phylo_betapart: Phylogenetic beta diversity partition

Description Usage Arguments Value

View source: R/pd.R

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

1
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/dli55 documentation built on Jan. 28, 2018, 3:48 a.m.