many changes!

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

diff --git a/R/dist.topo.R b/R/dist.topo.R
index 6741dcc8415f5ee1c33c1055aa58aa1e5fa55a49..86b396b9aa9814abade98b2c5bd86c3f75fe25ee 100644 (file)
--- a/R/dist.topo.R
+++ b/R/dist.topo.R
@@ -1,55 +1,64 @@
-## dist.topo.R (2009-05-10)
+## dist.topo.R (2010-05-25)
 
 ##      Topological Distances, Tree Bipartitions,
 ##   Consensus Trees, and Bootstrapping Phylogenies
 
-## Copyright 2005-2009 Emmanuel Paradis
+## Copyright 2005-2010 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
 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.")
-    n <- length(x$tip.label)
-    bp1 <- .Call("bipartition", x$edge, n, x$Nnode, PACKAGE = "ape")
+    if (method == "score" && (is.null(x$edge.length) || is.null(y$edge.length)))
+        stop("trees must have branch lengths for branch score distance.")
+    nx <- length(x$tip.label)
+    x <- unroot(x)
+    y <- unroot(y)
+    bp1 <- .Call("bipartition", x$edge, nx, x$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]))
+    ny <- length(y$tip.label) # fix by Otto Cordero
+    ## fix by Tim Wallstrom:
+    bp2.tmp <- .Call("bipartition", y$edge, ny, y$Nnode, PACKAGE = "ape")
+    bp2 <- lapply(bp2.tmp, function(xx) sort(y$tip.label[xx]))
+    bp2.comp <- lapply(bp2.tmp, function(xx) setdiff(1:ny, xx))
+    bp2.comp <- lapply(bp2.comp, function(xx) sort(y$tip.label[xx]))
+    ## End
     q1 <- length(bp1)
     q2 <- length(bp2)
     if (method == "PH85") {
         p <- 0
         for (i in 1:q1) {
             for (j in 1:q2) {
-                if (identical(all.equal(bp1[[i]], bp2[[j]]), TRUE)) {
+                if (identical(bp1[[i]], bp2[[j]]) | identical(bp1[[i]], bp2.comp[[j]])) {
                     p <- p + 1
                     break
                 }
             }
         }
-        dT <- if (q1 == q2) 2*(q1 - p) else 2*(min(q1, q2) - p) + abs(q1 - q2)
+        dT <- q1 + q2 - 2 * p # same than:
+        ##dT <- if (q1 == q2) 2*(q1 - p) else 2*(min(q1, q2) - p) + abs(q1 - q2)
     }
-    if (method == "BHV01") {
+    if (method == "score") {
         dT <- 0
         found1 <- FALSE
         found2 <- logical(q2)
         found2[1] <- TRUE
         for (i in 2:q1) {
             for (j in 2:q2) {
-                if (identical(bp1[[i]], bp2[[j]])) {
-                    dT <- dT + abs(x$edge.length[which(x$edge[, 2] == n + i)] -
-                                   y$edge.length[which(y$edge[, 2] == n + j)])
+                if (identical(bp1[[i]], bp2[[j]]) | identical(bp1[[i]], bp2.comp[[j]])) {
+                    dT <- dT + (x$edge.length[which(x$edge[, 2] == nx + i)] -
+                                y$edge.length[which(y$edge[, 2] == ny + j)])^2
                     found1 <- found2[j] <- TRUE
                     break
                 }
             }
             if (found1) found1 <- FALSE
-            else dT <- dT + x$edge.length[which(x$edge[, 2] == n + i)]
+            else dT <- dT + (x$edge.length[which(x$edge[, 2] == nx + i)])^2
         }
         if (!all(found2))
-          dT <- dT + sum(y$edge.length[y$edge[, 2] %in% (n + which(!found2))])
+            dT <- dT + sum((y$edge.length[y$edge[, 2] %in% (ny + which(!found2))])^2)
+        dT <- sqrt(dT)
     }
     dT
 }
@@ -63,17 +72,24 @@ dist.topo <- function(x, y, method = "PH85")
         stop("some tip labels are duplicated in tree no. 1")
     n <- length(ref)
     for (i in 2:length(x)) {
-        if (identical(x[[i]]$tip.label, ref)) next
-        ilab <- match(x[[i]]$tip.label, ref)
-        ## can use tabulate here because 'ilab' contains integers
-        if (any(tabulate(ilab) > 1))
-            stop(paste("some tip labels are duplicated in tree no.", i))
-        if (any(is.na(ilab)))
-            stop(paste("tree no.", i, "has different tip labels"))
-        ie <- match(1:n, x[[i]]$edge[, 2])
-        x[[i]]$edge[ie, 2] <- ilab
+        label <- x[[i]]$tip.label
+        if (!identical(label, ref)) {
+            if (length(label) != length(ref))
+                stop(paste("tree no.", i, "has a different number of tips"))
+            ilab <- match(label, ref)
+            ## can use tabulate here because 'ilab' contains integers
+            if (any(is.na(ilab)))
+                stop(paste("tree no.", i, "has different tip labels"))
+### <FIXME> the test below does not seem useful anymore
+###            if (any(tabulate(ilab) > 1))
+###                stop(paste("some tip labels are duplicated in tree no.", i))
+### </FIXME>
+            ie <- match(1:n, x[[i]]$edge[, 2])
+            x[[i]]$edge[ie, 2] <- ilab
+        }
+        x[[i]]$tip.label <- NULL
     }
-    for (i in 1:length(x)) x[[i]]$tip.label <- NULL
+    x[[1]]$tip.label <- NULL
     attr(x, "TipLabel") <- ref
     x
 }
@@ -195,7 +211,10 @@ boot.phylo <- function(phy, x, FUN, B = 100, block = 1, trees = FALSE)
     storage.mode(phy$Nnode) <- "integer"
     ans <- attr(.Call("prop_part", c(list(phy), boot.tree),
                       B + 1, FALSE, PACKAGE = "ape"), "number") - 1
-    if (trees) ans <- list(BP = ans, trees = boot.tree)
+    if (trees) {
+        class(boot.tree) <- "multiPhylo"
+        ans <- list(BP = ans, trees = boot.tree)
+    }
     ans
 }