MRCA: MRCA

In phylobase: Base Package for Phylogenetic Structures and Comparative Data

Description

Most Recent Common Ancestor (MRCA) of 2 or more nodes.

Usage

MRCA(phy, ...)

## S4 method for signature 'phylo4'
MRCA(phy, ...)

## S4 method for signature 'phylo'
MRCA(phy, ...)

Arguments

phy	a phylogenetic tree in phylo4, phylo4d or phylo format.
...	a vector of nodes

Details

Given some nodes (i.e., tips and/or internal), this function returns the node corresponding to the most recent common ancestor.

If phy is a phylo4 or phylo4d object, the nodes can contain both numeric or character values that will be used by getNode to retrieve the correct node. However, if phy is a phylo object, the nodes must be a numeric vector.

With phylo4 and phylo4d objects, if a single node is provided, it will be returned.

Value

the node corresponding to the most recent common ancestor

Examples

  data(geospiza)
  MRCA(geospiza, 1, 5)
  MRCA(geospiza, "fortis", 11)
  MRCA(geospiza, 2, 4, "fusca", 3)
  geo <- as(geospiza, "phylo")
  MRCA(geo, c(1,5))

Example output

N21 
 21 
N18 
 18 
N17 
 17 
Warning messages:
1: In asMethod(object) : losing data while coercing phylo4d to phylo
2: In asMethod(object) : trees with unknown order may be unsafe in ape
[1] 21

phylobase documentation built on March 26, 2020, 7:44 p.m.