a few changes...

[ape.git] / man / all.equal.phylo.Rd

diff --git a/man/all.equal.phylo.Rd b/man/all.equal.phylo.Rd
index 7c1003de174a447ae95d5f119fa2921cfaa60cce..9242c9f6450a093e4b16784ad78d781bf30064c9 100644 (file)
--- a/man/all.equal.phylo.Rd
+++ b/man/all.equal.phylo.Rd
@@ -4,9 +4,9 @@
 \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"}.}
@@ -34,16 +34,20 @@
   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}}
 \seealso{
-  \code{\link[base]{all.equal}} for the generic R function
+  \code{\link[base]{all.equal}} for the generic \R function
 }
 \examples{
 ### maybe the simplest example of two representations