rsomics-phydiv

Generalized phylogenetic alpha-diversity from a feature count table and a rooted Newick tree. Computes the McCoy & Matsen balance-weighted PD family (BWPD): the rooted/unrooted choice and the abundance-weighting exponent θ are both exposed, so a single binary covers Faith's PD, unrooted PD, and the weighted variants.

Faith's PD (rooted, unweighted) has its own crate, rsomics-faith-pd; this is the superset operation.

Usage

rsomics-phydiv counts.tsv --tree tree.nwk                       # rooted Faith's PD (auto)
rsomics-phydiv counts.tsv --tree tree.nwk --unrooted            # unrooted PD
rsomics-phydiv counts.tsv --tree tree.nwk --weight 1            # rooted, fully weighted
rsomics-phydiv counts.tsv --tree tree.nwk --unrooted --weight 0.25   # BWPD_0.25

The table is feature-by-sample TSV (first column feature IDs, header row sample names). Output is sample<TAB>phydiv, one row per sample.

--rooted / --unrooted override the default, which follows scikit-bio: rooted iff the tree's root is bifurcating. --weight is 0 (unweighted), 1 (fully weighted), or a θ in (0, 1) for partial weighting.

Origin

This crate is an independent Rust reimplementation of scikit-bio's skbio.diversity.alpha.phydiv based on:

• The published methods: Faith 1992 (DOI 10.1016/0006-3207(92)91201-3), McCoy & Matsen 2013 balance-weighted PD (DOI 10.7717/peerj.157), and the array-form node-abundance formulation of Hamady, Lozupone & Knight 2010 (DOI 10.1038/ismej.2009.97).
• The scikit-bio source (BSD-3-Clause), which was read and cited for the exact rooted-vs-unrooted branch selection, the 2·min(p, 1−p) balance fold, the θ-power semantics (skipped at θ=0 and θ=1), and the missing-length-as-zero convention.

Compatibility is value-exact against scikit-bio 0.7.2 within 1e-9 (deterministic branch-length summation weighted by closed-form node abundances).

License: MIT OR Apache-2.0. Upstream credit: scikit-bio (BSD-3-Clause).