various bug fixes

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

diff --git a/man/as.phylo.Rd b/man/as.phylo.Rd
index d7118f0d7bb8567e74d89e9ac6920f155ce9c276..4124046b3f71427064df77ea2e5d79b665be6895 100644 (file)
--- a/man/as.phylo.Rd
+++ b/man/as.phylo.Rd
@@ -5,39 +5,58 @@
 \alias{as.hclust.phylo}
 \alias{old2new.phylo}
 \alias{new2old.phylo}
-\title{Conversion Among Tree Objects}
-\usage{
-as.phylo(x, ...)
-\method{as.phylo}{hclust}(x, ...)
-\method{as.phylo}{phylog}(x, ...)
-\method{as.hclust}{phylo}(x, ...)
-old2new.phylo(phy)
-new2old.phylo(phy)
-}
-\arguments{
-  \item{x}{an object to be converted into another class.}
-  \item{...}{further arguments to be passed to or from other methods.}
-  \item{phy}{an object of class \code{"phylo"}.}
-}
+\alias{as.network.phylo}
+\alias{as.igraph}
+\alias{as.igraph.phylo}
+\title{Conversion Among Tree and Network Objects}
 \description{
   \code{as.phylo} is a generic function which converts an object into a
-  tree of class \code{"phylo"}. There are currently two methods for this
-  generic for objects of class \code{"hclust"} and of class
-  \code{"phylog"} (implemented in the package ade4).
+  tree of class \code{"phylo"}. There are currently two methods for
+  objects of class \code{"hclust"} and of class \code{"phylog"}
+  (implemented in the package ade4).
+
   \code{as.hclust.phylo} is a method of the generic
   \code{\link[stats]{as.hclust}} which converts an object of class
   \code{"phylo"} into one of class \code{"hclust"}. This can used to
   convert an object of class \code{"phylo"} into one of class
   \code{"dendrogram"} (see examples).
 
+  \code{as.network} and \code{as.igraph} convert trees of class
+  \code{"phylo"} into these respective classes defined in the packages
+  of the same names. Note that the generic of the former is defined in
+  \pkg{network}.
+
   \code{old2new.phylo} and \code{new2old.phylo} are utility functions
   for converting between the old and new coding of the class
   \code{"phylo"}.
 }
+\usage{
+as.phylo(x, ...)
+\method{as.phylo}{hclust}(x, ...)
+\method{as.phylo}{phylog}(x, ...)
+\method{as.hclust}{phylo}(x, ...)
+old2new.phylo(phy)
+new2old.phylo(phy)
+\method{as.network}{phylo}(x, directed = is.rooted(x), ...)
+as.igraph(x, ...)
+\method{as.igraph}{phylo}(x, directed = is.rooted(x), use.labels = TRUE, ...)
+}
+\arguments{
+  \item{x}{an object to be converted into another class.}
+  \item{directed}{a logical value: should the network be directed? By
+    default, this depends on whether the tree is rooted or not.}
+  \item{use.labels}{a logical specifying whether to use labels to build
+    the network of class \code{"igraph"}. If \code{TRUE} and the tree
+    has no node labels, then some default labels are created first. If
+    \code{FALSE}, the network is built with integers.}
+  \item{\dots}{further arguments to be passed to or from other methods.}
+  \item{phy}{an object of class \code{"phylo"}.}
+}
 \value{
-  An object of class \code{"hclust"} or \code{"phylo"}.
+  An object of class \code{"hclust"}, \code{"phylo"}, \code{"network"},
+  or \code{"igraph"}.
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \seealso{
   \code{\link[stats]{hclust}}, \code{\link[stats]{as.hclust}},
   \code{\link[stats]{dendrogram}}, \code{\link[ade4]{phylog}},
@@ -63,7 +82,24 @@ plot(dend)
 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))
+plot(dend, horiz = TRUE)
+layout(matrix(1))
+
+\dontrun{
+### convert into networks:
+if (require(network)) {
+    x <- as.network(rtree(10))
+    print(x)
+    plot(x, vertex.cex = 1:4)
+    plot(x, displaylabels = TRUE)
+}
+tr <- rtree(5)
+if (require(igraph)) {
+    print((x <- as.igraph(tr)))
+    plot(x)
+    print(as.igraph(tr, TRUE, FALSE))
+    print(as.igraph(tr, FALSE, FALSE))
+}
+}
 }
 \keyword{manip}