phy_struct: Calculate phylogenetic structure matrix

In boydorr/RDiversity: Measurement and Partitioning of Similarity-Sensitive Biodiversity

Calculate phylogenetic structure matrix

Description

Converts an object into class phylo into class phy_struct.

Usage

phy_struct(tree, partition)

Arguments

tree	object of class phylo
partition	two-dimensional matrix of mode numeric with rows as types (species), columns as subcommunities, and each element containing the relative abundance of types in each subcommunity relative to the metacommunity as a whole. In the phylogenetic case, this corresponds to the proportional abundance of historical species, which is calculated from the proportional abundance of terminal taxa

Value

phy_struct() returns a list containing:

$structure	- each row denotes historical species, columns denote terminal taxa, and elements contain 'branch lengths'
$tbar - the average distance from root to tip for all terminal taxa
$parameters	- information associated with each historical species
$tree	- object of class phylo

boydorr/RDiversity documentation built on May 6, 2022, 10:55 a.m.