\alias{is.rooted}
\title{Roots Phylogenetic Trees}
\usage{
-root(phy, outgroup)
+root(phy, outgroup, node = NULL, resolve.root = FALSE)
unroot(phy)
is.rooted(phy)
}
\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.}
+ \item{resolve.root}{a logical specifying whether to resolve the new
+ root as a bifurcating node.}
}
\description{
\code{root} reroots a phylogenetic tree with respect to the specified
- outgroup.
+ outgroup or at the node specified in \code{node}.
\code{unroot} unroots a phylogenetic tree, or returns it unchanged if
it is already unrooted.
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}.
}
\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
\seealso{
- \code{\link{bind.tree}}, \code{\link{drop.tip}}
+ \code{\link{bind.tree}}, \code{\link{drop.tip}},
+ \code{\link{nodelabels}}, \code{\link{identify.phylo}}
}
\examples{
data(bird.orders)
### 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:
+### ... 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)