# drop.tip

##### Remove Tips in a Phylogenetic Tree

`drop.tip`

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

`extract.clade`

does the inverse operation: it keeps all the tips
from a given node, and deletes all the other tips.

- Keywords
- manip

##### Usage

```
drop.tip(phy, tip, trim.internal = TRUE, subtree = FALSE,
root.edge = 0, rooted = is.rooted(phy), interactive = FALSE)
extract.clade(phy, node, root.edge = 0, interactive = FALSE)
```

##### 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`

. - rooted
- a logical indicating whether the tree must be treated as rooted or not. This allows to force the tree to be considered as unrooted (see examples).
- node
- a node number or label.
- interactive
- if
`TRUE`

the user is asked to select the tips or the node by clicking on the tree which must be plotted.

##### 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.

This also applies to `node`

, but if this argument is character
and the tree has no node label, this results in an error. If more than
one value is given with `node`

(i.e., a vector of length two or
more), only the first one is used with a warning.

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.

##### Value

- an object of class
`"phylo"`

.

##### See Also

##### 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))
data(bird.orders)
plot(drop.tip(bird.orders, 6:23, subtree = TRUE))
plot(drop.tip(bird.orders, c(1:5, 20:23), subtree = TRUE))
plot(drop.tip(bird.orders, c(1:20, 23), subtree = TRUE))
plot(drop.tip(bird.orders, c(1:20, 23), subtree = TRUE, rooted = FALSE))
### 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;
```

*Documentation reproduced from package ape, version 2.6-3, License: GPL (>= 2)*