\alias{plot.prop.part}
\title{Tree Bipartition and Bootstrapping Phylogenies}
\usage{
-boot.phylo(phy, x, FUN, B = 100, block = 1, trees = FALSE)
+boot.phylo(phy, x, FUN, B = 100, block = 1,
+ trees = FALSE, quiet = FALSE)
prop.part(..., check.labels = TRUE)
prop.clades(phy, ..., part = NULL)
\method{print}{prop.part}(x, ...)
together (see details).}
\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{\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
These functions analyse bipartitions found in a series of trees.
\code{prop.part} counts the number of bipartitions found in a series
- of trees given as \code{\dots}.
+ of trees given as \code{\dots}. If a single tree is passed, the
+ returned object is a list of vectors with the tips descending from
+ each node (i.e., clade compositions indexed by node number).
\code{prop.clades} counts the number of times the bipartitions present
in \code{phy} are present in a series of trees given as \code{\dots} or
Felsenstein, J. (1985) Confidence limits on phylogenies: an approach
using the bootstrap. \emph{Evolution}, \bold{39}, 783--791.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
\code{\link{dist.topo}}, \code{\link{consensus}}, \code{\link{nodelabels}}
}
\examples{
data(woodmouse)
-tr <- nj(dist.dna(woodmouse))
+f <- function(x) nj(dist.dna(x))
+tr <- f(woodmouse)
### Are bootstrap values stable?
for (i in 1:5)
- print(boot.phylo(tr, woodmouse, function(xx) nj(dist.dna(xx))))
+ print(boot.phylo(tr, woodmouse, f, quiet = TRUE))
### How many partitions in 100 random trees of 10 labels?...
TR <- replicate(100, rtree(10), FALSE)
pp10 <- prop.part(TR)