a few bug fixes especially in plot.phylo()

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

diff --git a/man/dist.topo.Rd b/man/dist.topo.Rd
index d10817c57fe82576a7dc867e618018b67821fb13..caf1b5b6f4eaf5d1757cde044a7a843f9003aa68 100644 (file)
--- a/man/dist.topo.Rd
+++ b/man/dist.topo.Rd
@@ -8,7 +8,7 @@ dist.topo(x, y, method = "PH85")
   \item{x}{an object of class \code{"phylo"}.}
   \item{y}{an object of class \code{"phylo"}.}
   \item{method}{a character string giving the method to be used: either
-    \code{"PH85"}, or \code{"BHV01"}.}
+    \code{"PH85"}, or \code{"score"}.}
 }
 \description{
   This function computes the topological distance between two
@@ -19,22 +19,33 @@ dist.topo(x, y, method = "PH85")
 }
 \details{
   Two methods are available: the one by Penny and Hendy (1985), and the
-  one by Billera et al. (2001).
+  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
   1985). Rzhetsky and Nei (1992) proposed a modification of the original
   formula to take multifurcations into account.
 
-  Billera et al. (2001) developed a distance from the geometry of a tree
-  space. The distance between two trees can be seen as the sum of the
-  branch lengths that need be erased to have two similar trees.
+  The branch length score may be seen as similar to the previous
+  distance but taking branch lengths into account. Kuhner and
+  Felsenstein (1994) proposed to calculate the square root of the sum of
+  the squared differences of the (internal) branch lengths defining
+  similar bipartitions (or splits) in both trees.
+}
+\note{
+  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
   space of phylogenetic trees. \emph{Advances in Applied Mathematics},
   \bold{27}, 733--767.
 
+  Kuhner, M. K. and Felsenstein, J. (1994) Simulation comparison of
+  phylogeny algorithms under equal and unequal evolutionary rates.
+  \emph{Molecular Biology and Evolution}, \bold{11}, 459--468.
+
   Nei, M. and Kumar, S. (2000) \emph{Molecular evolution and
   phylogenetics}. Oxford: Oxford University Press.
 
@@ -45,7 +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}}