R: Extract tip labels

TipLabels {TreeTools} | R Documentation

## Extract tip labels

### Description

`TipLabels()` extracts labels from an object: for example, names of taxa in a phylogenetic tree or data matrix. `AllTipLabels()` extracts all labels, where entries of a list of trees may pertain to different taxa.

### Usage

    TipLabels(x, single = TRUE)

    ## S3 method for class 'matrix'
    TipLabels(x, single = TRUE)

    ## S3 method for class 'phylo'
    TipLabels(x, single = TRUE)

    ## Default S3 method:
    TipLabels(x, single = TRUE)

    ## S3 method for class 'phyDat'
    TipLabels(x, single = TRUE)

    ## S3 method for class 'TreeNumber'
    TipLabels(x, single = TRUE)

    ## S3 method for class 'Splits'
    TipLabels(x, single = TRUE)

    ## S3 method for class 'list'
    TipLabels(x, single = FALSE)

    AllTipLabels(x)

    ## S3 method for class 'list'
    AllTipLabels(x)

    ## S3 method for class 'multiPhylo'
    AllTipLabels(x)

    ## S3 method for class 'phylo'
    AllTipLabels(x)

    ## S3 method for class 'Splits'
    AllTipLabels(x)

    ## S3 method for class 'TreeNumber'
    AllTipLabels(x)

    ## S3 method for class 'matrix'
    AllTipLabels(x)

    ## S3 method for class 'multiPhylo'
    TipLabels(x, single = FALSE)

    ## S3 method for class 'character'
    TipLabels(x, single = TRUE)

    ## S3 method for class 'numeric'
    TipLabels(x, single = TRUE)

    ## S3 method for class 'phyDat'
    TipLabels(x, single = TRUE)

    ## Default S3 method:
    TipLabels(x, single = TRUE)

### Arguments

`x` | An object of a supported class (see Usage section above).
`single` | Logical specifying whether to report the labels for the first object only (`TRUE`), or for each object in a list (`FALSE`).

### Value

`TipLabels()` returns a character vector listing the tip labels appropriate to `x`. If `x` is a single integer, this will be a vector `t1`, `t2` ... `tx`, to match the default of `ape::rtree()`.

### Author(s)

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

### See Also

Other tree properties: `ConsensusWithout()`, `NSplits()`, `NTip()`, `SplitsInBinaryTree()`, `TreeIsRooted()`

Other Splits operations: `LabelSplits()`, `NSplits()`, `NTip()`, `PolarizeSplits()`, `SplitFrequency()`, `SplitsInBinaryTree()`, `Splits`, `TipsInSplits()`, `match()`

### Examples

    TipLabels(BalancedTree(letters[5:1]))
    TipLabels(5)

    data('Lobo')
    head(TipLabels(Lobo.phy))

    AllTipLabels(c(BalancedTree(4), PectinateTree(8)))

[Package TreeTools version 1.5.1 Index]