phangorn (version 1.7-4)

Ancestors: tree utility function

Description

Functions for describing relationships among phylogenetic nodes.

Usage

Ancestors(x, node, type=c("all","parent"))
Children(x, node)
Siblings(x, node, include.self=FALSE)
Descendants(x, node, type=c("tips","children","all"))
mrca.phylo(x, node)

Arguments

x

a tree (a phylo object).

node

an integer or a vector of integers corresponding to a node ID

type

specify whether to return just direct children / parents or all

include.self

whether to include self in list of siblings

Value

• a vector or a list containing the indices of the nodes.

Details

These functions are inspired by treewalk in phylobase package, but work on the S3 phylo objects. The nodes are the indices as given in edge matrix of an phylo object. From taxon labels these indices can be easily derived matching against the tip.label argument of an phylo object, see example below. All the functions allow node to be either a scalar or vector.

See Also

treewalk, phylo

Examples

tree = rtree(10)
plot(tree, show.tip.label = FALSE)
nodelabels()
tiplabels()
Ancestors(tree, 1:3, "all")
Children(tree, 11)
Descendants(tree, 11, "tips")
Siblings(tree, 3)
mrca.phylo(tree, 1:3)
mrca.phylo(tree, match(c("t1", "t2", "t3"), tree$tip))