fix: #1797 address merge conflicts

Merge branch 'devel' into 1797_deprecate_derive_var_last_dose@devel

# Conflicts:
#	man/derive_var_last_dose_amt.Rd
#	man/derive_var_last_dose_date.Rd
#	man/derive_var_last_dose_grp.Rd

.Rprofile

@@ -1,5 +1,18 @@
+# Set renv profile base on R version.
+renv_profile <- paste(R.version$major, substr(R.version$minor, 1,1), sep = ".")
+if (file.exists("./renv/profile")){
+  message("Using renv profile from `renv/profile` file.")
+} else if (renv_profile %in% c("4.1", "4.2", "4.3")) {
+  message("Set renv profile to `", renv_profile, "`")
+  Sys.setenv("RENV_PROFILE" = renv_profile)
+} else {
+  message("This repository do not contains the renv profile for your R version.")
+}
+
 if (Sys.getenv("GITHUB_ACTIONS") == "") {
   source("renv/activate.R")
 } else {
   options(repos = c(CRAN = "https://cran.rstudio.com"))
 }
+
+

.github/workflows/common.yml

@@ -43,25 +43,25 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/style.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   spellcheck:
     name: Spelling
     uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   readme:
     name: Render README
     uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main
     if: github.event_name == 'push'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   validation:
     name: Validation
     uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main
     if: github.event_name == 'release'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
@@ -71,7 +71,7 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
     if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/v')
     with:
-      r-version: "4.0"
+      r-version: "4.1"
       # Whether to skip multiversion docs
       # Note that if you have multiple versions of docs,
       # your URL links are likely to break due to path changes
@@ -85,7 +85,7 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main
@@ -96,7 +96,7 @@ jobs:
     if: >
       github.event_name != 'release'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
       # Whether to skip code coverage badge creation
       # Setting to 'false' will require you to create
       # an orphan branch called 'badges' in your repository
@@ -106,4 +106,4 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"

.github/workflows/templates.yml

@@ -12,4 +12,4 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
     if: github.event.review.state == 'approved'
     with:
-      r-version: "4.0"
+      r-version: "4.1"

NAMESPACE

@@ -133,8 +133,10 @@ export(extend_source_datasets)
 export(extract_duplicate_records)
 export(extract_unit)
 export(filter_date_sources)
+export(filter_exist)
 export(filter_extreme)
 export(filter_joined)
+export(filter_not_exist)
 export(filter_relative)
 export(format_eoxxstt_default)
 export(format_reason_default)

NEWS.md

@@ -6,8 +6,14 @@
 
 - New function `compute_age_years()` for converting a vector of age values to years. (#1794)
 
+- New functions `filter_exist()` and `filter_not_exist()` for selecting records from
+a dataset dependent on the existence of the corresponding by groups in a filtered 
+source dataset. (#1699)
+
 - New function `derive_param_extreme_record()` that adds parameter based on the first or last record from multiple sources. (#1822)
 
+- New ADPPK template script available `ad_adppk.R` which creates Population PK Analysis Dataset (#1772) based on forthcoming CDISC Implementation guide.
+
 - New function `compute_egfr()` for calculating Estimated Glomerular Filtration Rate (eGFR) and Creatinine Clearance for Kidney Function (#1826)
 
 ## Updates of Existing Functions
@@ -83,9 +89,13 @@ the `filter_add` argument. (#1725)
 
 - Updated example dataset to trigger deterioration flags in the vignette "Creating Questionnaire ADaMs" (#1853, #1854)
 
+- Updated PK Programming vignette to include new Population PK Template `ad_adppk.R` (#1772)
+
 - Updated "Lab Grading" Vignette to link to grading metadata available in `{admiral}` and clarify how abnormal baseline
 values are assigned in NCI-CTCAEv5 (#1863).
 
