mpd: Mean pairwise distance

In mtalluto/mbm: Multifaceted Biodiversity Modelling

Description

Mean pairwise distance

Usage

mpd(comm, phylogeny, dis, dis.transform)

Arguments

comm	Community matrix giving sites (rows) by species (columns). Column names should match the names in the phylogeny
phylogeny	Phylogeny in the format used by ape; if missing dis is required
dis	Species distance matrix; if missing will be extracted from the phylogeny
dis.transform	Function (e.g., sqrt) to transform distance before computing mpd

Details

Computes mean pairwise distance (MPD) for all site pairs (including within and between site MPD)

Value

Matrix of pairwise distances; diagonal is witin site (alpha) MPD, other values are pairwise distances (beta MPD)

mtalluto/mbm documentation built on Aug. 13, 2019, 9:43 a.m.