final version for ape 2.6-1

[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
 }
 \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
 
   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{
   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
 }
 \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.
 }
   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}}
 \seealso{
   \code{\link{read.tree}} to read tree files in Newick format,
   \code{\link{cophenetic.phylo}}, \code{\link{prop.part}}