Do not include README.md, batch_copy.sh and .gitignore files into the final submission.

Overview

The objective of the R Consortium R Submission Pilot 3 Project is to test the concept that an R-language based submission package can meet the needs and the expectations of the FDA reviewers, including assessing code review and analyses reproducibility. All submission materials and communications from this pilot are publicly available, with the aim of providing a working example for future R-language based FDA submissions. This is an FDA-industry collaboration through the non-profit organisation R Consortium.

The RConsortium/submissions-pilot3-adam-to-fda repo demonstrates the eCTD submission package based on the RConsortium/submissions-pilot3-adam repo.

The RConsortium/submissions-pilot3-adam repo demonstrates an approach to organise an R-language based submission, including ADaMs, tables and figures. This is supported by internally-developed R functions, contained within an R package in the RConsortium/submissions-pilot3-utilities repo.

To learn more about other pilots, visit the R Consortium R Submission Working Group website and the R Consortium Working Groups webpage.

FDA Response

• Initial submission
  • version: [v0.1.0] (link TBC)
  • Cover letter (Draft version)

Re-run analysis

To re-run analysis, you can follow the steps described in the [ADRG] (link TBC) based on the programs saved in module 5.

Folder Structure

The folder is organized as a demo eCTD package following ICH guidance.

eCTD package:

• m1/: module 1 of the eCTD package

m1
└── us
    ├── cover-letter.pdf  # Submission cover letter
    └── report-tlf-pilot3.pdf    # Submission TLFs 

Note: the TLF format in report-tlf.pdf is not consistent, because it reflects different table layouts in different organizations.

• m5/: module 5 of the eCTD package

m5
└── datasets
    └── rconsortiumpilot3
        ├── tabulations
        |   └── sdtm
        |       ├── blankcrf.pdf
        |       ├── define-v1-updated-html.xsl
        |       ├── define.pdf
        |       ├── define.xml
        |       ├── ae.xpt                      # SDTM datasets in XPT format
        |       ├── cm.xpt
        |       ├── dm.xpt
        |       ├── ds.xpt
        |       ├── ex.xpt
        |       ├── lb.xpt
        |       ├── mh.xpt
        |       ├── qs.xpt
        |       ├── relrec.xpt
        |       ├── sc.xpt
        |       ├── se.xpt
        |       ├── suppae.xpt
        |       ├── suppdm.xpt
        |       ├── suppds.xpt
        |       ├── supplb.xpt
        |       ├── sv.xpt
        |       ├── ta.xpt
        |       ├── te.xpt
        |       ├── ti.xpt
        |       ├── ts.xpt
        |       ├── tv.xpt
        |       └── vs.xpt
        └── analysis
            └── adam
                ├── datasets
                |   ├── ADaM - Pilot 3.xlsx
                |   ├── define.xml
                |   ├── adrg.pdf
                |   ├── adadas.xpt                    # ADaM datasets in XPT format
                |   ├── adae.xpt
                |   ├── adlbc.xpt
                |   ├── adsl.xpt
                |   ├── adtte.xpt
                |   └── define2-0-0.xsl
                └── programs
                    ├── adadas.R                      # analysis R code for TLFs.   
                    ├── adae.R
                    ├── adlbc.R
                    ├── adsl.R
                    ├── adtte.R
                    ├── tlf-demographic.R
                    ├── tlf-efficacy.R
                    ├── tlf-kmplot.R
                    ├── tlf-primary.R
                    └── renv.lock

Other files: (Do not include in eCTD package)

• .gitignore: git ignore file
• batch_copy.sh: All files required for the eCTD submission are copied from the development repository to the submission repository by a running this batch script, located in the repository's root directory.
• README.md: readme file for github repo

News

Questions

Report issues in https://github.com/RConsortium/submissions-pilot3-adam-to-fda/issues.