https://github.com/cran/ape
Tip revision: 6fd9ab693f859dd738cc2de679a481797f575485 authored by Emmanuel Paradis on 17 July 2009, 00:00:00 UTC
version 2.3-2
version 2.3-2
Tip revision: 6fd9ab6
summary.phylo.Rd
\name{summary.phylo}
\alias{summary.phylo}
\alias{Ntip}
\alias{Nnode}
\alias{Nedge}
\title{Print Summary of a Phylogeny}
\usage{
\method{summary}{phylo}(object, \dots)
Ntip(phy)
Nnode(phy, internal.only = TRUE)
Nedge(phy)
}
\arguments{
\item{object, phy}{an object of class \code{"phylo"}.}
\item{...}{further arguments passed to or from other methods.}
\item{internal.only}{a logical indicating whether to return the number
of internal nodes only (the default), or of internal and terminal
(tips) nodes (if \code{FALSE}).}
}
\description{
The first function prints a compact summary of a phylogenetic tree (an
object of class \code{"phylo"}). The three other functions return the
number of tips, nodes, or edges, respectively.
}
\details{
The summary includes the numbers of tips and of nodes, summary
statistics of the branch lengths (if they are available) with mean,
variance, minimum, first quartile, median, third quartile, and
maximum, listing of the first ten tip labels, and (if available) of
the first ten node labels. It is also printed whether some of these
optional elements (branch lengths, node labels, and root edge) are not
found in the tree.
If the tree was estimated by maximum likelihood with
\code{\link{mlphylo}}, a summary of the model fit and the parameter
estimated is printed.
\code{summary} simply prints its results on the standard output and is
not meant for programming.
}
\value{
A NULL value in the case of \code{summary}, a single numeric value for
the three other functions.
}
\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
\seealso{
\code{\link{read.tree}}, \code{\link[base]{summary}} for the generic R
function
}
\examples{
data(bird.families)
summary(bird.families)
Ntip(bird.families)
Nnode(bird.families)
Nedge(bird.families)
}
\keyword{manip}