R: Renumber a tree's nodes and tips

Renumber {TreeTools} | R Documentation

## 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 (martin.smith@durham.ac.uk)

### 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()`, `SingleTaxonTree()`, `SortTree()`, `Subtree()`

### Examples

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

[Package TreeTools version 1.7.0 Index]