MicrobiomeStat

MicrobiomeStat is an R package for statistical analysis and visualization of microbiome and multi-omics data.

Repository Layout

• 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.

Organizing Principles

• 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/.

Benchmarks

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.