esubdemo

Overview

esubdemo is a demo project to illustrate how to organize analysis scripts in an R package folder structure.

The demo project follows the concepts discussed in:

• Marwick, B., Boettiger, C., & Mullen, L. (2018). Packaging data analytical work reproducibly using R (and friends). The American Statistician, 72(1), 80-88.
• Wu, P., Palukuru, U. P., Luo, Y., Nepal, S., & Zhang, Y. (2021) Analysis and reporting in regulated clinical trial environment using R. PharmaSUG 2021
• R for Clinical Study Reports and Submission

Folder Structure

By using an R package folder structure and the associated development tools, we are able to achieve:

• Consistency
• Automation
• Reproducibility
• Compliance

Below are the minimal sufficient folders and files leveraging the R package folder structure.

• *.Rproj: RStudio project file for opening the project.
• DESCRIPTION: Metadata for a package including authors, license, dependencies, etc.
• vignettes/: Analysis scripts using R Markdown.
• R/: Project-specific R functions.
• man/: Manual of project-specific R functions.

There are additional folders and files required in this demo for an analysis project.

People may use different folder names as it is not a standard R package folder. These folders and files often need to be added in .Rbuildignore to pass automated checking.

• vignettes/data-adam/: ADaM datasets in .sas7bdat format.
  • One may also put it in inst/extdata/ following R package convention
  • In reality, we suggest to have real data saved outside of this project (e.g., in a database)
• vignettes/tlf/: TLF outputs
• renv.lock and renv/: R package management using the renv package (introduction).
• _pkgdown.yml: pkgdown configuration file
• .Rprofile: Project startup file to setup running environment including R version, package repository, folder paths, etc.
  • We further use inst/startup.R and R/zzz.R to ensure the startup file is executed both when running devtools::load_all() and running regular build & reload.