\alias{compar.gee}
\alias{print.compar.gee}
\alias{drop1.compar.gee}
+\alias{predict.compar.gee}
\title{Comparative Analysis with GEEs}
+\description{
+ \code{compar.gee} performs the comparative analysis using generalized
+ estimating equations as described by Paradis and Claude (2002).
+
+ \code{drop1} tests single effects of a fitted model output from
+ \code{compar.gee}.
+
+ \code{predict} returns the predicted (fitted) values of the model.
+}
\usage{
-compar.gee(formula, data = NULL, family = "gaussian", phy,
+compar.gee(formula, data = NULL, family = "gaussian", phy, corStruct,
scale.fix = FALSE, scale.value = 1)
\method{drop1}{compar.gee}(object, scope, quiet = FALSE, ...)
+\method{predict}{compar.gee}(object, type = c("link", "response"), ...)
}
\arguments{
\item{formula}{a formula giving the model to be fitted.}
\item{data}{the name of the data frame where the variables in
\code{formula} are to be found; by default, the variables are looked
for in the global environment.}
- \item{family}{a character string specifying the distribution assumed
- for the response; by default a Gaussian distribution (with link
- identity) is assumed (see \code{?family} for details on specifying
- the distribution, and on changing the link function).}
- \item{phy}{an object of class \code{"phylo"}.}
+ \item{family}{a function specifying the distribution assumed for the
+ response; by default a Gaussian distribution (with link identity) is
+ assumed (see \code{?family} for details on specifying the
+ distribution, and on changing the link function).}
+ \item{phy}{an object of class \code{"phylo"} (ignored if
+ \code{corStruct} is used).}
+ \item{corStruct}{a (phylogenetic) correlation structure.}
\item{scale.fix}{logical, indicates whether the scale parameter should
be fixed (TRUE) or estimated (FALSE, the default).}
\item{scale.value}{if \code{scale.fix = TRUE}, gives the value for the
\item{scope}{<unused>.}
\item{quiet}{a logical specifying whether to display a warning message
about eventual ``marginality principle violation''.}
+ \item{type}{a character string specifying the type of predicted
+ values. By default, the linear (link) prediction is returned.}
\item{\dots}{further arguments to be passed to \code{drop1}.}
}
-\description{
- \code{compar.gee} performs the comparative analysis using generalized
- estimating equations as described by Paradis and Claude (2002).
-
- \code{drop1} tests single effects of a fitted model output from
- \code{compar.gee}.
-}
\details{
If a data frame is specified for the argument \code{data}, then its
rownames are matched to the tip labels of \code{phy}. The user must be
If \code{data = NULL}, then it is assumed that the variables are in
the same order than the tip labels of \code{phy}.
}
+\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.
+}
\value{
\code{compar.gee} returns an object of class \code{"compar.gee"} with
the following components:
\item{effect.assign}{a vector of integers assigning the coefficients
to the effects (used by \code{drop1}).}
\item{nobs}{the number of observations.}
+ \item{QIC}{the quasilikelihood information criterion as defined by Pan
+ (2001).}
\item{coefficients}{the estimated coefficients (or regression parameters).}
\item{residuals}{the regression residuals.}
\item{family}{a character string, the distribution assumed for the response.}
\code{drop1} returns an object of class \code{"\link[stats]{anova}"}.
}
\references{
+ Pan, W. (2001) Akaike's information criterion in generalized
+ estimating equations. \emph{Biometrics}, \bold{57}, 120--125.
+
Paradis, E. and Claude J. (2002) Analysis of comparative data using
generalized estimating equations. \emph{Journal of theoretical
Biology}, \bold{218}, 175--185.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
\code{\link{read.tree}}, \code{\link{pic}},