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Extract tip labels

Source: R/SplitFunctions.R
TipLabels.Rd

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)

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

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

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

# S3 method for class 'phylo'
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)

# 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)

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)

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 rtree().

See also

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

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

Author

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

Examples

TipLabels(BalancedTree(letters[5:1]))
#> [1] "e" "d" "c" "b" "a"
TipLabels(5)
#> [1] "t1" "t2" "t3" "t4" "t5"

data("Lobo")
head(TipLabels(Lobo.phy))
#> [1] "Tubiluchus_Priapulida"  "Cricocosmia"            "Aysheaia"              
#> [4] "Siberion"               "Onychodictyon_ferox"    "Onychodictyon_gracilis"

AllTipLabels(c(BalancedTree(4), PectinateTree(8)))
#> [1] "t1" "t2" "t3" "t4" "t5" "t6" "t7" "t8"