multiRF {phytools}R Documentation

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". If trees contains a large number of phylogenies (say 100 or 1,000) this will be much faster than calling RF.dist in the phangorn package for all pairwise comparisons because it avoids repeating some internal calculations. Nonetheless for large numbers multiRF is slow, and will use lots of memory.

Usage

multiRF(trees)

Arguments

trees

object of class "multiPhylo" consisting of two or more fully bifurcating, unrooted trees. If trees are rooted, they will be unrooted.

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 distance matrix.

Author(s)

Liam Revell liam.revell@umb.edu

References

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

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

[Package phytools version 0.4-60 Index]