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corGrafen

Grafen's (1989) Correlation Structure

Description

Grafen's (1989) covariance structure. Branch lengths are computed using Grafen's method (see compute.brlen). The covariance matrice is then the traditional variance-covariance matrix for a phylogeny.

Usage

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

Arguments

`value`	The rho parameter
`phy`	An object of class `phylo` representing the phylogeny (branch lengths are ignored) to consider
`object`	An (initialized) object of class `corGrafen`
`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, or kept fixed at their initial value. Defaults to 'FALSE', in which case the coefficients are allowed to vary.
`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 corGrafen or the rho coefficient from an object of this class or the correlation matrix of an initialized object of this class.

Author(s)

Julien Dutheil dutheil@evolbio.mpg.de

References

Grafen, A. (1989) The phylogenetic regression. Philosophical Transactions of the Royal society of London. Series B. Biological Sciences, 326, 119–157.

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24