various updates for ape 2.7-2 (fixed)

[ape.git] / R / root.R

diff --git a/R/root.R b/R/root.R
index d02044fa627360bafaedf5055e8bfe3dce3d7d8c..5691bb518f01e9b1105b7b886c5ca48952b02e61 100644 (file)
--- a/R/root.R
+++ b/R/root.R
@@ -1,8 +1,8 @@
-## root.R (2009-11-15)
+## root.R (2011-04-29)
 
 ##   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")
@@ -247,7 +252,7 @@ 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 +288,7 @@ 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