-## dist.topo.R (2010-01-25)
+## dist.topo.R (2010-05-25)
## 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("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
}
x[[1]]$tip.label <- NULL