Expected covariance under a Brownian model (Felsenstein 1985, Martins and Hansen 1997)
$$V_{ij} = \gamma \times t_a$$
where \(t_a\) is the distance on the phylogeny between the root and the most recent common ancestor of taxa \(i\) and \(j\) and \(\gamma\) is a constant.
corBrownian(value=1, phy, form=~1)
# S3 method for corBrownian
coef(object, unconstrained = TRUE, ...)
# S3 method for corBrownian
corMatrix(object, covariate = getCovariate(object), corr = TRUE, ...)The \(\gamma\) parameter (default to 1)
An object of class phylo representing the phylogeny
(with branch lengths) to consider
An (initialized) object of class corBrownian
a logical value. If 'TRUE' the function returns the correlation matrix, otherwise it returns the variance/covariance matrix.
ignored for now.
ignored for now.
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'
some methods for these generics require additional arguments. None are used in these methods.
An object of class corBrownian, or the coefficient from an
object of this class (actually sends numeric(0)), or the
correlation matrix of an initialized object of this class.
Felsenstein, J. (1985) Phylogenies and the comparative method. American Naturalist, 125, 1--15.
Martins, E. P. and Hansen, T. F. (1997) Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. American Naturalist, 149, 646--667.