TipLabels {TreeTools}

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 'MixedBase'
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 ([e-mail])

See Also

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

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

Examples

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

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

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