3 \alias{coef.corMartins}
4 \alias{corMatrix.corMartins}
5 \title{Martins's (1997) Correlation Structure}
7 corMartins(value, phy, form = ~1, fixed = FALSE)
8 \method{coef}{corMartins}(object, unconstrained = TRUE, ...)
9 \method{corMatrix}{corMartins}(object,
10 covariate = getCovariate(object), corr = TRUE, ...)
13 \item{value}{The \eqn{\alpha}{alpha} parameter}
14 \item{phy}{An object of class \code{phylo} representing the phylogeny
15 (with branch lengths) to consider}
16 \item{object}{An (initialized) object of class \code{corMartins}}
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, ok 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 returned
27 in unconstrained form (the same used in the optimization
28 algorithm). If 'FALSE' the coefficients are returned in
29 "natural", possibly constrained, form. Defaults to 'TRUE'}
30 \item{\dots}{some methods for these generics require additional arguments.
31 None are used in these methods.}
34 Martins and Hansen's (1997) covariance structure:
35 \deqn{V_{ij} = \gamma \times e^{-\alpha t_{ij}}}{%
36 Vij = gamma . exp(-alpha . tij)}
37 where \eqn{t_{ij}}{tij} is the phylogenetic distance between taxa \eqn{i}{i} and \eqn{j}{j} and \eqn{\gamma}{gamma} is a constant.
40 An object of class \code{corMartins} or the alpha coefficient from an object of this class
41 or the correlation matrix of an initialized object of this class.
43 \author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr}}
45 \code{\link{corClasses}}.
48 Martins, E. P. and Hansen, T. F. (1997) Phylogenies and the comparative
49 method: a general approach to incorporating phylogenetic information
50 into the analysis of interspecific data. \emph{American Naturalist},