previous `{admiral}` versions, have been removed: (#2098)
@@ -32,6 +44,8 @@
 
 ## Documentation
 
+- A way to standardize roxygen labels and descriptions for function arguments was implemented and tested (#2034)
+
 ## Various
 
 # admiral 0.12.2

diff --git a/R/call_derivation.R b/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

diff --git a/R/create_single_dose_dataset.R b/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
 #'

diff --git a/R/derive_adeg_params.R b/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`

diff --git a/R/derive_advs_params.R b/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`

diff --git a/R/derive_basetype_records.R b/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

diff --git a/R/derive_date_vars.R b/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).
 #'

diff --git a/R/derive_expected_records.R b/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.
 #'

diff --git a/R/derive_extreme_records.R b/R/derive_extreme_records.R
@@ -7,7 +7,7 @@
 #' distinguishes `derive_extreme_records()` from `derive_summary_records()`,
 #' where only the by variables are populated for the new records.
 #'
-#' @param dataset Input dataset
+#' @param dataset `r roxygen_param_dataset()`
 #'
 #'   If `dataset_add` is not specified, the new records are selected from the
 #'   input dataset. In this case the variables specified by `by_vars` and
@@ -92,6 +92,14 @@
 #'   automatically.
 #'
 #'
+#' @param keep_source_vars Variables to be kept in the new records
+#'
+#'   A named list or tidyselect expressions created by `exprs()` defining the
+#'   variables to be kept for the new records. The variables specified for
+#'   `by_vars` and `set_values_to` need not be specified here as they are kept
+#'   automatically.
+#'
+#'
 #' @inheritParams filter_extreme
 #' @inheritParams derive_summary_records
 #'

diff --git a/R/derive_joined.R b/R/derive_joined.R
@@ -6,9 +6,8 @@
 #' variables from both datasets. For example, add the lowest value (nadir)
 #' before the current observation.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by `by_vars` are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars"))`
 #'
 #' @param dataset_add Additional dataset
 #'

diff --git a/R/derive_locf_records.R b/R/derive_locf_records.R
@@ -3,10 +3,8 @@
 #' Adds LOCF records as new observations for each 'by group' when the dataset
 #' does not contain observations for missed visits/time points.
 #'
-#' @param dataset Input dataset
-#'
-#'   The columns specified by the `by_vars`, `analysis_var`, `order`,
-#'   `keep_vars` parameters are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars", "analysis_var", "order", "keep_vars"))`
 #'
 #' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
 #'