Collecting all the data!

Where is all the data? An intermittent attempt to continuously compile, collate, consolidate, and curate publicly available CDISC data useful for Clinical Reporting in R
SDTM
ADaM
Community
Technical
Author

Ben Straub

Published

February 17, 2025

The purpose of this blog is to maintain an ongoing list of publicly available data packages, data in packages or data sources that align to CDISC standards. My hope is that this could be a resource for:

The data presented below is just a start and is shown in order of how I found them. Feel free to get in touch with me for additions or clarifications. You can find me on pharmaverse slack by joining here. In fact, I encourage, nay implore you, to get in touch as this can’t be all the data that we have available to us!

pharmaversesdtm: SDTM Test Data for the Pharmaverse Family of Packages

A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing and developing Analysis Data Model (ADaM) datasets inside the pharmaverse family of packages. A CDISC Pilot was conducted somewhere between 2008 and 2010. This is that Pilot data but slowly brought up to current CDISC standards. There are also new datasets in the same style (same STUDYID, USUBJIDs, etc.) added by the {admiral} and the {admiral} extension package teams that provide test data for new domains or specific TAs (ophthalmology, vaccines, etc.).

Most common SDTM datasets can be found as well as some specific disease area SDTMs that are not available in the CDISC pilot datasets.

Available on CRAN. This package is actively maintained on GitHub

pharmaverseadam: ADaM Test Data for the Pharmaverse Family of Packages

A set of Analysis Data Model (ADaM) datasets constructed using the Study Data Tabulation Model (SDTM) datasets contained in the {pharmaversesdtm} package and the template scripts from the {admiral} family of packages.

Available on CRAN. This package is actively maintained on GitHub

admiral: ADaM in R Asset Library

A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the “Analysis Data Model Implementation Guide.

Limited datasets like ADSL, ADLB are provided in {admiral} , because the template scripts available in this package are used to create the ADaMs in {pharmaverseadam} .

Available on CRAN. This package is actively maintained on GitHub.

random.cdisc.data: Create Random ADaM Datasets

A set of functions to create random Analysis Data Model (ADaM) datasets and cached datasets. You can find a list of the possible random CDISC datasets generated here. ADaM dataset specifications are described by the Clinical Data Interchange Standards Consortium (CDISC) Analysis Data Model Team. These datasets are used to power the TLG Catalog, though the NEST team is actively substituting them for {pharmaverseadam} datasets instead - see a recent blog post about this very effort!

Available on CRAN. The package is actively maintained on GitHub by the NEST team.

safetyData: Clinical Trial Data

The package re-formats PHUSE’s sample ADaM and SDTM datasets as an R package following R data best practices.

PHUSE released the data under the permissive MIT license, so reuse with attribution is encouraged. The data are especially useful for prototyping new tables, listings and figures and for writing automated tests.

Basic documentation for each data file is provided in help files (e.g. ?adam_adae). Full data specifications in the form of define.xml files can also be found at the links above (pdf for ADaM and pdf for SDTM).

Available on CRAN. The package is available on GitHub.

NEST: Accelerating Clinical Reporting

NEST is a collection of open-sourced R packages, which enables faster and more efficient insights generation under clinical research settings, for both exploratory and regulatory purposes.

They have a wealth of data generated for documentation, demonstrations and testing. You can find all the datasets and what packages they live in here.

Collect all the data!

As you can see the list is short! Let me know if you have sources (big and small) and we can add to this list.

Last updated

2025-02-17 17:27:35.060369

Details

Source, Session info

Reuse

Citation

BibTeX citation:
@online{straub2025,
  author = {Straub, Ben},
  title = {Collecting All the Data!},
  date = {2025-02-17},
  url = {https://pharmaverse.github.io/blog/posts/2025-02-17_data__packages/data__packages.html},
  langid = {en}
}
For attribution, please cite this work as:
Straub, Ben. 2025. “Collecting All the Data!” February 17, 2025. https://pharmaverse.github.io/blog/posts/2025-02-17_data__packages/data__packages.html.