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\name{comparePhylo}
\alias{comparePhylo}
\alias{print.comparePhylo}
\title{Compare Two "phylo" Objects}
\description{
This function compares two phylogenetic trees, rooted or unrooted, and
returns a detailed report of this comparison.
}
\usage{
comparePhylo(x, y, plot = FALSE, force.rooted = FALSE,
use.edge.length = FALSE, commons = TRUE,
location = "bottomleft", ...)
\method{print}{comparePhylo}(x, ...)
}
\arguments{
\item{x, y}{two objects of class \code{"phylo"}.}
\item{plot}{a logical value. If \code{TRUE}, the two trees are plotted
on the same device and their similarities are shown.}
\item{force.rooted}{a logical value. If \code{TRUE}, the trees are
considered rooted even if \code{is.rooted} returns \code{FALSE}.}
\item{use.edge.length}{a logical value passed to
\code{\link{plot.phylo}} (see below).}
\item{commons}{whether to show the splits (the default), or the splits
specific to each tree (applies only for unrooted trees).}
\item{location}{location of where to position the \code{\link{legend}}.}
\item{\dots}{further parameters used by \code{\link{plot.phylo}}, in function
\code{print.comparePhylo} unused.}
}
\details{
In all cases, the numbers of tips and of nodes and the tip labels are
compared.
If both trees are rooted, or if \code{force.rooted = TRUE}, the clade
compositions of each tree are compared. If both trees are also
ultrametric, their branching times are compared.
If both trees are unrooted and have the same number of nodes, the
bipartitions (aka splits) are compared.
If \code{plot = TRUE}, the edge lengths are not used by default
because in some situations with unrooted trees, some splits might not
be visible if the corresponding internal edge length is very short. To
use edge lengths, set \code{use.edge.length = TRUE}.
}
\value{
an object of class \code{"comparePhylo"} which is a list with messages
from the comparison and, optionally, tables comparing branching times.
}
\author{Emmanuel Paradis, Klaus Schliep}
\seealso{\code{\link{all.equal.phylo}}}
\examples{
## two unrooted trees but force comparison as rooted:
a <- read.tree(text = "(a,b,(c,d));")
b <- read.tree(text = "(a,c,(b,d));")
comparePhylo(a, b, plot = TRUE, force.rooted = TRUE)
## two random unrooted trees:
c <- rtree(5, rooted = FALSE)
d <- rtree(5, rooted = FALSE)
comparePhylo(c, d, plot = TRUE)
}
\keyword{manip}
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