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\name{rtree}
\alias{rtree}
\alias{rcoal}
\alias{rmtree}
\alias{rtopology}
\alias{rmtopology}
\title{Generate Random Trees}
\description{
These functions generate trees by splitting randomly the edges
(\code{rtree} and \code{rtopology}) or randomly clustering the tips
(\code{rcoal}). \code{rtree} and \code{rtopology} generate general
trees, and \code{rcoal} generates coalescent trees. The algorithms are
described in Paradis (2012) and in a vignette in this package.
}
\usage{
rtree(n, rooted = TRUE, tip.label = NULL, br = runif, equiprob = FALSE, ...)
rtopology(n, rooted = FALSE, tip.label = NULL, br = runif, ...)
rcoal(n, tip.label = NULL, br = "coalescent", ...)
rmtree(N, n, rooted = TRUE, tip.label = NULL, br = runif,
equiprob = FALSE, ...)
rmtopology(N, n, rooted = FALSE, tip.label = NULL, br = runif, ...)
}
\arguments{
\item{n}{an integer giving the number of tips in the tree.}
\item{rooted}{a logical indicating whether the tree should be rooted
(the default).}
\item{tip.label}{a character vector giving the tip labels; if not
specified, the tips "t1", "t2", ..., are given.}
\item{br}{one of the following: (i) an \R function used to generate the
branch lengths (\code{rtree}; use \code{NULL} to simulate only a
topology), or the coalescence times (\code{rcoal}); (ii) a character
to simulate a genuine coalescent tree for \code{rcoal} (the
default); or (iii) a numeric vector for the branch lengths or the
coalescence times.}
\item{equiprob}{(new since \pkg{ape} 5.4-1) a logical specifying
whether topologies are generated in equal frequencies. If,
\code{FALSE}, the unbalanced topologies are generated in higher
proportions than the balanced ones.}
\item{\dots}{further argument(s) to be passed to \code{br}.}
\item{N}{an integer giving the number of trees to generate.}
}
\details{
The trees generated are bifurcating. If \code{rooted = FALSE} in
(\code{rtree}), the tree is trifurcating at its root.
The option \code{equiprob = TRUE} generates \emph{unlabelled}
topologies in equal frequencies. This is more complicated for the
labelled topologies (see the vignette \dQuote{RandomTopologies}).
The default function to generate branch lengths in \code{rtree} is
\code{runif}. If further arguments are passed to \code{br}, they need
to be tagged (e.g., \code{min = 0, max = 10}).
\code{rmtree} calls successively \code{rtree} and set the class of
the returned object appropriately.
}
\value{
An object of class \code{"phylo"} or of class \code{"multiPhylo"} in
the case of \code{rmtree} or \code{rmtopology}.
}
\references{
Paradis, E. (2012) \emph{Analysis of Phylogenetics and Evolution with
R (Second Edition).} New York: Springer.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{stree}}, \code{\link{rlineage}}, vignette
\dQuote{RandomTopologies}.
}
\examples{
layout(matrix(1:9, 3, 3))
### Nine random trees:
for (i in 1:9) plot(rtree(20))
### Nine random cladograms:
for (i in 1:9) plot(rtree(20, FALSE), type = "c")
### generate 4 random trees of bird orders:
data(bird.orders)
layout(matrix(1:4, 2, 2))
for (i in 1:4)
plot(rcoal(23, tip.label = bird.orders$tip.label), no.margin = TRUE)
layout(1)
par(mar = c(5, 4, 4, 2))
}
\keyword{datagen}
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