various bug fixes

[ape.git] / R / root.R

diff --git a/R/root.R b/R/root.R
index aadd6c15454454947c4e5fc1e2d3a3d0124ede26..5691bb518f01e9b1105b7b886c5ca48952b02e61 100644 (file)
--- a/R/root.R
+++ b/R/root.R
@@ -1,8 +1,8 @@
-## root.R (2009-09-09)
+## 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$root.edge <- NULL
@@ -35,11 +35,11 @@ unroot <- function(phy)
     ## nodes by adding 1, except the root (this remains the
     ## origin of the tree).
     nb.tip <- length(phy$tip.label)
-    ROOT <- nb.tip + 1
+    ROOT <- nb.tip + 1L
     EDGEROOT <- which(phy$edge[, 1] == ROOT)
     ## j: the target where to stick the edge
     ## i: the edge to delete
-    if (phy$edge[EDGEROOT[1], 2] == ROOT + 1) {
+    if (phy$edge[EDGEROOT[1], 2] == ROOT + 1L) {
         j <- EDGEROOT[2]
         i <- EDGEROOT[1]
     } else {
@@ -50,24 +50,29 @@ unroot <- function(phy)
     ## cladewise order.
     phy$edge <- phy$edge[-i, ]
     nodes <- phy$edge > ROOT # renumber all nodes except the root
-    phy$edge[nodes] <- phy$edge[nodes] - 1
+    phy$edge[nodes] <- phy$edge[nodes] - 1L
     if (!is.null(phy$edge.length)) {
         phy$edge.length[j] <- phy$edge.length[j] + phy$edge.length[i]
         phy$edge.length <- phy$edge.length[-i]
     }
-    phy$Nnode <- phy$Nnode - 1
+    phy$Nnode <- phy$Nnode - 1L
     if (!is.null(phy$node.label))
       phy$node.label <- phy$node.label[-2]
     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