clade.matrix: Create a clade matrix from a phylogeny

In caper: Comparative Analyses of Phylogenetics and Evolution in R

Create a clade matrix from a phylogeny

Description

Takes a phylogeny in the 'ape' package format and converts it into a binary matrix showing which tips (matrix columns) subtend from each node in the phylogeny (matrix rows). This is a useful format for quickly calculating branch length information for subsets of the phylogeny.

Usage

clade.matrix(phy)

Arguments

phy	A object of class 'phylo'

Details

The clade matrix shows the tips from a phylogeny that subtend from each internal and external node. Each tip is represented as column showing the nodes of which it is a member and hence each row shows the tips that are members of a given node. Dropping columns gives a quick and easy way to find out which edges are retained in a particular subset of the tree and this structure is used for quickly calculating branch lengths calculations or clade statistics.

Value

A list of class 'clade.matrix' containing the following components:

clade.matrix	A binary m x n matrix, where m is the total number of nodes in the phylogeny and n is the number of tips. An element is 1 if tip $n_i$ subtends from a node $m_j$.
edge.length	A numeric vector of length m showing the edge length leading to each node in the phylogeny and named with the node number.
tip.label	A character vector of length n giving the labels assigned to the tips of the phylogeny.
edge	The edge matrix from the original phylogeny.

Author(s)

David Orme

Examples

data(perissodactyla)
clade.matrix(perissodactyla.tree)

caper documentation built on Sept. 26, 2023, 5:10 p.m.