+- Increased documentation for those functions which are regarded as wrapper functions (#1726)
+
 ## Various
 
 - `vars()` which was used in the admiral function calls that expected a list of

R/derive_adeg_params.R

@@ -1,9 +1,11 @@
 #' Adds a Parameter for Corrected QT (an ECG measurement)
 #'
-#' Adds a record for corrected QT using either Bazett's, Fridericia's or Sagie's
+#' @description Adds a record for corrected QT using either Bazett's, Fridericia's or Sagie's
 #' formula for each by group (e.g., subject and visit) where the source parameters
 #' are available.
 #'
+#' **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,
@@ -238,9 +240,11 @@ compute_qtc <- function(qt, rr, method) {
 
 #' Adds a Parameter for Derived RR (an ECG measurement)
 #'
-#' Adds a record for derived RR based on heart rate for each by group (e.g.,
+#' @description Adds a record for derived RR based on heart rate for each by group (e.g.,
 #' subject and visit) where the source parameters are available.
 #'
+#' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
+#'
 #' The analysis value of the new parameter is derived as
 #' \deqn{\frac{60000}{HR}}{60000 / HR}
 #'

R/derive_advs_params.R

@@ -1,8 +1,10 @@
 #' Adds a Parameter for Mean Arterial Pressure
 #'
-#' Adds a record for mean arterial pressure (MAP) for each by group
+#' @description Adds a record for mean arterial pressure (MAP) for each by group
 #' (e.g., subject and visit) where the source parameters are available.
 #'
+#' **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
@@ -204,8 +206,11 @@ compute_map <- function(diabp, sysbp, hr = NULL) {
 
 #' Adds a Parameter for BSA (Body Surface Area) Using the Specified Method
 #'
-#' Adds a record for BSA (Body Surface Area) using the specified derivation method
-#' for each by group (e.g., subject and visit) where the source parameters are available.
+#' @description Adds a record for BSA (Body Surface Area) using the specified derivation
+#' method for each by group (e.g., subject and visit) where the source parameters are
+#' available.
+#'
+#' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
 #' @param dataset Input dataset
 #'
@@ -453,9 +458,11 @@ compute_bsa <- function(height = height,
 
 #' Adds a Parameter for BMI
 #'
-#' Adds a record for BMI/Body Mass Index using Weight and Height each by group
+#' @description Adds a record for BMI/Body Mass Index using Weight and Height each by group
 #' (e.g., subject and visit) where the source parameters are available.
 #'
+#' **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

R/derive_date_vars.R

@@ -1058,7 +1058,10 @@ convert_dtc_to_dtm <- function(dtc,
 
 #' Convert a Date into a Datetime Object
 #'
-#' Convert a date (datetime, date, or date character) into a Date vector (usually `'--DTM'`).
+#' @description Convert a date (datetime, date, or date character) into a Date
+#' vector (usually `'--DTM'`).
+#'
+#' **Note:** This is a wrapper function for the function `convert_dtc_to_dtm()`.
 #'
 #' @param dt The date to convert.
 #'

R/derive_merged.R

@@ -448,8 +448,11 @@ derive_var_merged_cat <- function(dataset,
 
 #' Merge an Existence Flag
 #'
-#' Adds a flag variable to the input dataset which indicates if there exists at
-#' least one observation in another dataset fulfilling a certain condition.
+#' @description Adds a flag variable to the input dataset which indicates if
+#' there exists at least one observation in another dataset fulfilling a certain
+#' condition.
+#'
+#' **Note:** This is a wrapper function for the more generic `derive_vars_merged()`.
 #'
 #' @param dataset_add Additional dataset
 #'
@@ -811,7 +814,9 @@ get_not_mapped <- function() {
 
 #' Merge a Summary Variable
 #'
-#' Merge a summary variable from a dataset to the input dataset.
+#' @description Merge a summary variable from a dataset to the input dataset.
+#'
+#' **Note:** This is a wrapper function for the more generic `derive_vars_merged`.
 #'
 #' @param dataset Input dataset
 #'

R/derive_param_doseint.R

@@ -1,8 +1,10 @@
 #' Adds a Parameter for Dose Intensity
 #'
-#' Adds a record for the dose intensity for each by group
+#' @description Adds a record for the dose intensity for each by group
 #' (e.g., subject and visit) where the source parameters are available.
 #'
+#' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
+#'
 #' The analysis value of the new parameter is derived as
 #' Total Dose / Planned Dose * 100
 #'

R/derive_param_tte.R

@@ -809,9 +809,11 @@ tte_source <- function(dataset_name,
 
 #' Create an `event_source` Object
 #'
-#' `event_source` objects are used to define events as input for the
+#' @description `event_source` objects are used to define events as input for the
 #' `derive_param_tte()` function.
 #'
+#' **Note:** This is a wrapper function for the more generic `tte_source()`.
+#'
 #' @inheritParams tte_source
 #'
 #'
@@ -854,9 +856,11 @@ event_source <- function(dataset_name,
 
