Usage
corGrafen(value, phy, form=~1, fixed = FALSE)
"coef"(object, unconstrained = TRUE, ...)
"corMatrix"(object, covariate = getCovariate(object), corr = TRUE, ...)
Arguments
phy
An object of class phylo representing the phylogeny
(branch lengths are ignored) to consider
object
An (initialized) object of class corGrafen
corr
a logical value. If 'TRUE' the function returns the
correlation matrix, otherwise it returns the variance/covariance
matrix.
fixed
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.
covariate
ignored for now.
unconstrained
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.