\title{Tree Bipartition and Bootstrapping Phylogenies}
\usage{
boot.phylo(phy, x, FUN, B = 100, block = 1,
- trees = FALSE, quiet = FALSE)
+ trees = FALSE, quiet = FALSE, rooted = FALSE)
prop.part(..., check.labels = TRUE)
-prop.clades(phy, ..., part = NULL)
+prop.clades(phy, ..., part = NULL, rooted = FALSE)
\method{print}{prop.part}(x, ...)
\method{summary}{prop.part}(object, ...)
\method{plot}{prop.part}(x, barcol = "blue", leftmar = 4, ...)
\item{trees}{a logical specifying whether to return the bootstraped
trees (\code{FALSE} by default).}
\item{quiet}{a logical: a progress bar is displayed by default.}
+ \item{rooted}{a logical specifying whether the trees should be treated
+ as rooted or not (the default).}
\item{\dots}{either (i) a single object of class \code{"phylo"}, (ii) a
series of such objects separated by commas, or (iii) a list
containing such objects. In the case of \code{plot} further
passed as \code{\dots} fulfills conditions (i) and (ii) above, then it
might be faster to first call, e.g., \code{pp <- prop.part(...)}, then
use the option \code{part}: \code{prop.clades(phy, part = pp)}.
+
+ You have to be careful that by default \code{prop.clades} considers
+ the trees as unrooted and this may result in spurious results if the
+ trees are rooted (see examples).
}
\value{
\code{prop.part} returns an object of class \code{"prop.part"} which
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)
plot(pp20, pch = "x", col = 2)
+
+set.seed(1)
+tr <- rtree(10) # rooted by default
+prop.clades(tr, tr) # clearly wrong
+prop.clades(tr, tr, rooted = TRUE)
+tr <- rtree(10, rooted = FALSE)
+prop.clades(tr, tr) # correct
}
\keyword{manip}
\keyword{htest}