final wrap for ape 3.0

[ape.git] / R / as.phylo.R

diff --git a/R/as.phylo.R b/R/as.phylo.R
index e0ee65fec8575654d1cb1e56637006b7625093fc..5d541bce67f3de75f947ba59caa0ea256921e4eb 100644 (file)
--- a/R/as.phylo.R
+++ b/R/as.phylo.R
@@ -1,8 +1,8 @@
-## as.phylo.R (2007-03-05)
+## as.phylo.R (2011-03-25)
 
 ##     Conversion Among Tree Objects
 
-## Copyright 2005-2007 Emmanuel Paradis
+## Copyright 2005-2011 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -29,7 +29,8 @@ new2old.phylo <- function(phy)
 
 as.phylo <- function (x, ...)
 {
-    if (class(x) == "phylo") return(x)
+    if (length(class(x)) == 1 && class(x) == "phylo")
+        return(x)
     UseMethod("as.phylo")
 }
 
@@ -47,20 +48,21 @@ as.phylo.hclust <- function(x, ...)
         edge[j:(j + 1), 1] <- node[i]
         for (l in 1:2) {
             k <- j + l - 1L
-            if (x$merge[i, l] > 0) {
-                edge[k, 2] <- node[x$merge[i, l]] <- cur.nod
+            y <- x$merge[i, l]
+            if (y > 0) {
+                edge[k, 2] <- node[y] <- cur.nod
                 cur.nod <- cur.nod + 1L
-                edge.length[k] <- x$height[i] - x$height[x$merge[i, l]]
+                edge.length[k] <- x$height[i] - x$height[y]
             } else {
-                edge[k, 2] <- -x$merge[i, l]
+                edge[k, 2] <- -y
                 edge.length[k] <- x$height[i]
             }
         }
         j <- j + 2L
     }
     if (is.null(x$labels))
-      x$labels <- as.character(1:(N + 1))
-    obj <- list(edge = edge, edge.length = edge.length,
+        x$labels <- as.character(1:(N + 1))
+    obj <- list(edge = edge, edge.length = edge.length / 2,
                 tip.label = x$labels, Nnode = N)
     class(obj) <- "phylo"
     reorder(obj)
@@ -87,21 +89,46 @@ as.hclust.phylo <- function(x, ...)
 {
     if (!is.ultrametric(x)) stop("the tree is not ultrametric")
     if (!is.binary.tree(x)) stop("the tree is not binary")
+    if (!is.rooted(x)) stop("the tree is not rooted")
     n <- length(x$tip.label)
-    bt <- rev(branching.times(x))
-    N <- length(bt)
-    nm <- as.numeric(names(bt))
+    x$node.label <- NULL # by Jinlong Zhang (2010-12-15)
+    bt <- sort(branching.times(x))
+    inode <- as.numeric(names(bt))
+    N <- n - 1L
+    nm <- numeric(N + n) # hash table
+    nm[inode] <- 1:N
     merge <- matrix(NA, N, 2)
     for (i in 1:N) {
-        ind <- which(x$edge[, 1] == nm[i])
-        for (k in 1:2)
-          merge[i, k] <- if (x$edge[ind[k], 2] <= n) -x$edge[ind[k], 2]
-          else which(nm == x$edge[ind[k], 2])
+        ind <- which(x$edge[, 1] == inode[i])
+        for (k in 1:2) {
+            tmp <- x$edge[ind[k], 2]
+            merge[i, k] <- if (tmp <= n) -tmp else nm[tmp]
+        }
     }
     names(bt) <- NULL
-    obj <- list(merge = merge, height = bt, order = 1:(N + 1),
-                labels = x$tip.label, call = match.call(),
-                method = "unknown")
+    obj <- list(merge = merge, height = bt, order = 1:n, labels = x$tip.label,
+                call = match.call(), method = "unknown")
     class(obj) <- "hclust"
     obj
 }
+
+as.network.phylo <- function(x, directed = is.rooted(x), ...)
+{
+    if (is.null(x$node.label)) x <- makeNodeLabel(x)
+    res <- network(x$edge, directed = directed, ...)
+    network.vertex.names(res) <- c(x$tip.label, x$node.label)
+    res
+}
+
+as.igraph <- function(x, ...) UseMethod("as.igraph")
+
+as.igraph.phylo <- function(x, directed = is.rooted(x), use.labels = TRUE, ...)
+{
+    ## local copy because x will be changed before evaluating is.rooted(x):
+    directed <- directed
+    if (use.labels) {
+        if (is.null(x$node.label)) x <- makeNodeLabel(x)
+        x$edge <- matrix(c(x$tip.label, x$node.label)[x$edge], ncol = 2)
+    } else x$edge <- x$edge - 1L
+    graph.edgelist(x$edge, directed = directed, ...)
+}