R: Generate a tree with a specific outgroup

EnforceOutgroup {TreeTools} | R Documentation

## Generate a tree with a specific outgroup

### Description

Given a tree or a list of taxa, `EnforceOutgroup()` rearranges the ingroup and outgroup taxa such that the two are sister taxa across the root, without changing the relationships within the ingroup or within the outgroup.

### Usage

    EnforceOutgroup(tree, outgroup)

    ## S3 method for class 'phylo'
    EnforceOutgroup(tree, outgroup)

    ## S3 method for class 'character'
    EnforceOutgroup(tree, outgroup)

### Arguments

`tree` | Either a tree of class `phylo`; or (for `EnforceOutgroup()`) a character vector listing the names of all the taxa in the tree, from which a random tree will be generated.
`outgroup` | Character vector containing the names of taxa to include in the outgroup.

### Value

`EnforceOutgroup()` returns a tree of class `phylo` where all outgroup taxa are sister to all remaining taxa, without modifying the ingroup topology.

### Author(s)

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

### See Also

For a more robust implementation, see `RootTree()`, which will eventually replace this function (#30).

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

### Examples

    tree <- EnforceOutgroup(letters[1:9], letters[1:3])
    plot(tree)

[Package TreeTools version 1.3.1 Index]