phytools (version 1.2-0)

findMRCA: Get the MRCA of a set of taxa

Description

This function returns node number of the most recent common ancestor of a set of taxa. If tips=NULL the function is redundant with mrca (for type="node") or vcv.phylo, but much slower (for type="height").

Usage

findMRCA(tree, tips=NULL, type=c("node","height"))

Value

The node number of the MRCA, or a matrix of node numbers (if tips==NULL) - for type="node"; or the height of the MRCA, or a matrix of heights (if tips==NULL) - for type="height".

Arguments

tree

a phylogenetic tree as an object of class "phylo".

tips

a vector containing a set of tip labels.

type

either "node" to return the node of the MRCA; or "height" to return the height above the root of the MRCA of tips.

Author

Liam Revell

Details

If tips==NULL and type="node" (the default) it will return the result of a normal function call to mrca.

If tips=NULL and type="height" it will return a matrix equal to that produced by vcv.phylo.

From phytools 0.5-66 forward findMRCA uses getMRCA in the ape package internally, which results in a big speed-up. Even though the two functions are thus totally redundant I have left findMRCA in the package to ensure backward compatibility.

References

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

See Also

findMRCA, mrca

Examples

data(anoletree)
anc<-findMRCA(anoletree,c("cristatellus","cooki",
    "gundlachi"))
plotTree(anoletree,type="fan",fsize=0.7,lwd=1)
nodelabels(node=anc,frame="circle",pch=21,cex=1.5,
    bg="blue")
legend("topleft","common ancestor of\nPuerto Rican TG anoles",
	pch=21,pt.cex=1.5,pt.bg="blue",cex=0.7,bty="n")
par(mar=c(5.1,4.1,4.1,2.1)) ## reset margin to default