3 \alias{coef.corBrownian}
4 \alias{corMatrix.corBrownian}
5 \title{Brownian Correlation Structure}
7 corBrownian(value=1, phy, form=~1)
8 \method{coef}{corBrownian}(object, unconstrained = TRUE, ...)
9 \method{corMatrix}{corBrownian}(object, covariate = getCovariate(object), corr = TRUE, ...)
12 \item{value}{The \eqn{\gamma}{gamma} parameter (default to 1)}
13 \item{phy}{An object of class \code{phylo} representing the phylogeny
14 (with branch lengths) to consider}
15 \item{object}{An (initialized) object of class \code{corBrownian}}
16 \item{corr}{a logical value. If 'TRUE' the function returns the
17 correlation matrix, otherwise it returns the variance/covariance matrix.}
18 \item{form}{ignored for now.}
19 \item{covariate}{ignored for now.}
20 \item{unconstrained}{a logical value. If 'TRUE' the coefficients are returned
21 in unconstrained form (the same used in the optimization
22 algorithm). If 'FALSE' the coefficients are returned in
23 "natural", possibly constrained, form. Defaults to 'TRUE'}
24 \item{\dots}{some methods for these generics require additional arguments.
25 None are used in these methods.}
28 Expected covariance under a Brownian model (Felsenstein 1985, Martins
31 \deqn{V_{ij} = \gamma \times t_a}{Vij = gamma . ta}
33 where \eqn{t_a}{ta} is the distance on the phylogeny between the root
34 and the most recent common ancestor of taxa \eqn{i}{i} and \eqn{j}{j}
35 and \eqn{\gamma}{gamma} is a constant.
38 An object of class \code{corBrownian}, or the coefficient from an
39 object of this class (actually sends \code{numeric(0)}), or the
40 correlation matrix of an initialized object of this class.
42 \author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr}}
44 \code{\link{corClasses}}
47 Felsenstein, J. (1985) Phylogenies and the comparative method.
48 \emph{American Naturalist}, \bold{125}, 1--15.
50 Martins, E. P. and Hansen, T. F. (1997) Phylogenies and the comparative
51 method: a general approach to incorporating phylogenetic information
52 into the analysis of interspecific data. \emph{American Naturalist},