phytools (version 2.4-4)

fastMRCA: Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa

Description

Finds the most recent common ancestor (MRCA) for a pair of tip taxa.

Usage

fastMRCA(tree, sp1, sp2)
fastHeight(tree, sp1, sp2)
fastDist(tree, sp1, sp2)

Value

The node number of the MRCA, the height above the root (for fastHeight), or the patristic distance between two taxa (for fastDist).

Arguments

tree

an object of class "phylo".

sp1

species one name.

sp2

species two name.

Author

Liam Revell

Details

Function (fastMRCA) returns the most recent common ancestor (node number) for a pair of taxa; or, in the case of fastHeight, the height above the root of the MRCA of a pair of taxa; or, in the case of fastDist, the patristic distance between a pair of taxa.

This function is mostly redundant with findMRCA (or findMRCA(...,type="height") in the case of fastHeight), but for very large trees will be considerably faster.

(Also see getMRCA in the ape package.)

References

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

See Also

getMRCA, findMRCA, mrca

Examples

## simulate 2000-tip tree
tree<-pbtree(n=2000)

## find the MRCA of two randomly chosen tips
tips<-sample(tree$tip.label,2)
anc<-fastMRCA(tree,tips[1],tips[2])