R: Brownian Correlation Structure

corBrownian {ape}

R Documentation

Brownian Correlation Structure

Description

Expected covariance under a Brownian model (Felsenstein 1985, Martins and Hansen 1997)

V_{ij} = \gamma \times t_a

where t_a is the distance on the phylogeny between the root and the most recent common ancestor of taxa i and j and \gamma is a constant.

Usage

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

Arguments

`value`	The `\gamma` parameter (default to 1). The exact value has no effect on model fitting with PGLS.
`phy`	An object of class `phylo` representing the phylogeny (with branch lengths) to consider.
`object`	An (initialized) object of class `corBrownian`.
`corr`	a logical value. If 'TRUE' the function returns the correlation matrix, otherwise it returns the variance/covariance matrix.
`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.
`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).
`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 corBrownian, or the coefficient from an object of this class (actually sends numeric(0)), or the correlation matrix of an initialized object of this class.

Author(s)

Julien Dutheil dutheil@evolbio.mpg.de

References

Felsenstein, J. (1985) Phylogenies and the comparative method. American Naturalist, 125, 1–15.

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.