R: Martins's (1997) Correlation Structure

corMartins {ape} | R Documentation

## Martins's (1997) Correlation Structure

### Description

Martins and Hansen's (1997) covariance structure:

Vij = gamma . exp(-alpha . tij)

where tij is the phylogenetic distance between taxa i and j and gamma is a constant.

### Usage

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

### Arguments

`value` | The alpha parameter
`phy` | An object of class `phylo` representing the phylogeny (with branch lengths) to consider
`object` | An (initialized) object of class `corMartins`
`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, ok 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 `corMartins` or the alpha coefficient from an object of this class or the correlation matrix of an initialized object of this class.

### Author(s)

Julien Dutheil julien.dutheil@univ-montp2.fr

### References

Martins, E. P. and Hansen, T. F. (1997) Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. American Naturalist, 149, 646–667.

### See Also

`corClasses`.

[Package ape version 5.0 Index]