fix bug in prop.clades

[ape.git] / man / as.phylo.Rd

diff --git a/man/as.phylo.Rd b/man/as.phylo.Rd
index 86b48ba6988aa1b0d03c19d32f4f90e949d89106..1c9f6e5a7f096d29352bcf1eb0ff25d6cb5f9a43 100644 (file)
--- a/man/as.phylo.Rd
+++ b/man/as.phylo.Rd
@@ -56,6 +56,12 @@ as.igraph(x, ...)
   An object of class \code{"hclust"}, \code{"phylo"}, \code{"network"},
   or \code{"igraph"}.
 }
+\note{
+  In an object of class \code{"hclust"}, the \code{height} gives the
+  distance between the two sets that are being agglomerated. So these
+  distances are divided by two when setting the branch lengths of a
+  phylogenetic tree.
+}
 \author{Emmanuel Paradis}
 \seealso{
   \code{\link[stats]{hclust}}, \code{\link[stats]{as.hclust}},
@@ -83,8 +89,9 @@ layout(matrix(1:2, 2, 1))
 plot(bird.orders, font = 1, no.margin = TRUE)
 par(mar = c(0, 0, 0, 8))
 plot(dend, horiz = TRUE)
-layout(matrix(1, 1, 1))
+layout(matrix(1))
 
+\dontrun{
 ### convert into networks:
 if (require(network)) {
     x <- as.network(rtree(10))
@@ -100,4 +107,5 @@ if (require(igraph)) {
     print(as.igraph(tr, FALSE, FALSE))
 }
 }
+}
 \keyword{manip}