drop.tip {ape}R Documentation

Remove Tips in a Phylogenetic Tree

Description

This function removes the terminal branches of a phylogenetic tree, possibly removing the corresponding internal branches.

Usage

drop.tip(phy, tip, trim.internal = TRUE)

Arguments

phy an object of class "phylo".
tip a vector of mode numeric or character specifying the tips to delete.
trim.internal a logical specifying whether to delete the corresponding internal branches.

Details

The argument tip can be either character or numeric. In the first case, it gives the labels of the tips to be deleted; in the second case the numbers of these labels in the vector phy$tip.label are given.

If trim.internal = FALSE, the new tips are given "NA" as labels, unless there are node labels in the tree in which case they are used.

Value

an object of class "phylo".

Author(s)

Emmanuel Paradis paradis@isem.univ-montp2.fr

See Also

bind.tree, root, rotate

Examples

data(bird.families)
tip <- c(
"Eopsaltriidae", "Acanthisittidae", "Pittidae", "Eurylaimidae",
"Philepittidae", "Tyrannidae", "Thamnophilidae", "Furnariidae",
"Formicariidae", "Conopophagidae", "Rhinocryptidae", "Climacteridae",
"Menuridae", "Ptilonorhynchidae", "Maluridae", "Meliphagidae",
"Pardalotidae", "Petroicidae", "Irenidae", "Orthonychidae",
"Pomatostomidae", "Laniidae", "Vireonidae", "Corvidae",
"Callaeatidae", "Picathartidae", "Bombycillidae", "Cinclidae",
"Muscicapidae", "Sturnidae", "Sittidae", "Certhiidae",
"Paridae", "Aegithalidae", "Hirundinidae", "Regulidae",
"Pycnonotidae", "Hypocoliidae", "Cisticolidae", "Zosteropidae",
"Sylviidae", "Alaudidae", "Nectariniidae", "Melanocharitidae",
"Paramythiidae","Passeridae", "Fringillidae")
plot(drop.tip(bird.families, tip))
plot(drop.tip(bird.families, tip, trim.internal = FALSE))

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