\alias{plot.prop.part}
\title{Tree Bipartition and Bootstrapping Phylogenies}
\usage{
-boot.phylo(phy, x, FUN, B = 100, block = 1, trees = FALSE)
-prop.part(..., check.labels = FALSE)
-prop.clades(phy, ..., part = NULL)
+boot.phylo(phy, x, FUN, B = 100, block = 1,
+ trees = FALSE, quiet = FALSE, rooted = FALSE)
+prop.part(..., check.labels = TRUE)
+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, ...)
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{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
arguments for the plot (see details).}
\item{check.labels}{a logical specifying whether to check the labels
- of each tree. If \code{FALSE} (the default), it is assumed that all
- trees have the same tip labels, and that they are in the same order
- (see details).}
+ of each tree. If \code{FALSE}, it is assumed that all trees have the
+ same tip labels, and that they are in the same order (see details).}
\item{part}{a list of partitions as returned by \code{prop.part}; if
this is used then \code{\dots} is ignored.}
\item{object}{an object of class \code{"prop.part"}.}
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
be resampled altogether. For instance, if one wants to resample at the
codon-level, then \code{block = 3} must be used.
- Using (the default) \code{check.labels = FALSE} in \code{prop.part}
- results in considerable decrease in computing times. This requires that
- (i) all trees have the same tip labels, \emph{and} (ii) these labels
- are ordered similarly in all trees (in other words, the element
- \code{tip.label} are identical in all trees).
+ Using \code{check.labels = FALSE} in \code{prop.part} decreases
+ computing times. This requires that (i) all trees have the same tip
+ labels, \emph{and} (ii) these labels are ordered similarly in all
+ trees (in other words, the element \code{tip.label} are identical in
+ all trees).
The plot function represents a contingency table of the different
partitions (on the \emph{x}-axis) in the lower panel, and their observed
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
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)
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}