o read.dna(, "fasta") may add '\r' in labels: this is fixed.
+ o prop.clades() returned wrong numbers when the tip labels of
+ 'phy' are not in the same order than the list of trees (thanks
+ to Rupert Collins for the report).
+
CHANGES IN APE VERSION 3.0-7
-## dist.topo.R (2012-12-12)
+## dist.topo.R (2013-02-09)
## Topological Distances, Tree Bipartitions,
## Consensus Trees, and Bootstrapping Phylogenies
-## Copyright 2005-2012 Emmanuel Paradis
+## Copyright 2005-2013 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
y$tip.label <- NULL
y
}
+ x <- unclass(x) # another killer improvement by Tucson's hackathon (1/2/2013)
x <- lapply(x, relabel)
attr(x, "TipLabel") <- ref
class(x) <- "multiPhylo"
part <- prop.part(obj, check.labels = TRUE)
}
+ ## until ape 3.0-7 it was assumed implicitly that the labels in phy
+ ## are in the same order than in 'part' (bug report by Rupert Collins)
+ if (!identical(phy$tip.label, attr(part, "labels"))) {
+ i <- match(phy$tip.label, attr(part, "labels"))
+ j <- match(seq_len(Ntip(phy)), phy$edge[, 2])
+ phy$edge[j, 2] <- i
+ phy$tip.label <- attr(part, "labels")
+ }
bp <- prop.part(phy)
if (!rooted) {
bp <- postprocess.prop.part(bp)
for (i in 1:5)
print(boot.phylo(tr, woodmouse, f, quiet = TRUE))
### How many partitions in 100 random trees of 10 labels?...
-TR <- replicate(100, rtree(10), FALSE)
+TR <- rmtree(100, 10)
pp10 <- prop.part(TR)
length(pp10)
### ... and in 100 random trees of 20 labels?
-TR <- replicate(100, rtree(20), FALSE)
+TR <- rmtree(100, 20)
pp20 <- prop.part(TR)
length(pp20)
plot(pp10, pch = "x", col = 2)