-## dist.topo.R (2009-07-06)
+## dist.topo.R (2010-01-22)
## 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)))
+ 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.")
- n <- length(x$tip.label)
- bp1 <- .Call("bipartition", x$edge, n, x$Nnode, PACKAGE = "ape")
+ nx <- length(x$tip.label)
+ 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
## fix by Tim Wallstrom:
- bp2.tmp <- .Call("bipartition", y$edge, n, y$Nnode, PACKAGE = "ape")
+ bp2.tmp <- .Call("bipartition", y$edge, ny, y$Nnode, PACKAGE = "ape")
bp2 <- lapply(bp2.tmp, function(xx) sort(y$tip.label[xx]))
- bp2.comp <- lapply(bp2.tmp, function(xx) setdiff(1:n, xx))
+ bp2.comp <- lapply(bp2.tmp, function(xx) setdiff(1:ny, xx))
bp2.comp <- lapply(bp2.comp, function(xx) sort(y$tip.label[xx]))
## End
q1 <- length(bp1)
p <- 0
for (i in 1:q1) {
for (j in 1:q2) {
- if (identical(bp1[[i]], bp2[[j]]) |
- identical(bp1[[i]], bp2.comp[[j]])) {
+ if (identical(bp1[[i]], bp2[[j]]) | identical(bp1[[i]], bp2.comp[[j]])) {
p <- p + 1
break
}
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]])) {
+ 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
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
}