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\name{as.bitsplits}
\alias{as.bitsplits}
\alias{as.bitsplits.prop.part}
\alias{print.bitsplits}
\alias{sort.bitsplits}
\alias{bitsplits}
\alias{countBipartitions}
\alias{as.prop.part}
\alias{as.prop.part.bitsplits}
\title{Split Frequencies and Conversion Among Split Classes}
\description{
\code{bitsplits} returns the bipartitions (aka splits) for a single
tree or a list of trees. If at least one tree is rooted, an error is
returned.
\code{countBipartitions} returns the frequencies of the bipartitions
from a reference tree (phy) observed in a list of trees (X), all unrooted.
\code{as.bitsplits} and \code{as.prop.part} are generic functions for
converting between the \code{"bitsplits"} and \code{"prop.part"}
classes.
}
\usage{
bitsplits(x)
countBipartitions(phy, X)
as.bitsplits(x)
\method{as.bitsplits}{prop.part}(x)
\method{print}{bitsplits}(x, ...)
\method{sort}{bitsplits}(x, decreasing = FALSE, ...)
as.prop.part(x, ...)
\method{as.prop.part}{bitsplits}(x, include.trivial = FALSE, ...)
}
\arguments{
\item{x}{an object of the appropriate class.}
\item{phy}{an object of class \code{"phylo"}.}
\item{X}{an object of class \code{"multiPhylo"}.}
\item{decreasing}{a logical value to sort the bipartitions in
increasing (the default) or decreasing order of their frequency.}
\item{include.trivial}{a logical value specifying whether to include
the trivial split with all tips in the returned object.}
\item{\dots}{further arguments passed to or from other methods.}
}
\details{
These functions count bipartitions as defined by internal branches, so
they not work only with unrooted trees. The structure of the class
\code{"bitsplits"} is described in a separate document on ape's web
site.
}
\value{
\code{bitsplits}, \code{as.bitsplits}, and \code{sort} return an object
of class \code{"bitsplits"}.
\code{countBipartitions} returns a vector of integers.
\code{as.prop.part} returns an object of class \code{"prop.part"}.
}
\author{Emmanuel Paradis}
\seealso{\code{\link{prop.part}}, \code{\link{is.compatible}}}
\examples{
tr <- rtree(20)
pp <- prop.part(tr)
as.bitsplits(pp)
## works only with unrooted trees (ape 5.5):
countBipartitions(rtree(10, rooted = FALSE), rmtree(100, 10, rooted = FALSE))
}
\keyword{manip}
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