-## dist.topo.R (2010-01-25)
+## dist.topo.R (2010-05-06)
## Topological Distances, Tree Bipartitions,
## Consensus Trees, and Bootstrapping Phylogenies
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(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
}