Extract a subtree

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 unpredictably. 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(), ImposeConstraint(), KeptPaths(), KeptVerts(), LeafLabelInterchange(), MakeTreeBinary(), Renumber(), RenumberTips(), RenumberTree(), RootTree(), SortTree(), TipTimedTree(), TrivialTree

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

tree <- Preorder(BalancedTree(8))
plot(tree)
ape::nodelabels()
ape::nodelabels(13, 13, bg="yellow")


plot(Subtree(tree, 13))