corGrafen: Grafen's (1989) Correlation Structure

In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description

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.

Usage

corGrafen(value, phy, form=~1, fixed = FALSE)
## S3 method for class 'corGrafen'
coef(object, unconstrained = TRUE, ...)
## S3 method for class 'corGrafen'
corMatrix(object,
                  covariate = getCovariate(object), corr = TRUE, ...)

Arguments

value	The rho parameter
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.
form	ignored for now.
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.

Value

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.

Author(s)

Julien Dutheil [e-mail]

References

Grafen, A. (1989) The phylogenetic regression. Philosophical Transactions of the Royal society of London. Series B. Biological Sciences, 326, 119–157.

See Also

corClasses, compute.brlen, vcv.phylo.

gjuggler/ape documentation built on May 17, 2019, 6:03 a.m.