multiRF: Computes Robinson-Foulds distance between a set of trees

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Computes Robinson-Foulds distance between a set of trees

Description

Computes the Robinson-Foulds (Robinson & Foulds 1981) distance between a set of trees in an object of class "multiPhylo".

Usage

multiRF(trees,quiet=FALSE,multi2di=FALSE)

Arguments

trees	object of class "multiPhylo" consisting of two or more fully bifurcating, unrooted trees. If trees are rooted, they will be unrooted.
quiet	logical argument indicating whether or not to run quietly. (Defaults to FALSE.)
multi2di	logical argument indicating whether or not to resolve multifurcating trees. (Defaults to FALSE.)

Details

Computes the Robinson-Foulds distance between all phylogenies in an object of class "multiPhylo". Uses prop.part internally for most of the heavy lifting.

Value

A matrix containing distances.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

Robinson, D. R., Foulds, L. R. (1981) Comparison of phylogenetic trees. Mathematical Biosciences, 53, 131-147.

phytools documentation built on June 22, 2024, 10:39 a.m.