ADaM Test Data for the Pharmaverse Family of Packages • pharmaverseadam

Test data (ADaM) for the pharmaverse family of packages

Purpose

To provide a one-stop-shop for ADaM test data in the pharmaverse family of packages.

Package Contents

The ADaM contents of this package is populated by an script that executes the admiral, admiralonco, admiralophtha, admiralvaccine and admiralpeds templates and saves the resulting datasets here. This script can be executed by the package maintainers in two scenarios:

Regularly, upon new releases of these packages;
Ad-hoc, whenever templates in the above packages have been updated but releases are far away in the calendar. In this case, the ADaM datasets are created using a development version of the templates.

Please check the Changelog to see the versions of the packages used to generate the ADaM datasets in current or past version of pharmaverseadam. Please see the Dataset Creation and Documentation Process for details on the script.

Installation

The package is available from CRAN and can be installed by running install.packages("pharmaverseadam"). To install the latest development version of the package directly from GitHub use the following code:

if (!requireNamespace("remotes", quietly = TRUE)) {
      install.packages("remotes")
    }

remotes::install_github("pharmaverse/pharmaverseadam", ref = "main")

Dataset Creation and Documentation Process

The execution of the ADaM templates and creation of the package documentation in pharmaverseadam is semi-automated for consistency and ease of maintenance. Metadata for each dataset such as names, labels, descriptions, authors, and sources, is managed in a centralized XLSX file (inst/extdata/adams-specs.xlsx) and used to generate .R documentation files. These are then used to populate the reference pages in the package documentation.

The workflow consists of two main steps:

1. Metadata Preparation

Firstly, the user reviews inst/extdata/adams-specs.xlsx and ensures its contents is up-to-date. If a new template has been added to an existing package, or if a new extension package has been created whose ADaM templates they wish to execute in pharmaverseadam, then the user should update adams-specs.xlsx with specifications for the new dataset(s). Note that any missing metadata fields will be set by default to “No label/description/source available.”

2. Execute `create_adams_data.R`

Secondly, the user runs data-raw/create_adams_data.R. This script handles the installation of each package, the execution of the templates, the saving of the ADaM datasets and the creation of the documentation pages.

Script steps

Save specs as JSON
The script saves the specs stored in inst/extdata/adams-specs.xlsx as a JSON file located here: inst/extdata/adams-specs.json. This is so that the specs themselves, as well as any diffs across commits, are easily viewable on Github and R Studio.
Installs Required Packages
The script installs the following packages:
- admiral
- admiralonco
- admiralophtha
- admiralvaccine
- admiralpeds
- pharmaversesdtm By default, the latest development versions of each package will be used, but the user can also select a different version instead (e.g. a released version) with which to refresh pharmaverseadam. The user may also deselect some packages whose templates they do not wish to run. If a new extension package has been created, this should be added to the script in each relevant section (see the script itself for more details).
Executes Templates from Each Package
Processes and Saves Datasets into {pharmaverseadam}
Generates Dataset Documentation
For every dataset, a matching .R file is created in the R/ folder containing:
- Dataset name and title,
- Variable-level documentation (names and labels),
- Source information indicating which template and package generated it,
- Example usage with data("<dataset>").

pharmaverseadam