R: Drop tips from tree

DropTip {TreeTools} | R Documentation

## Drop tips from tree

### Description

`DropTip()` removes specified tips from a phylogenetic tree, collapsing incident branches.

### Usage

    DropTip(tree, tip, preorder = TRUE)

    ## S3 method for class 'phylo'
    DropTip(tree, tip, preorder = TRUE)

    ## S3 method for class 'multiPhylo'
    DropTip(tree, tip, preorder = TRUE)

    KeepTip(tree, tip, preorder = TRUE)

### Arguments

`tree` | A tree of class `phylo`.
`tip` | Character vector specifying labels of leaves in tree to be dropped, or integer vector specifying the indices of leaves to be dropped. Specifying the index of an internal node will drop all descendants of that node.
`preorder` | Logical specifying whether to Preorder the tree before dropping tips. Necessary if a tree's edges may be unconventionally numbered.

### Details

This function is more robust than `ape::drop.tip()` as it does not require any particular internal node numbering schema.

### Value

`DropTip()` returns a tree of class `phylo`, with the requested leaves removed.

`KeepTip()` returns `tree` with all leaves not in `tip` removed, in preorder.

### Author(s)

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

### See Also

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

### Examples

    tree <- BalancedTree(8)
    plot(tree)
    plot(DropTip(tree, c('t4', 't5')))

[Package TreeTools version 1.5.1 Index]