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First Publicly Available R-Based Submission Package Submitted to FDA (Pilot 3)

By September 11, 2023Announcement, Blog

The R Consortium is pleased to announce that on August 28, 2023, the R Submissions Working Group successfully submitted an R-based test submission pilot 3 package through the FDA eCTD gateway! The FDA CDER staff are now able to begin their evaluation process. All submission materials can be found at: 

The pilot 3 test submission is an example of an all R submission package following eCTD specifications. These include the installation and loading of the proprietary {pilot3} R package and other open-source R packages, R scripts for the analysis data model (ADaM) datasets from pilot 3 and tables, listings, figures (TLFs) from pilot 1, analysis data reviewer’s guide (adrg), and other required eCTD components. To our knowledge, this is the first publicly available R-based FDA submission package, which includes R scripts to generate ADaM datasets and TLFs. We hope this submission package and our learnings can serve as a good reference for future R-based regulatory submissions from different sponsors. Additional agency feedback will be shared in future communications.  For any future questions, you may contact the pilot 3 team here:

The working group also began working on a pilot 4 project to explore the use of novel technologies such as Linux containers and WebAssembly software to bundle a Shiny application into a self-contained package in order to facilitate a smoother process for transferring and executing the application. Stay tuned for more about pilot 4 in the future.

For past announcements on pilot 1 and pilot 2, see below.

Announcement of the R Consortium R submission pilot 1:

Announcement of the R Consortium R submission pilot 2, an R based test submission with a shiny component:

About the R consortium R submission working group

The R Consortium R Submissions Working Group is focused on improving practices for R-based clinical trial regulatory submissions.

To bring an experimental clinical product to market, electronic submission of data, computer programs, and relevant documentation is required by health authority agencies from different countries. In the past, submissions have been mainly based on the SAS language. 

In recent years, the use of open source languages, especially the R language, has become very popular in the pharmaceutical industry and research institutions. Although the health authorities accept submissions based on open source programming languages, sponsors may be hesitant to conduct submissions using open source languages due to a lack of working examples.

Therefore, the R Consortium R Submissions Working Group aims at providing R-based submission examples and identifying potential gaps during submission of these example packages. All materials, including submission examples and communications, are publicly available on the R consortium Github page:

The R consortium R submission working group includes members from more than 10 pharmaceutical companies, as well as regulatory agencies. More details of the working group can be found at:

The R consortium R submission working group is open to anyone who is interested in joining. If interested, please contact Joseph Rickert at