phy2branch {rdiversity}

Phylogenetic similarity

Description

Packages all inputs into an object of class similarity.

Usage

phy2branch(tree, partition, depth = 1)

Arguments

tree

object of class phylo.

partition

two-dimensional matrix of mode numeric with rows as types (terminal taxa), columns as subcommunities, and each element containing the relative abundance of types in each subcommunity relative to the metacommunity as a whole.

depth

proportion of total tree height to be conserved (taken as a proportion from the highest tip). Describes how much evolutionary history should be retained, with 0 marking the date of the most recent tip, and 1 (the default) marking the most recent common ancestor. Numbers greater than 1 extend the root of the tree.

Value

phy2branch() returns an object of class similarity.