Renumber: Renumber a tree's nodes and tips

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

Renumber a tree's nodes and tips

Description

Renumber() numbers the nodes and tips in a tree to conform with the phylo standards.

Usage

Renumber(tree)

Arguments

tree	A tree of class phylo.

Details

The ape class phylo is not formally defined, but expects trees' internal representation to conform to certain principles: for example, nodes should be numbered sequentially, with values increasing away from the root.

Renumber() attempts to reformat any tree into a representation that will not cause ape functions to produce unwanted results or to crash R.

Value

Renumber() returns a tree of class phylo, numbered in a Cladewise fashion consistent with the expectations of ape functions.

Author(s)

Martin R. Smith ([e-mail])

See Also

Preorder() provides a faster and simpler alternative, but also rotates nodes.

Other tree manipulation: AddTip(), CollapseNode(), ConsensusWithout(), DropTip(), EnforceOutgroup(), ImposeConstraint(), KeptPaths(), KeptVerts(), LeafLabelInterchange(), MakeTreeBinary(), RenumberTips(), RenumberTree(), RootTree(), SortTree(), Subtree(), TipTimedTree(), TrivialTree

Examples

tree <- RandomTree(letters[1:10])
Renumber(tree)

TreeTools documentation built on Sept. 11, 2024, 8:27 p.m.