bug fix in root()

[ape.git] / R / root.R

diff --git a/R/root.R b/R/root.R
index d02044fa627360bafaedf5055e8bfe3dce3d7d8c..8526b8f3d4f74add15240b88eca14a8267785496 100644 (file)
--- a/R/root.R
+++ b/R/root.R
@@ -1,8 +1,8 @@
-## root.R (2009-11-15)
+## root.R (2011-08-05)
 
 ##   Root of Phylogenetic Trees
 
-## Copyright 2004-2009 Emmanuel Paradis
+## Copyright 2004-2011 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -10,19 +10,19 @@
 is.rooted <- function(phy)
 {
     if (!inherits(phy, "phylo"))
-      stop('object "phy" is not of class "phylo"')
+        stop('object "phy" is not of class "phylo"')
     if (!is.null(phy$root.edge)) TRUE
     else
-      if (tabulate(phy$edge[, 1])[length(phy$tip.label) + 1] > 2)
-        FALSE else TRUE
+        if (tabulate(phy$edge[, 1])[length(phy$tip.label) + 1] > 2)
+            FALSE else TRUE
 }
 
 unroot <- function(phy)
 {
     if (!inherits(phy, "phylo"))
-      stop('object "phy" is not of class "phylo"')
+        stop('object "phy" is not of class "phylo"')
     if (dim(phy$edge)[1] < 3)
-      stop("cannot unroot a tree with two edges.")
+        stop("cannot unroot a tree with less than three edges.")
     ## delete FIRST the root.edge (in case this is sufficient to
     ## unroot the tree, i.e. there is a multichotomy at the root)
     if (!is.null(phy$root.edge)) phy$root.edge <- NULL
@@ -61,13 +61,18 @@ unroot <- function(phy)
     phy
 }
 
-root <- function(phy, outgroup, node = NULL, resolve.root = FALSE)
+root <- function(phy, outgroup, node = NULL,
+                 resolve.root = FALSE, interactive = FALSE)
 {
     if (!inherits(phy, "phylo"))
-      stop('object "phy" is not of class "phylo"')
+        stop('object "phy" is not of class "phylo"')
     phy <- reorder(phy)
     n <- length(phy$tip.label)
-    ROOT <- n + 1
+    ROOT <- n + 1L
+    if (interactive) {
+        node <- identify(phy)$nodes
+        cat("You have set resolve.root =", resolve.root, "\n")
+    }
     if (!is.null(node)) {
         if (node <= n)
             stop("incorrect node#: should be greater than the number of taxa")
@@ -86,34 +91,21 @@ root <- function(phy, outgroup, node = NULL, resolve.root = FALSE)
         ## First check that the outgroup is monophyletic--
         ## unless there's only one tip specified of course
         if (length(outgroup) > 1) {
-            seq.nod <- .Call("seq_root2tip", phy$edge, n,
-                             phy$Nnode, PACKAGE = "ape")
-            sn <- seq.nod[outgroup]
-            ## We go from the root to the tips: the sequence of nodes
-            ## is identical until the MRCA:
-            newroot <- ROOT
-            i <- 2 # we start at the 2nd position since the root
-                   # of the tree is a common ancestor to all tips
-            repeat {
-                x <- unique(unlist(lapply(sn, "[", i)))
-                if (length(x) != 1) break
-                newroot <- x
-                i <- i + 1
-            }
-            ## Check that all descendants of this node
-            ## are included in the outgroup.
-            ## (below is slightly faster than calling "bipartition")
-            desc <- which(unlist(lapply(seq.nod,
-                                        function(x) any(x %in% newroot))))
-            msg <- "the specified outgroup is not monophyletic"
+            pp <- prop.part(phy)
             ingroup <- (1:n)[-outgroup]
-            ## 'outgroup' and 'desc' are already sorted:
-            if (newroot != ROOT) {
-                if (!identical(outgroup, desc) && !identical(ingroup, desc))
-                    stop(msg)
-            } else { # otherwise check monophyly of the ingroup
-                if (!is.monophyletic(phy, ingroup)) stop(msg)
+            newroot <- 0L
+            for (i in 2:phy$Nnode) {
+                if (identical(pp[[i]], ingroup)) {
+                    newroot <- i + n
+                    break
+                }
+                if (identical(pp[[i]], outgroup)) {
+                    newroot <- phy$edge[which(phy$edge[, 2] == i + n), 1]
+                    break
+                }
             }
+            if (!newroot)
+                stop("the specified outgroup is not monophyletic")
         } else newroot <- phy$edge[which(phy$edge[, 2] == outgroup), 1]
     }
     N <- Nedge(phy)
@@ -247,7 +239,7 @@ root <- function(phy, outgroup, node = NULL, resolve.root = FALSE)
     o[NEXT:(NEXT + ne - 1L)] <- s
 
     if (fuseRoot) {
-        phy$Nnode <- oldNnode - 1
+        phy$Nnode <- oldNnode - 1L
         N <- N - 1L
     }
     phy$edge[INV, ] <- phy$edge[INV, 2:1]
@@ -283,7 +275,7 @@ root <- function(phy, outgroup, node = NULL, resolve.root = FALSE)
             }
         }
         ## N <- N + 1L ... not needed
-        phy$Nnode <- phy$Nnode + 1
+        phy$Nnode <- phy$Nnode + 1L
     }
 
     ## The block below renumbers the nodes so that they conform