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\name{corBlomberg}
\alias{corBlomberg}
\alias{coef.corBlomberg}
\alias{corMatrix.corBlomberg}
\title{Blomberg et al.'s Correlation Structure}
\usage{
corBlomberg(value, phy, form = ~1, fixed = FALSE)
\method{corMatrix}{corBlomberg}(object, covariate = getCovariate(object),
corr = TRUE, ...)
\method{coef}{corBlomberg}(object, unconstrained = TRUE, \dots)
}
\arguments{
\item{value}{the (initial) value of the parameter \eqn{g}{g}.}
\item{phy}{an object of class \code{"phylo"}.}
\item{form}{a one sided formula of the form ~ t, or ~ t | g,
specifying the taxa covariate t and, optionally, a grouping factor
g. A covariate for this correlation structure must be character
valued, with entries matching the tip labels in the phylogenetic
tree. When a grouping factor is present in form, the correlation
structure is assumed to apply only to observations within the same
grouping level; observations with different grouping levels are
assumed to be uncorrelated. Defaults to ~ 1, which corresponds to
using the order of the observations in the data as a covariate, and
no groups.}
\item{fixed}{a logical specifying whether \code{gls} should
estimate \eqn{\gamma}{gamma} (the default) or keep it fixed.}
\item{object}{an (initialized) object of class \code{"corBlomberg"}.}
\item{covariate}{an optional covariate vector (matrix), or list of
covariate vectors (matrices), at which values the correlation
matrix, or list of correlation matrices, are to be
evaluated. Defaults to getCovariate(object).}
\item{corr}{a logical value specifying whether to return the
correlation matrix (the default) or the variance-covariance matrix.}
\item{unconstrained}{a logical value. If \code{TRUE} (the default),
the coefficients are returned in unconstrained form (the same used
in the optimization algorithm). If \code{FALSE} the coefficients are
returned in ``natural'', possibly constrained, form.}
\item{\dots}{further arguments passed to or from other methods.}
}
\description{
The ``ACDC'' (accelerated/decelerated) model assumes that continuous
traits evolve under a Brownian motion model which rates accelerates
(if \eqn{g}{g} < 1) or decelerates (if \eqn{g}{g} > 1) through
time. If \eqn{g}{g} = 1, then the model reduces to a Brownian motion
model.
}
\value{
an object of class \code{"corBlomberg"}, the coefficients from an
object of this class, or the correlation matrix of an initialized
object of this class. In most situations, only \code{corBlomberg} will
be called by the user.
}
\author{Emmanuel Paradis}
\references{
Blomberg, S. P., Garland, Jr, T., and Ives, A. R. (2003) Testing for
phylogenetic signal in comparative data: behavioral traits are more
labile. \emph{Evolution}, \bold{57}, 717--745.
}
\keyword{models}
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