corGrafen

From ape v2.1-1
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 class 'corGrafen':
coef(object, unconstrained = TRUE, ...)
## S3 method for class 'corGrafen':
corMatrix(object,
covariate = getCovariate(object), corr = TRUE, ...)
Arguments
value
The $\alpha$ 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.