https://github.com/cran/ape
Tip revision: c44657c7122de6f1ff126170a82fdac9211b53d5 authored by Emmanuel Paradis on 01 August 2012, 00:00:00 UTC
version 3.0-5
version 3.0-5
Tip revision: c44657c
root.Rd
\name{root}
\alias{root}
\alias{unroot}
\alias{is.rooted}
\title{Roots Phylogenetic Trees}
\usage{
root(phy, outgroup, node = NULL, resolve.root = FALSE, interactive = FALSE)
unroot(phy)
is.rooted(phy)
}
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
\item{outgroup}{a vector of mode numeric or character specifying the
new outgroup.}
\item{node}{alternatively, a node number where to root the tree (this
should give the MRCA of the ingroup).}
\item{resolve.root}{a logical specifying whether to resolve the new
root as a bifurcating node.}
\item{interactive}{if \code{TRUE} the user is asked to select the node
by clicking on the tree which must be plotted.}
}
\description{
\code{root} reroots a phylogenetic tree with respect to the specified
outgroup or at the node specified in \code{node}.
\code{unroot} unroots a phylogenetic tree, or returns it unchanged if
it is already unrooted.
\code{is.rooted} tests whether a tree is rooted.
}
\details{
The argument \code{outgroup} can be either character or numeric. In
the first case, it gives the labels of the tips of the new outgroup;
in the second case the numbers of these labels in the vector
\code{phy$tip.label} are given.
If \code{outgroup} is of length one (i.e., a single value), then the
tree is rerooted using the node below this tip as the new root.
If \code{outgroup} is of length two or more, the most recent common
ancestor (MRCA) \emph{of the ingroup} is used as the new root. Note
that the tree is unrooted before being rerooted, so that if
\code{outgroup} is already the outgroup, then the returned tree is not
the same than the original one (see examples). If \code{outgroup} is
not monophyletic, the operation fails and an error message is issued.
If \code{resolve.root = TRUE}, \code{root} adds a zero-length branch
below the MRCA of the ingroup.
A tree is considered rooted if either only two branches connect to the
root, or if there is a \code{root.edge} element. In all other cases,
\code{is.rooted} returns \code{FALSE}.
}
\value{
an object of class \code{"phylo"} for \code{root} and \code{unroot}; a
single logical value for \code{is.rooted}.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{bind.tree}}, \code{\link{drop.tip}},
\code{\link{nodelabels}}, \code{\link{identify.phylo}}
}
\examples{
data(bird.orders)
plot(root(bird.orders, 1))
plot(root(bird.orders, 1:5))
tr <- root(bird.orders, 1)
is.rooted(bird.orders) # yes!
is.rooted(tr) # no!
### This is because the tree has been unrooted first before rerooting.
### You can delete the outgroup...
is.rooted(drop.tip(tr, "Struthioniformes"))
### ... or resolve the basal trichotomy in two ways:
is.rooted(multi2di(tr))
is.rooted(root(bird.orders, 1, r = TRUE))
### To keep the basal trichotomy but forcing the tree as rooted:
tr$root.edge <- 0
is.rooted(tr)
}
\keyword{manip}