-## dist.topo.R (2010-01-22)
+## dist.topo.R (2011-02-21)
## Topological Distances, Tree Bipartitions,
## Consensus Trees, and Bootstrapping Phylogenies
-## Copyright 2005-2010 Emmanuel Paradis
+## Copyright 2005-2011 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 == "score" && (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 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]))
ny <- length(y$tip.label) # fix by Otto Cordero
for (i in 2:q1) {
for (j in 2:q2) {
if (identical(bp1[[i]], bp2[[j]]) | identical(bp1[[i]], bp2.comp[[j]])) {
- if (i == 19) browser()
dT <- dT + (x$edge.length[which(x$edge[, 2] == nx + i)] -
y$edge.length[which(y$edge[, 2] == ny + j)])^2
found1 <- found2[j] <- TRUE
stop("some tip labels are duplicated in tree no. 1")
n <- length(ref)
for (i in 2:length(x)) {
- if (identical(x[[i]]$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]]$tip.label <- NULL
attr(x, "TipLabel") <- ref
x
}
if (length(obj) == 1 && class(obj[[1]]) != "phylo")
obj <- obj[[1]]
## <FIXME>
- ## class(obj) <- NULL # needed?
+ ## class(obj) <- NULL # needed? apparently not, see below (2010-11-18)
## </FIXME>
ntree <- length(obj)
if (ntree == 1) check.labels <- FALSE
- if (check.labels) obj <- .compressTipLabel(obj)
+ if (check.labels) obj <- .compressTipLabel(obj) # fix by Klaus Schliep (2011-02-21)
for (i in 1:ntree) storage.mode(obj[[i]]$Nnode) <- "integer"
## <FIXME>
## The 1st must have tip labels
## Maybe simply pass the number of tips to the C code??
- if (!is.null(attr(obj, "TipLabel")))
- for (i in 1:ntree) obj[[i]]$tip.label <- attr(obj, "TipLabel")
+ obj <- .uncompressTipLabel(obj) # fix a bug (2010-11-18)
## </FIXME>
clades <- .Call("prop_part", obj, ntree, TRUE, PACKAGE = "ape")
attr(clades, "number") <- attr(clades, "number")[1:length(clades)]
storage.mode(phy$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
}