4 \alias{corMatrix.corGrafen}
5 \title{Grafen's (1989) Correlation Structure}
7 corGrafen(value, phy, form=~1, fixed = FALSE)
8 \method{coef}{corGrafen}(object, unconstrained = TRUE, ...)
9 \method{corMatrix}{corGrafen}(object,
10 covariate = getCovariate(object), corr = TRUE, ...)
13 \item{value}{The \eqn{\alpha}{rho} parameter}
14 \item{phy}{An object of class \code{phylo} representing the phylogeny
15 (branch lengths are ignored) to consider}
16 \item{object}{An (initialized) object of class \code{corGrafen}}
17 \item{corr}{a logical value. If 'TRUE' the function returns the
18 correlation matrix, otherwise it returns the variance/covariance
20 \item{fixed}{an optional logical value indicating whether the
21 coefficients should be allowed to vary in the optimization, or kept
22 fixed at their initial value. Defaults to 'FALSE', in which case the
23 coefficients are allowed to vary.}
24 \item{form}{ignored for now.}
25 \item{covariate}{ignored for now.}
26 \item{unconstrained}{a logical value. If 'TRUE' the coefficients are
27 returned in unconstrained form (the same used in the optimization
28 algorithm). If 'FALSE' the coefficients are returned in "natural",
29 possibly constrained, form. Defaults to 'TRUE'}
30 \item{...}{some methods for these generics require additional
31 arguments. None are used in these methods.}
34 Grafen's (1989) covariance structure. Branch lengths are computed using
35 Grafen's method (see \code{\link{compute.brlen}}). The covariance
36 matrice is then the traditional variance-covariance matrix for a
40 An object of class \code{corGrafen} or the rho coefficient from an
41 object of this class or the correlation matrix of an initialized
44 \author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr}}
46 \code{\link{corClasses}}, \code{\link{compute.brlen}}, \code{\link{vcv.phylo}}.
49 Grafen, A. (1989) The phylogenetic regression. \emph{Philosophical
50 Transactions of the Royal society of London. Series B. Biological
51 Sciences}, \bold{326}, 119--157.