phytools: multiRF – R documentation

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multiRF

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 argumenet 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 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.

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19