R: Renumber a tree's tips

RenumberTips {TreeTools} | R Documentation

## Renumber a tree's tips

### Description

`RenumberTips(tree, tipOrder)` sorts the tips of a phylogenetic tree `tree` such that the indices in `tree$edge[, 2]` correspond to the order of leaves given in `tipOrder`.

### Usage

    RenumberTips(tree, tipOrder)

    ## S3 method for class 'phylo'
    RenumberTips(tree, tipOrder)

    ## S3 method for class 'multiPhylo'
    RenumberTips(tree, tipOrder)

    ## S3 method for class 'list'
    RenumberTips(tree, tipOrder)

### Arguments

`tree` | A tree of class `phylo`.
`tipOrder` | A character vector containing the values of `tree$tip.label` in the desired sort order, or an object (perhaps of class `phylo` or `Splits`) with tip labels.

### Value

`RenumberTips()` returns `tree`, with the tips' internal representation numbered to match `tipOrder`.

### Author(s)

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

### See Also

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

### Examples

    data('Lobo') # Loads the phyDat object Lobo.phy
    tree <- RandomTree(Lobo.phy)
    tree <- RenumberTips(tree, names(Lobo.phy))

[Package TreeTools version 1.2.0 Index]