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compar.gee

Comparative Analysis with GEEs

Description

compar.gee performs the comparative analysis using generalized estimating equations as described by Paradis and Claude (2002).

drop1 tests single effects of a fitted model output from compar.gee.

predict returns the predicted (fitted) values of the model.

Usage

compar.gee(formula, data = NULL, family = "gaussian", phy, corStruct,
          scale.fix = FALSE, scale.value = 1)
## S3 method for class 'compar.gee'
drop1(object, scope, quiet = FALSE, ...)
## S3 method for class 'compar.gee'
predict(object, newdata = NULL, type = c("link", "response"), ...)

Arguments

`formula`	a formula giving the model to be fitted.
`data`	the name of the data frame where the variables in `formula` are to be found; by default, the variables are looked for in the global environment.
`family`	a function specifying the distribution assumed for the response; by default a Gaussian distribution (with link identity) is assumed (see `?family` for details on specifying the distribution, and on changing the link function).
`phy`	an object of class `"phylo"` (ignored if `corStruct` is used).
`corStruct`	a (phylogenetic) correlation structure.
`scale.fix`	logical, indicates whether the scale parameter should be fixed (TRUE) or estimated (FALSE, the default).
`scale.value`	if `scale.fix = TRUE`, gives the value for the scale (default: `scale.value = 1`).
`object`	an object of class `"compar.gee"` resulting from fitting `compar.gee`.
`scope`	<unused>.
`quiet`	a logical specifying whether to display a warning message about eventual “marginality principle violation”.
`newdata`	a data frame with column names matching the variables in the formula of the fitted object (see `predict` for details).
`type`	a character string specifying the type of predicted values. By default, the linear (link) prediction is returned.
`...`	further arguments to be passed to `drop1`.

Details

If a data frame is specified for the argument data, then its rownames are matched to the tip labels of phy. The user must be careful here since the function requires that both series of names perfectly match, so this operation may fail if there is a typing or syntax error. If both series of names do not match, the values in the data frame are taken to be in the same order than the tip labels of phy, and a warning message is issued.

If data = NULL, then it is assumed that the variables are in the same order than the tip labels of phy.

Value

compar.gee returns an object of class "compar.gee" with the following components:

`call`	the function call, including the formula.
`effect.assign`	a vector of integers assigning the coefficients to the effects (used by `drop1`).
`nobs`	the number of observations.
`QIC`	the quasilikelihood information criterion as defined by Pan (2001).
`coefficients`	the estimated coefficients (or regression parameters).
`residuals`	the regression residuals.
`family`	a character string, the distribution assumed for the response.
`link`	a character string, the link function used for the mean function.
`scale`	the scale (or dispersion parameter).
`W`	the variance-covariance matrix of the estimated coefficients.
`dfP`	the phylogenetic degrees of freedom (see Paradis and Claude for details on this).

drop1 returns an object of class "anova".

predict returns a vector or a data frame if newdata is used.

Note

The calculation of the phylogenetic degrees of freedom is likely to be approximative for non-Brownian correlation structures (this will be refined soon).

The calculation of the quasilikelihood information criterion (QIC) needs to be tested.

Author(s)

Emmanuel Paradis

References

Pan, W. (2001) Akaike's information criterion in generalized estimating equations. Biometrics, 57, 120–125.

Paradis, E. and Claude J. (2002) Analysis of comparative data using generalized estimating equations. Journal of theoretical Biology, 218, 175–185.

Examples

### The example in Phylip 3.5c (originally from Lynch 1991)
### (the same analysis than in help(pic)...)
tr <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);"
tree.primates <- read.tree(text = tr)
X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
### Both regressions... the results are quite close to those obtained
### with pic().
compar.gee(X ~ Y, phy = tree.primates)
compar.gee(Y ~ X, phy = tree.primates)
### Now do the GEE regressions through the origin: the results are quite
### different!
compar.gee(X ~ Y - 1, phy = tree.primates)
compar.gee(Y ~ X - 1, phy = tree.primates)

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