https://github.com/cran/ape
Tip revision: 1330e272d62c723b8073c95b066950b294f59697 authored by Emmanuel Paradis on 20 October 2012, 00:00:00 UTC
version 3.0-6
version 3.0-6
Tip revision: 1330e27
corGrafen.Rd
\name{corGrafen}
\alias{corGrafen}
\alias{coef.corGrafen}
\alias{corMatrix.corGrafen}
\title{Grafen's (1989) Correlation Structure}
\usage{
corGrafen(value, phy, form=~1, fixed = FALSE)
\method{coef}{corGrafen}(object, unconstrained = TRUE, ...)
\method{corMatrix}{corGrafen}(object,
covariate = getCovariate(object), corr = TRUE, ...)
}
\arguments{
\item{value}{The \eqn{\rho}{rho} parameter}
\item{phy}{An object of class \code{phylo} representing the phylogeny
(branch lengths are ignored) to consider}
\item{object}{An (initialized) object of class \code{corGrafen}}
\item{corr}{a logical value. If 'TRUE' the function returns the
correlation matrix, otherwise it returns the variance/covariance
matrix.}
\item{fixed}{an optional logical value indicating whether the
coefficients should be allowed to vary in the optimization, or kept
fixed at their initial value. Defaults to 'FALSE', in which case the
coefficients are allowed to vary.}
\item{form}{ignored for now.}
\item{covariate}{ignored for now.}
\item{unconstrained}{a logical value. If 'TRUE' the coefficients are
returned in unconstrained form (the same used in the optimization
algorithm). If 'FALSE' the coefficients are returned in "natural",
possibly constrained, form. Defaults to 'TRUE'}
\item{\dots}{some methods for these generics require additional
arguments. None are used in these methods.}
}
\description{
Grafen's (1989) covariance structure. Branch lengths are computed using
Grafen's method (see \code{\link{compute.brlen}}). The covariance
matrice is then the traditional variance-covariance matrix for a
phylogeny.
}
\value{
An object of class \code{corGrafen} or the rho coefficient from an
object of this class or the correlation matrix of an initialized
object of this class.
}
\author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr}}
\seealso{
\code{\link{corClasses}}, \code{\link{compute.brlen}}, \code{\link{vcv.phylo}}.
}
\references{
Grafen, A. (1989) The phylogenetic regression. \emph{Philosophical
Transactions of the Royal society of London. Series B. Biological
Sciences}, \bold{326}, 119--157.
}
\keyword{models}