various bug fixes

[ape.git] / man / dist.topo.Rd

diff --git a/man/dist.topo.Rd b/man/dist.topo.Rd
index 3fbedcd0761dc0649bf62775394ecb6a373d9f21..caf1b5b6f4eaf5d1757cde044a7a843f9003aa68 100644 (file)
--- a/man/dist.topo.Rd
+++ b/man/dist.topo.Rd
@@ -19,7 +19,8 @@ dist.topo(x, y, method = "PH85")
 }
 \details{
   Two methods are available: the one by Penny and Hendy (1985), and the
-  branch length score by Kuhner and Felsenstein (1994).
+  branch length score by Kuhner and Felsenstein (1994). The trees are
+  always considered as unrooted.
 
   The topological distance is defined as twice the number of internal
   branches defining different bipartitions of the tips (Penny and Hendy
@@ -33,7 +34,8 @@ dist.topo(x, y, method = "PH85")
   similar bipartitions (or splits) in both trees.
 }
 \note{
-  The geodesic distance of Billera et al. (2001) has been disabled.
+  The geodesic distance of Billera et al. (2001) has been disabled: see
+  the package \pkg{distory} on CRAN.
 }
 \references{
   Billera, L. J., Holmes, S. P. and Vogtmann, K. (2001) Geometry of the
@@ -54,7 +56,7 @@ dist.topo(x, y, method = "PH85")
   testing minimum-evolution trees. \emph{Molecular Biology and
     Evolution}, \bold{9}, 945--967.
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \seealso{
   \code{\link{read.tree}} to read tree files in Newick format,
   \code{\link{cophenetic.phylo}}, \code{\link{prop.part}}