-\name{vcv.phylo}
+\name{vcv}
+\alias{vcv}
\alias{vcv.phylo}
+\alias{vcv.corPhyl}
\title{Phylogenetic Variance-covariance or Correlation Matrix}
\usage{
-vcv.phylo(phy, model = "Brownian", cor = FALSE)
+vcv(phy, ...)
+\method{vcv}{phylo}(phy, model = "Brownian", corr = FALSE, ...)
+\method{vcv}{corPhyl}(phy, corr = FALSE, ...)
}
\arguments{
- \item{phy}{an object of class \code{"phylo"}.}
+ \item{phy}{an object of the correct class (see above).}
\item{model}{a character giving the model used to compute the
- variances and covariances of the phynotype; by default
- \code{"Brownian"}. Currently only the Brownian model is available.}
- \item{cor}{a logical indicating whether the correlation matrix should
+ 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 phenotype assuming it evolves under a given model
- (currently only the model of Brownian motion is available).
+ 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 given by the \code{tip.label}
- of the argument \code{phy}) as colnames and rownames.
+ 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
comparative methods. \emph{American Naturalist}, \bold{155}, 346--364.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\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{read.tree}} to read tree files in Newick format
+ \code{\link{corBrownian}}, \code{\link{corMartins}},
+ \code{\link{corGrafen}}, \code{\link{corPagel}},
+ \code{\link{corBlomberg}}
+}
+\examples{
+tr <- rtree(5)
+## all are the same:
+vcv(tr)
+vcv(corBrownian(1, tr))
+vcv(corPagel(1, tr))
}
\keyword{manip}
\keyword{multivariate}