The objective of the R Consortium R submission pilot 1 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 a FDA-industry collaboration through the non-profit organization R Consortium.
The RConsortium/submissions-pilot1 repo demonstrates an approach to organize internal developed R functions and tables, listings, and figures (TLFs) generation programs using an R package.
The project is developed and tested in the environment below:
The work in this repo is organized as an R package following the concepts discussed in:
More details related to organize a clinical project and submission package can be found in Chapter 10–15 of the R for Clinical Study Reports and Submission book.
In short, the project is organized as an R package.
pilot1wrappers.Rproj: RStudio project file used to open the project.
DESCRIPTION: Metadata for a package including authors, license, dependency, etc.
vignettes/: Analysis scripts using R Markdown.
R/: Project-specific R functions.
man/: Manual of project-specific R functions.
The source dataset is in the
adam/ folder. The original data is from the PHUSE Github repository.
inst/startup.R: The primary startup file. It configures the running environment, including R version, package repository, folder paths, and other parameters.
.Rprofile: An entry point file ensuring
inst/startup.R execution during development, such as opening the project in RStudio, using
devtools::load_all(), or using RStudio build panel features.
R/zzz.R: Another entry point file, triggering
inst/startup.R during package loading via
The original code is prepared and executed on Ubuntu 20.04.3 LTS. We use renv to ensure reproducibility for R version and R package versions.
renv/ folder: R package management using the renv package. (Introduction)
_pkgdown.yml: pkgdown configuration file.