bayesian-reproducible-file-structure

project
|- DESCRIPTION          # project metadata and dependencies
|- README.md            # top-level description of content and guide to users
|- NAMESPACE            # exports R functions in the package for repeated use
|- LICENSE              # specify the conditions of use and reuse of the code, data & text
|- data/                # raw data, not changed once created
|  +- my_data.csv       # data files in open formats such as TXT, CSV, TSV, etc.
|
|- analysis/            # Series of folders for each step of the analysis
|  +- 01_tidy/          # Tidying scripts
|     +- 01_tidy.Rmd
|  +- 02_fit/           # model fitting scripts
|     +- 02_fit.Rmd
|  +- 03_process/       # Model processing scripts
|     +- 03_process.Rmd
|  +- 04_paper/         # Paper - which pulls code from
|     +- 04_paper.Rmd
|  +- 05_diagnostics/
|     +- 05_diagnostics.Rmd
|  +- Makefile          # builds a PDF/HTML/DOCX file from the Rmd, code, and data files
|
| - analysis_output/    # folder for the 
|   +- 01_tidy_output/
|   +- 02_fit_output/
|   +- 03_process_output/
|   +- 04_paper_output/
|   +- 05_diagnostics_output/
|
|- R/
|  +- my_functions.R    # custom R functions that are used more than once throughout the project
|
|- man/
|  +- my_functions.Rd   # documentation for the R functions (auto-generated when using devtools)
|
| Things that I don't have implemented yet...
|
|- tests/
|  +- testthat.R        # unit tests of R functions to ensure they perform as expected
|- .travis.yml          # continuous integration service hook for auto-testing at each commit
|- dockerfile           # makes a custom isolated computational environment for the project


With making this more general, it could be a good idea to describe how this sort of file along with the make file could be sent to a HPC facility, or AWS or similar.