The objective of the R Consortium R submission Pilot 1 Project is to test the concept that a 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 function and table, listing, figure generation program 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 RStudio project.
DESCRIPTION: Metadata for a package including authors, license, dependency etc.
vignettes/: Analysis scripts using Rmarkdown.
R/: Project specific R functions.
man/: Manual of project specific R functions.
The source dataset is in
adam\ folder. The original data is from the PHUSE Github Repository
.Rprofile: Project startup file to setup running environment including R version, repository, folder path etc.
R/zzz.Rto allow the startup file is executed while running.
devtools::load_all()and RStudio build panel.
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 version.
renv\folder: R package management using
_pkgdown.yml: pkgdown configuration file.