corPagel: Pagel's "lambda" Correlation Structure

In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description

The correlation structure from the present model is derived from the Brownian motion model by multiplying the off-diagonal elements (i.e., the covariances) by lambda. The variances are thus the same than for a Brownian motion model.

Usage

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

Arguments

value	the (initial) value of the parameter lambda.
phy	an object of class "phylo".
form	(ignored).
fixed	a logical specifying whether gls should estimate lambda (the default) or keep it fixed.
object	an (initialized) object of class "corPagel".
covariate	(ignored).
corr	a logical value specifying whether to return the correlation matrix (the default) or the variance-covariance matrix.
unconstrained	a logical value. If TRUE (the default), 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.
...	further arguments passed to or from other methods.

Value

an object of class "corPagel", the coefficients from an object of this class, or the correlation matrix of an initialized object of this class. In most situations, only corPagel will be called by the user.

Author(s)

Emmanuel Paradis

References

Freckleton, R. P., Harvey, P. H. and M. Pagel, M. (2002) Phylogenetic analysis and comparative data: a test and review of evidence. American Naturalist, 160, 712–726.

Pagel, M. (1999) Inferring the historical patterns of biological evolution. Nature, 401,877–884.

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