a collection of bug fixes

[ape.git] / R / dist.topo.R

diff --git a/R/dist.topo.R b/R/dist.topo.R
index 88110c59c8c7304444b06395cc4645eec33cabf9..f82dd65193695e63301d706ac71bd63395212a5c 100644 (file)
--- a/R/dist.topo.R
+++ b/R/dist.topo.R
@@ -1,9 +1,9 @@
-## dist.topo.R (2008-06-28)
+## dist.topo.R (2009-07-06)
 
 ##      Topological Distances, Tree Bipartitions,
 ##   Consensus Trees, and Bootstrapping Phylogenies
 
-## Copyright 2005-2008 Emmanuel Paradis
+## Copyright 2005-2009 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -11,25 +11,31 @@
 dist.topo <- function(x, y, method = "PH85")
 {
     if (method == "BHV01" && (is.null(x$edge.length) || is.null(y$edge.length)))
-      stop("trees must have branch lengths for Billera et al.'s distance.")
+        stop("trees must have branch lengths for Billera et al.'s distance.")
     n <- length(x$tip.label)
     bp1 <- .Call("bipartition", x$edge, n, x$Nnode, PACKAGE = "ape")
     bp1 <- lapply(bp1, function(xx) sort(x$tip.label[xx]))
-    bp2 <- .Call("bipartition", y$edge, n, y$Nnode, PACKAGE = "ape")
-    bp2 <- lapply(bp2, function(xx) sort(y$tip.label[xx]))
+    ## fix by Tim Wallstrom:
+    bp2.tmp <- .Call("bipartition", y$edge, n, y$Nnode, PACKAGE = "ape")
+    bp2 <- lapply(bp2.tmp, function(xx) sort(y$tip.label[xx]))
+    bp2.comp <- lapply(bp2.tmp, function(xx) setdiff(1:n, xx))
+    bp2.comp <- lapply(bp2.comp, function(xx) sort(y$tip.label[xx]))
+    ## End
     q1 <- length(bp1)
     q2 <- length(bp2)
     if (method == "PH85") {
         p <- 0
         for (i in 1:q1) {
             for (j in 1:q2) {
-                if (identical(all.equal(bp1[[i]], bp2[[j]]), TRUE)) {
+                if (identical(bp1[[i]], bp2[[j]]) |
+                    identical(bp1[[i]], bp2.comp[[j]])) {
                     p <- p + 1
                     break
                 }
             }
         }
-        dT <- if (q1 == q2) 2*(q1 - p) else 2*(min(q1, q2) - p) + abs(q1 - q2)
+        dT <- q1 + q2 - 2 * p # same than:
+        ##dT <- if (q1 == q2) 2*(q1 - p) else 2*(min(q1, q2) - p) + abs(q1 - q2)
     }
     if (method == "BHV01") {
         dT <- 0
@@ -87,6 +93,7 @@ prop.part <- function(..., check.labels = TRUE)
     ## class(obj) <- NULL # needed?
     ## </FIXME>
     ntree <- length(obj)
+    if (ntree == 1) check.labels <- FALSE
     if (check.labels) obj <- .compressTipLabel(obj)
     for (i in 1:ntree) storage.mode(obj[[i]]$Nnode) <- "integer"
     ## <FIXME>
@@ -167,8 +174,8 @@ prop.clades <- function(phy, ..., part = NULL)
 
 boot.phylo <- function(phy, x, FUN, B = 100, block = 1, trees = FALSE)
 {
-    if (is.list(x)) {
-        if (class(x) == "DNAbin") x <- as.matrix(x)
+    if (is.list(x) && !is.data.frame(x)) {
+        if (inherits(x, "DNAbin")) x <- as.matrix(x)
         else {
             nm <- names(x)
             n <- length(x)