final fixes for ape 2.7-3

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

diff --git a/man/all.equal.phylo.Rd b/man/all.equal.phylo.Rd
index f11afeb6ea4047a4ed352784937a75bef6bb0407..41351daa6a8dbf856511793080cff09ceec308fc 100644 (file)
--- a/man/all.equal.phylo.Rd
+++ b/man/all.equal.phylo.Rd
@@ -21,7 +21,7 @@
     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.}
+  \item{\dots}{further arguments passed to or from other methods.}
 }
 \description{
   This function makes a global comparison of two phylogenetic trees.
@@ -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