make.clade.tree {diversitree}

Make a "Clade Tree"

Description

This function makes a “clade tree”, where tips represent clades. It is designed to make working with unresolved clade information in make.bisse more straightforward. clade.tree objects have their own plotting methods.

Usage

make.clade.tree(tree, clades)
clades.from.polytomies(tree)
clades.from.classification(tree, class, check=TRUE)

Arguments

tree

An ultrametric phylogenetic tree, in ape “phylo” format.

clades

A list, where the name of each element represents a tip in tree and each element is a character vector containing the names of species contained within that clade.

class

A vector along tree$tip.label, indicating the class to which each tip belongs.

check

Logical, indicating whether a (potentially slow) check will be done to ensure that all resulting clades are reciprocally monophyletic within the tree.

Details

The idea here is that make.bisse takes a tree and a named character state vector. If the phylogenetic tree contains information about the membership of clades, then the unresolved clade information can be constructed automatically. The names chosen should therefore reflect the names used in the state information.

Note

Currently, clade.tree objects work poorly with some ape functions.

Author(s)

Richard G. FitzJohn