-## dist.topo.R (2008-06-28)
+## dist.topo.R (2010-05-06)
## Topological Distances, Tree Bipartitions,
## Consensus Trees, and Bootstrapping Phylogenies
-## Copyright 2005-2008 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$edge.length)))
+ stop("trees must have branch lengths for Billera et al.'s distance.")
+ nx <- length(x$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$edge[, 2] %in% (ny + which(!found2))])^2)
+ dT <- sqrt(dT)
}
dT
}
stop(paste("tree no.", i, "has different tip labels"))
ie <- match(1:n, x[[i]]$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
}
## 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>
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)