corPagel {ape} | R Documentation

## Pagel's “lambda” Correlation Structure

### 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.

[Package ape version 5.0 Index]