# corGrafen

From ape v5.3
0th

Percentile

##### Grafen's (1989) Correlation Structure

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.

Keywords
models
##### Usage
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, ...)
##### 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.

##### References

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

corClasses, compute.brlen, vcv.phylo.