TreeTools: TipLabels – R documentation

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TipLabels

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 '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)

Examples

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

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

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

TreeTools

Create, Modify and Analyse Phylogenetic Trees

v1.4.4

GPL (>= 3)

Authors

Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)

Initial release