new alex()

[ape.git] / man / bind.tree.Rd

diff --git a/man/bind.tree.Rd b/man/bind.tree.Rd
index ff8cafe8d1b95c0864680b6fc2deb8ee39418679..b1e9908c65ab9beaf80261c57142541ae8720147 100644 (file)
--- a/man/bind.tree.Rd
+++ b/man/bind.tree.Rd
@@ -1,9 +1,10 @@
 \name{bind.tree}
 \alias{bind.tree}
+\alias{+.phylo}
 \title{Binds Trees}
 \usage{
 bind.tree(x, y, where = "root", position = 0, interactive = FALSE)
-\method{+}{phylo}(x, y)
+\special{x + y}
 }
 \arguments{
   \item{x}{an object of class \code{"phylo"}.}
@@ -34,6 +35,17 @@ bind.tree(x, y, where = "root", position = 0, interactive = FALSE)
     bind.tree(x, y, position = if (is.null(x$root.edge)) 0 else
     x$root.edge)
   }
+
+  If only one of the trees has no branch length, the branch lengths of
+  the other one are ignored with a warning.
+
+  If one (or both) of the trees has no branch length, it is possible to
+  specify a value of 'position' to graft 'y' below the node of 'x'
+  specified by 'where'. In this case, the exact value of 'position' is
+  not important as long as it is greater than zero. The new node will be
+  multichotomous if 'y' has no root edge. This can be solved by giving
+  an arbitrary root edge to 'y' beforehand (e.g., \code{y$root.edge <-
+  1}): it will be deleted during the binding operation.
 }
 \value{
   an object of class \code{"phylo"}.
@@ -88,8 +100,8 @@ title("x")
 plot(z, show.node.label = TRUE, font = 1, root.edge = TRUE)
 title("z <- bind.tree(x, y, 2, .1)")
 
-x <- rtree(100)
-y <- rtree(100)
+x <- rtree(50)
+y <- rtree(50)
 x$root.edge <- y$root.edge <- .2
 z <- x + y
 plot(y, show.tip.label = FALSE, root.edge = TRUE); axisPhylo()