R: Extract a subtree

Subtree {TreeTools} | R Documentation

## Extract a subtree

### Description

`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.

### Details

Modified from the ape function `extract.clade`, which sometimes behaves erratically. Unlike extract.clade, this function supports the extraction of 'clades' that constitute a single tip.

### Value

`Subtree()` returns a tree of class `phylo` that represents a clade extracted from the original tree.

### Author(s)

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

### See Also

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

### Examples

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

    plot(Subtree(tree, 13))

[Package TreeTools version 1.2.0 Index]