Grafen's (1989) covariance structure. Branch lengths are computed using
Grafen's method (see compute.brlen). The covariance
matrice is then the traditional variance-covariance matrix for a
phylogeny.
corGrafen(value, phy, form=~1, fixed = FALSE)
# S3 method for corGrafen
coef(object, unconstrained = TRUE, ...)
# S3 method for corGrafen
corMatrix(object,
covariate = getCovariate(object), corr = TRUE, ...)The \(\rho\) parameter
An object of class phylo representing the phylogeny
(branch lengths are ignored) to consider
An (initialized) object of class corGrafen
a logical value. If 'TRUE' the function returns the correlation matrix, otherwise it returns the variance/covariance matrix.
an optional logical value indicating whether the coefficients should be allowed to vary in the optimization, or kept fixed at their initial value. Defaults to 'FALSE', in which case the coefficients are allowed to vary.
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 corGrafen or the rho coefficient from an
object of this class or the correlation matrix of an initialized
object of this class.
Grafen, A. (1989) The phylogenetic regression. Philosophical Transactions of the Royal society of London. Series B. Biological Sciences, 326, 119--157.