\alias{rTraitCont}
\title{Continuous Character Simulation}
\usage{
-rTraitCont(phy, model = "BM", sigma = 0.1, alpha = 1,
- theta = 0, ancestor = FALSE, root.value = 0)
+rTraitCont(phy, model = "BM", sigma = 0.1, alpha = 1, theta = 0,
+ ancestor = FALSE, root.value = 0, ...)
}
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
values at the nodes as well (by default, only the values at the tips
are returned).}
\item{root.value}{a numeric giving the value at the root.}
+ \item{\dots}{further arguments passed to \code{model} if it is a
+ function.}
}
\description{
This function simulates the evolution of a continuous character along a
\item{\code{"OU"}:}{an Ornstein-Uhlenbeck model is used. The above
indexing rule is used for the three parameters \code{sigma},
- \code{alpha}, and \code{theta}. This may be more interesting for the
- last one to model varying phenotypic optima. Be careful that large
- values of \code{alpha} may give unrealistic output.}
+ \code{alpha}, and \code{theta}. This may be interesting for the last
+ one to model varying phenotypic optima. The exact updating formula
+ from Gillespie (1996) are used which are reduced to BM formula if
+ \code{alpha = 0}.}
\item{A function:}{it must be of the form \code{foo(x, l)} where
\code{x} is the trait of the ancestor and \code{l} is the branch
length. It must return the value of the descendant. The arguments
\code{sigma}, \code{alpha}, and \code{theta} are ignored.}
}}
-\note{
- Currently, the OU model is a bit difficult to tune. Hopefully, this
- may be improved in the future.
-}
\value{
A numeric vector with names taken from the tip labels of
\code{phy}. If \code{ancestor = TRUE}, the node labels are used if
present, otherwise, ``Node1'', ``Node2'', etc.
}
\references{
+ Gillespie, D. T. (1996) Exact numerical simulation of the
+ Ornstein-Uhlenbeck process and its integral. \emph{Physical Review E},
+ \bold{54}, 2084--2091.
+
Paradis, E. (2006) \emph{Analyses of Phylogenetics and Evolution with
R.} New York: Springer.
}
\author{Emmanuel Paradis}
\seealso{
- \code{\link{rTraitDisc}}, \code{\link{ace}}
+ \code{\link{rTraitDisc}}, \code{\link{rTraitMult}}, \code{\link{ace}}
}
\examples{
data(bird.orders)