\name{as.matching}
\alias{as.matching}
\alias{as.matching.phylo}
\alias{as.phylo.matching}
\title{Conversion Between Phylo and Matching Objects}
\description{
  These functions convert objects between the classes "phylo" and
  "matching".
}
\usage{
as.matching(x, ...)
\method{as.matching}{phylo}(x, labels = TRUE, ...)
\method{as.phylo}{matching}(x, ...)
}
\arguments{
  \item{x}{an object to convert as an object of class "matching" or of
    class "phylo".}
  \item{labels}{a logical specifying whether the tip and node labels
    should be included in the returned matching.}
  \item{\dots}{further arguments to be passed to or from other methods.}
}
\details{
  A matching is a representation where each tip and each node are given
  a number, and sibling groups are grouped in a ``matching pair'' (see
  Diaconis and Holmes 1998, for details). This coding system can be used
  only for binary (fully dichotomous) trees.

  Diaconis and Holmes (1998) gave some conventions to insure that a
  given tree has a unique representation as a matching. I have tried to
  follow them in the present functions.
}
\value{
  \code{as.matching} returns an object of class "matching" with the
  following component:

  \item{matching}{a three-columns numeric matrix where the first two
    columns represent the sibling pairs, and the third one the
    corresponding ancestor.}
  \item{edge.length}{(optional) a numeric vector representing the branch
    lengths where the ith element is the length of the branch below the
    element (tip or node) numbered i in \code{matching}.}
  \item{tip.label}{(optional) a character vector giving the tip labels
    where the ith element is the label of the tip numbered i in
    \code{matching}.}
  \item{node.label}{(optional) a character vector giving the node
    labels in the same order than in \code{matching} (i.e. the ith
    element is the label of the node numbered i + n in \code{matching},
    with n the number of tips).}

  \code{as.phylo.matching} returns an object of class "phylo".
}
\author{Emmanuel Paradis \email{paradis@isem.univ-montp2.fr}}
\references{
  Diaconis, P. W. and Holmes, S. P. (1998) Matchings and phylogenetic
  trees. \emph{Proceedings of the National Academy of Sciences USA},
  \bold{95}, 14600--14602.
}
\seealso{\code{\link{as.phylo}}}
\examples{
data(bird.orders)
m <- as.matching(bird.orders)
str(m)
m
tr <- as.phylo(m)
all.equal(tr, bird.orders)
}
\keyword{manip}