as.phylo {aphylo}

Extensions to the as.phylo function

Description

This function takes an edgelist and recodes (relabels) the nodes following ape's coding convention.

Usage

## S3 method for class 'matrix'
as.phylo(x, edge.length = NULL, root.edge = NULL, ...)

## S3 method for class 'aphylo'
as.phylo(x, ...)

Arguments

x

Either an edgelist or an object of class aphylo.

edge.length

A vector with branch lengths (optional).

root.edge

A numeric scalar with the length for the root node (optional).

...

Further arguments passed to the method.

Value

An integer matrix of the same dimmension as edges with the following aditional attribute:

labels

Named integer vector of size n. Original labels of the edgelist where the first n are leaf nodes, n+1 is the root node, and the reminder are the internal nodes.

Examples

# A simple example ----------------------------------------------------------
# This tree has a coding different from ape's

mytree <- matrix(c(1, 2, 1, 3, 2, 4, 2, 5), byrow = TRUE, ncol=2)
mytree

ans <- as.phylo(mytree)
ans
plot(ans)