# drop.tip

##### Remove Tips in a Phylogenetic Tree

`drop.tip`

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

does the opposite operation (i.e., returns the induced tree).

`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), collapse.singles = TRUE,
interactive = FALSE)
keep.tip(phy, tip)
extract.clade(phy, node, root.edge = 0, collapse.singles = TRUE,
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).

- collapse.singles
a logical specifying whether to delete the internal nodes of degree 2.

- 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

```
# NOT RUN {
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 5.3, License: GPL (>= 2)*