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\name{devfun2}
\alias{devfun2}
\title{Deviance Function in Terms of Standard Deviations/Correlations}
\description{
The deviance is profiled with respect to the fixed-effects
parameters but not with respect to sigma; that is, the
function takes parameters for the variance-covariance parameters
and for the residual standard deviation. The random-effects
variance-covariance parameters are on the standard deviation/correlation
scale, not the theta (Cholesky factor) scale.
}
\usage{
devfun2(fm, useSc = if(isLMM(fm)) TRUE else NA,
scale = c("sdcor", "varcov"), ...)
}
\arguments{
\item{fm}{a fitted model inheriting from class \code{"\linkS4class{merMod}"}.}
\item{useSc}{(\code{\link{logical}}) indicating whether a scale parameter
has been in the model or should be used.}% FIXME, see also ../R/profile.R
\item{scale}{a character string indicating the scale of the argument
of the deviance function.}
\item{\dots}{
arguments passed to the internal \code{profnames} function
(\code{signames=TRUE} to use old-style \code{.sigxx names},
\code{FALSE} uses (sd_cor|xx);
also \code{prefix=c("sd","cor")})
}
}
\value{
Returns a function that takes a vector of standard deviations and
correlations and returns the deviance (or REML criterion). The
function has additional attributes
\describe{
\item{optimum}{a named vector giving the parameter values
at the optimum}
\item{basedev}{the deviance at the optimum, (i.e., \emph{not} the
REML criterion).}
\item{thopt}{the optimal variance-covariance parameters on the
\dQuote{theta} (Cholesky factor) scale}
\item{stderr}{standard errors of fixed effect parameters}
}
}
\note{
Even if the original model was fitted using \code{REML=TRUE} as by default
with \code{\link{lmer}()}, this returns the deviance, i.e., the objective
function for maximum (log) likelihood (ML).
For the REML objective function, use \code{\link{getME}(fm, "devfun")}
instead.
}
\examples{
m1 <- lmer(Reaction~Days+(Days|Subject),sleepstudy)
dd <- devfun2(m1, useSc=TRUE)
pp <- attr(dd, "optimum")
## extract variance-covariance and residual std dev parameters
sigpars <- pp[grepl("^\\\\.sig", names(pp))]
all.equal(unname(dd(sigpars)),deviance(refitML(m1)))
}
\keyword{utilities}
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