-## dist.topo.R (2011-02-21)
+## dist.topo.R (2011-06-14)
## Topological Distances, Tree Bipartitions,
## Consensus Trees, and Bootstrapping Phylogenies
if (any(table(ref) != 1))
stop("some tip labels are duplicated in tree no. 1")
n <- length(ref)
- for (i in 2:length(x)) {
- label <- x[[i]]$tip.label
- if (!identical(label, ref)) {
- if (length(label) != length(ref))
- stop(paste("tree no.", i, "has a different number of tips"))
- ilab <- match(label, ref)
- ## can use tabulate here because 'ilab' contains integers
- if (any(is.na(ilab)))
- stop(paste("tree no.", i, "has different tip labels"))
+ Ntree <- length(x)
+ if (Ntree > 1) {
+ for (i in 2:Ntree) {
+ label <- x[[i]]$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
+ ie <- match(1:n, x[[i]]$edge[, 2])
+ x[[i]]$edge[ie, 2] <- ilab
+ }
+ x[[i]]$tip.label <- NULL
}
- x[[i]]$tip.label <- NULL
}
x[[1]]$tip.label <- NULL
attr(x, "TipLabel") <- ref
n
}
-boot.phylo <- function(phy, x, FUN, B = 100, block = 1, trees = FALSE)
+boot.phylo <- function(phy, x, FUN, B = 100, block = 1,
+ trees = FALSE, quiet = FALSE)
{
if (is.list(x) && !is.data.frame(x)) {
if (inherits(x, "DNAbin")) x <- as.matrix(x)
}
}
boot.tree <- vector("list", B)
+ if (!quiet) progbar <- utils::txtProgressBar(style = 3) # suggestion by Alastair Potts
for (i in 1:B) {
if (block > 1) {
y <- seq(block, ncol(x), block)
boot.samp[y - j] <- boot.i - j
} else boot.samp <- sample(ncol(x), replace = TRUE)
boot.tree[[i]] <- FUN(x[, boot.samp])
+ if (!quiet) utils::setTxtProgressBar(progbar, i/B)
}
+ if (!quiet) close(progbar)
for (i in 1:B) storage.mode(boot.tree[[i]]$Nnode) <- "integer"
storage.mode(phy$Nnode) <- "integer"
- ans <- attr(.Call("prop_part", c(list(phy), boot.tree),
- B + 1, FALSE, PACKAGE = "ape"), "number") - 1
+ ans <- prop.clades(phy, boot.tree)
+ ##ans <- attr(.Call("prop_part", c(list(phy), boot.tree),
+ ## B + 1, FALSE, PACKAGE = "ape"), "number") - 1
if (trees) {
class(boot.tree) <- "multiPhylo"
ans <- list(BP = ans, trees = boot.tree)