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\name{vcv}
\alias{vcv}
\alias{vcv.phylo}
\alias{vcv.corPhyl}
\title{Phylogenetic Variance-covariance or Correlation Matrix}
\usage{
vcv(phy, ...)
\method{vcv}{phylo}(phy, model = "Brownian", corr = FALSE, ...)
\method{vcv}{corPhyl}(phy, corr = FALSE, ...)
}
\arguments{
\item{phy}{an object of the correct class (see above).}
\item{model}{a character giving the model used to compute the
variances and covariances; only \code{"Brownian"} is available (for
other models, a correlation structure may be used).}
\item{corr}{a logical indicating whether the correlation matrix should
be returned (\code{TRUE}); by default the variance-covariance matrix
is returned (\code{FALSE}).}
\item{\dots}{further arguments to be passed to or from other methods.}
}
\description{
This function computes the expected variances and covariances of a
continuous trait assuming it evolves under a given model.
This is a generic function with methods for objects of class
\code{"phylo"} and \code{"corPhyl"}.
}
\value{
a numeric matrix with the names of the tips as colnames and rownames.
}
\references{
Garland, T. Jr. and Ives, A. R. (2000) Using the past to predict the
present: confidence intervals for regression equations in phylogenetic
comparative methods. \emph{American Naturalist}, \bold{155}, 346--364.
}
\author{Emmanuel Paradis}
\note{
Do not confuse this function with \code{\link[stats]{vcov}} which
computes the variance-covariance matrix among parameters of a fitted
model object.
}
\seealso{
\code{\link{corBrownian}}, \code{\link{corMartins}},
\code{\link{corGrafen}}, \code{\link{corPagel}},
\code{\link{corBlomberg}}, \code{\link{vcv2phylo}}
}
\examples{
tr <- rtree(5)
## all are the same:
vcv(tr)
vcv(corBrownian(1, tr))
vcv(corPagel(1, tr))
}
\keyword{manip}
\keyword{multivariate}
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