https://github.com/cran/ape
Tip revision: b2e768879a4de1e6742930fa884ac9578bc3d930 authored by Emmanuel Paradis on 19 November 2006, 00:00:00 UTC
version 1.9
version 1.9
Tip revision: b2e7688
all.equal.phylo.Rd
\name{all.equal.phylo}
\alias{all.equal.phylo}
\title{Global Comparison of two Phylogenies}
\usage{
\method{all.equal}{phylo}(target, current, use.edge.length = TRUE,
use.tip.label = TRUE, index.return = FALSE,
tolerance = .Machine$double.eps ^ 0.5,
scale = NULL, \dots)
}
\arguments{
\item{target}{an object of class \code{"phylo"}.}
\item{current}{an object of class \code{"phylo"}.}
\item{use.edge.length}{if \code{FALSE} only the topologies are
compared; the default is \code{TRUE}.}
\item{use.tip.label}{if \code{FALSE} the unlabelled trees are
compared; the default is \code{TRUE}.}
\item{index.return}{if \code{TRUE} the function returns a two-column
matrix giving the correspondence between the nodes of both trees.}
\item{tolerance}{the numeric tolerance used to compare the branch
lengths.}
\item{scale}{a positive number, comparison of branch lengths is made
after scaling (i.e., dividing) them by this number.}
\item{...}{further arguments passed to or from other methods.}
}
\description{
This function makes a global comparison of two phylogenetic trees.
}
\details{
This function is meant to be an adaptation of the generic function
\code{all.equal} for the comparison of phylogenetic trees.
A single phylogenetic tree may have several representations in the Newick
format and in the \code{"phylo"} class of objects used in `ape'. One
aim of the present function is to be able to identify whether two
objects of class \code{"phylo"} represent the same phylogeny.
Only the labelled topologies are compared (i.e. branch lengths are not
considered.
}
\value{
A logical value, or a two-column matrix.
}
\author{Beno¯t Durand \email{b.durand@alfort.AFSSA.FR}}
\seealso{
\code{\link[base]{all.equal}} for the generic R function
}
\examples{
### maybe the simplest example of two representations
### for the same rooted tree...:
t1 <- read.tree(text = "(a:1,b:1);")
t2 <- read.tree(text = "(b:1,a:1);")
all.equal(t1, t2)
### ... compare with this:
identical(t1, t2)
### one just slightly more complicated...:
t3 <- read.tree(text = "((a:1,b:1):1,c:2);")
t4 <- read.tree(text = "(c:2,(a:1,b:1):1);")
all.equal(t3, t4) # == all.equal.phylo(t3, t4)
### ... here we force the comparison as lists:
all.equal.list(t3, t4)
t5 <- read.tree(text = "(a:2,(c:1,b:1):1);")
### note that this does NOT return FALSE...:
all.equal(t3, t5)
### ... do this instead:
identical(all.equal(t3, t5), TRUE)
}
\keyword{manip}