ape: corPagel – R documentation

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corPagel

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`	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 lambda (the default) or keep it fixed.
`object`	an (initialized) object of class `"corPagel"`.
`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 "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.

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

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