\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{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
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) is used as the new root. Note that the tree is really
- 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.
+ 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.
an object of class \code{"phylo"} for \code{root} and \code{unroot}; a
single logical value for \code{is.rooted}.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
\code{\link{bind.tree}}, \code{\link{drop.tip}},
\code{\link{nodelabels}}, \code{\link{identify.phylo}}