R: Blomberg et al.'s Correlation Structure

corBlomberg {ape} | R Documentation

## Blomberg et al.'s Correlation Structure

### Description

The “ACDC” (accelerated/decelerated) model assumes that continuous traits evolve under a Brownian motion model which rates accelerates (if g < 1) or decelerates (if g > 1) through time. If g = 1, then the model reduces to a Brownian motion model.

### Usage

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

### Arguments

`value` | the (initial) value of the parameter g.
`phy` | an object of class `"phylo"`.
`form` | a one sided formula of the form ~ t, or ~ t | g, specifying the taxa covariate t and, optionally, a grouping factor g. A covariate for this correlation structure must be character valued, with entries matching the tip labels in the phylogenetic tree. When a grouping factor is present in form, the correlation structure is assumed to apply only to observations within the same grouping level; observations with different grouping levels are assumed to be uncorrelated. Defaults to ~ 1, which corresponds to using the order of the observations in the data as a covariate, and no groups.
`fixed` | a logical specifying whether `gls` should estimate gamma (the default) or keep it fixed.
`object` | an (initialized) object of class `"corBlomberg"`.
`covariate` | an optional covariate vector (matrix), or list of covariate vectors (matrices), at which values the correlation matrix, or list of correlation matrices, are to be evaluated. Defaults to getCovariate(object).
`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 `"corBlomberg"`, the coefficients from an object of this class, or the correlation matrix of an initialized object of this class. In most situations, only `corBlomberg` will be called by the user.

### Author(s)

Emmanuel Paradis

### References

Blomberg, S. P., Garland, Jr, T., and Ives, A. R. (2003) Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution, 57, 717–745.

[Package ape version 5.4 Index]