 #' Create a `censor_source` Object
 #'
-#' `censor_source` objects are used to define censorings as input for the
+#' @description `censor_source` objects are used to define censorings as input for the
 #' `derive_param_tte()` function.
 #'
+#' **Note:** This is a wrapper function for the more generic `tte_source()`.
+#'
 #' @inheritParams tte_source
 #'
 #'

R/derive_var_base.R

@@ -1,6 +1,8 @@
 #' Derive Baseline Variables
 #'
-#' Derive baseline variables, e.g. `BASE` or `BNRIND`, in a BDS dataset
+#' @description Derive baseline variables, e.g. `BASE` or `BNRIND`, in a BDS dataset.
+#'
+#' **Note:** This is a wrapper function for the more generic `derive_vars_merged()`.
 #'
 #' @param dataset The input dataset
 #'

R/derive_var_extreme_date.R

@@ -258,8 +258,10 @@ derive_var_extreme_dtm <- function(dataset,
 
 #' Derive First or Last Date from Multiple Sources
 #'
-#' Add the first or last date from multiple sources to the dataset, e.g.,
-#' the last known alive date (`LSTALVDT`).
+#' @description Add the first or last date from multiple sources to the
+#' dataset, e.g., the last known alive date (`LSTALVDT`).
+#'
+#' **Note:** This is a wrapper function for the function `derive_var_extreme_dtm()`.
 #'
 #' @inheritParams derive_var_extreme_dtm
 #'

R/derive_var_last_dose_amt.R

@@ -1,6 +1,8 @@
 #' Derive Last Dose Amount
 #'
-#' Add a variable for dose amount from the last dose to the input dataset.
+#' @description Add a variable for dose amount from the last dose to the input dataset.
+#'
+#' **Note:** This is a wrapper function for the function `derive_vars_last_dose()`.
 #'
 #' @description
 #' `r lifecycle::badge("deprecated")`

R/derive_var_last_dose_date.R

@@ -1,6 +1,9 @@
 #' Derive Last Dose Date-Time
 #'
-#' Add a variable for the dose date or datetime of the last dose to the input dataset.
+#' @description Add a variable for the dose date or datetime of the last dose to
+#' the input dataset.
+#'
+#' **Note:** This is a wrapper function for the function `derive_vars_last_dose()`.
 #'
 #' @description
 #' `r lifecycle::badge("deprecated")`

R/derive_var_last_dose_grp.R

@@ -1,6 +1,9 @@
 #' Derive Last Dose with User-Defined Groupings
 #'
-#' Add a variable for user-defined dose grouping of the last dose to the input dataset.
+#' @description Add a variable for user-defined dose grouping of the last dose
+#' to the input dataset.
+#'
+#' **Note:** This is a wrapper function for the function `derive_vars_last_dose()`.
 #'
 #' @description
 #' `r lifecycle::badge("deprecated")`

R/derive_var_trtdurd.R

@@ -1,6 +1,8 @@
 #' Derive Total Treatment Duration (Days)
 #'
-#' Derives total treatment duration (days) (`TRTDURD`)
+#' @description Derives total treatment duration (days) (`TRTDURD`).
+#'
+#' **Note:** This is a wrapper function for the more generic `derive_vars_duration()`.
 #'
 #' @param dataset Input dataset
 #'

R/derive_vars_aage.R

@@ -1,6 +1,8 @@
 #' Derive Analysis Age
 #'
-#' Derives analysis age (`AAGE`) and analysis age unit (`AAGEU`)
+#' @description Derives analysis age (`AAGE`) and analysis age unit (`AAGEU`).
+#'
+#' **Note:** This is a wrapper function for the more generic `derive_vars_duration()`.
 #'
 #' @param dataset Input dataset
 #'

R/derive_vars_transposed.R

@@ -98,7 +98,9 @@ derive_vars_transposed <- function(dataset,
 
 #' Derive ATC Class Variables
 #'
-#' Add Anatomical Therapeutic Chemical class variables from `FACM` to `ADCM`
+#' @description Add Anatomical Therapeutic Chemical class variables from `FACM` to `ADCM`.
+#'
+#' **Note:** This is a wrapper function for the more generic `derive_vars_transposed()`.
 #'
 #' @param dataset Input dataset
 #'