-## dist.topo.R (2011-03-26)
+## dist.topo.R (2011-06-14)
## Topological Distances, Tree Bipartitions,
## Consensus Trees, and Bootstrapping Phylogenies
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)