\name{drop.tip}
\alias{drop.tip}
+\alias{extract.clade}
\title{Remove Tips in a Phylogenetic Tree}
\usage{
drop.tip(phy, tip, trim.internal = TRUE, subtree = FALSE,
- root.edge = 0)
+ root.edge = 0, rooted = is.rooted(phy))
+extract.clade(phy, node, root.edge = 0)
}
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
\item{root.edge}{an integer giving the number of internal branches to
be used to build the new root edge. This has no effect if
\code{trim.internal = FALSE}.}
+ \item{rooted}{a logical indicated whether the tree must be treated as
+ rooted or not. This allows to force the tree to be considered as
+ unrooted (see examples).}
+ \item{node}{a node number or label.}
}
\description{
- This function removes the terminal branches of a phylogenetic tree,
+ \code{drop.tip} removes the terminal branches of a phylogenetic tree,
possibly removing the corresponding internal branches.
+
+ \code{extract.clade} does the inverse operation: it keeps all the tips
+ from a given node, and deletes all the other tips.
}
\details{
The argument \code{tip} can be either character or numeric. In the
second case the numbers of these labels in the vector
\code{phy$tip.label} are given.
+ This also applies to \code{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 \code{node} (i.e., a vector of length two or
+ more), only the first one is used with a warning.
+
If \code{trim.internal = FALSE}, the new tips are given \code{"NA"} as
labels, unless there are node labels in the tree in which case they
are used.
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)
-
+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);