phylo_betapart: Phylogenetic beta diversity partition

In daijiang/lirrr: Functions collected/wrote by Daijiang Li

Phylogenetic beta diversity partition

Description

Calculate Phylogenetic beta diversity and its partition, adapted from betapart::phylo.belt.xx(). Since the pairwise and multisie version share the same core computation process, it makes more sense to return both. Then we can choose which one to use.

Usage

phylo_betapart(comm = dat_1, tree)

Arguments

comm	A site by species data frame, site names as row names.
tree	A phylogeny of class "phylo".

Value

A list of four: pairwise beta of jaccard and sorense; and multisite beta of jaccard and sorensen. Pairwise beta has three distance matrix. For jaccard, phylo.beta.jtu is the turnover-fraction of Jaccard, phylo.beta.jne is the nestedness-fraction. For sorensen, phylo.beta.sim is the turnover part measured as Simpson derived pairwise dissimilarity, phylo.beta.sne is the nestedness-fraction. Similarly for the multisite version.

daijiang/lirrr documentation built on Feb. 3, 2024, 5:42 p.m.