\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$double.eps ^ 0.5,
- scale = NULL, \dots)
+ use.tip.label = TRUE, index.return = FALSE,
+ tolerance = .Machine$double.eps ^ 0.5,
+ scale = NULL, \dots)
}
\arguments{
\item{target}{an object of class \code{"phylo"}.}
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.
+}
+\note{
+ The algorithm used here does not work correctly for the comparison of
+ topologies (i.e., ignoring tip labels) of unrooted trees. This also
+ affects \code{\link{unique.multiPhylo}} which calls the present function. See:
- Only the labelled topologies are compared (i.e. branch lengths are not
- considered.
+ \url{https://stat.ethz.ch/pipermail/r-sig-phylo/2011-August/001562.html}
}
\value{
A logical value, or a two-column matrix.
}
-\author{\enc{Benoît}{Benoit} \email{b.durand@alfort.AFSSA.FR}}
+\author{\enc{Benoît}{Benoit} Durand \email{b.durand@alfort.AFSSA.FR}}
\seealso{
\code{\link[base]{all.equal}} for the generic \R function
}