ape (version 1.10-2)

drop.tip: 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, subtree = FALSE,
         root.edge = 0)

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.
subtree
a logical specifying whether to output in the tree how many tips have been deleted and where.
root.edge
an integer giving the number of internal branches to be used to build the new root edge. This has no effect if trim.internal = FALSE.

Value

  • an object of class "phylo".

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.

If subtree = TRUE, the returned tree has one or several terminal branches indicating how many tips have been removed (with a label "[x_tips]"). This is done for as many monophyletic groups that have been deleted.

Note that subtree = TRUE implies trim.internal = TRUE.

To undestand how the option root.edge works, see the examples below.

See Also

bind.tree, root

Examples

Run this code
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))
data(bird.orders)
plot(drop.tip(bird.orders, 6:23, subtree = TRUE), font = 1)
plot(drop.tip(bird.orders, c(1:5, 20:23), subtree = TRUE), font = 1)

### Examples of the use of `root.edge'
tr <- read.tree(text = "(A:1,(B:1,(C:1,(D:1,E:1):1):1):1):1;")
drop.tip(tr, c("A", "B"), root.edge = 0) # = (C:1,(D:1,E:1):1);
drop.tip(tr, c("A", "B"), root.edge = 1) # = (C:1,(D:1,E:1):1):1;
drop.tip(tr, c("A", "B"), root.edge = 2) # = (C:1,(D:1,E:1):1):2;
drop.tip(tr, c("A", "B"), root.edge = 3) # = (C:1,(D:1,E:1):1):3;

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