Appendix C — Technical appendix

Published

Oct 2026

Requirements

R, Quarto, and the packages recorded in root renv.lock. Restore with renv::restore(). The domain uses one shared environment.

Reuse

Both scripts accept optional input and output directories. Run from the repository root. Keep original study data separate from data/example/.

Feature tables must contain integer counts. Metadata must include sample_id and group; taxonomy must include matching feature_id and nonblank taxon. Zero-total samples fail validation.

Scope

The workflow starts from a feature table. It does not process raw reads, assign taxonomy, test group significance, adjust for repeated measures or confounding, or perform differential abundance analysis.

Included preview figures and tables were computed independently with Python. Run the supplied R scripts to regenerate equivalent numerical summaries and R-styled figures. Quarto code fences do not execute analysis.