MicrobiomeStat is an R package for statistical analysis and visualization of microbiome and multi-omics data.
R/: package implementation.man/: generated Rd documentation.tests/testthat/: regression and unit tests.vignettes/: end-user long-form documentation.data/: packaged example datasets.inst/: installed assets, templates, external example files, and pkgdown source assets.dev/: developer-only scripts and benchmarks that are tracked in Git but excluded from package builds.docs/: generated pkgdown site committed for GitHub Pages.
- Keep package-shipping content in standard R package directories only.
- Keep reusable developer automation and reproducibility helpers under
dev/. - Keep large benchmark inputs outside the Git repository in the sibling workspace directory
../datasets/. - Keep throwaway local exploration outside the package tree in
../scratch/.
The Hackathon benchmark harness lives in dev/hackathon/. Those scripts resolve paths relative to themselves and expect the following workspace layout:
MicrobiomeStat/
├── repo/
└── datasets/
└── benchmark_data/
├── Hackathon/
└── results/
See dev/README.md and dev/hackathon/README.md for the developer-facing workflow.