TreeTools (version 1.4.2)

Subtree: Extract a subtree

Description

Subtree() safely extracts a clade from a phylogenetic tree.

Usage

Subtree(tree, node)

Arguments

tree

A tree of class phylo, with internal numbering in cladewise order (use Preorder(tree) or (slower) Cladewise(tree)) .

node

The number of the node at the base of the clade to be extracted.

Value

Subtree() returns a tree of class phylo that represents a clade extracted from the original tree.

Details

Modified from the ape function extract.clade, which sometimes behaves erratically. Unlike extract.clade, this function supports the extraction of 'clades' that constitute a single tip.

See Also

Other tree manipulation: AddTip(), CollapseNode(), ConsensusWithout(), DropTip(), EnforceOutgroup(), LeafLabelInterchange(), MakeTreeBinary(), RenumberTips(), RenumberTree(), Renumber(), RootTree(), SingleTaxonTree(), SortTree()

Examples

# NOT RUN {
tree <- Preorder(BalancedTree(8))
plot(tree)
ape::nodelabels()
ape::nodelabels(13, 13, bg='yellow')

plot(Subtree(tree, 13))

# }