lme4 (version 2.0-6)

devfun2: 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"), ...)

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

optimum

a named vector giving the parameter values at the optimum

basedev

the deviance at the optimum, (i.e., not the REML criterion).

thopt

the optimal variance-covariance parameters on the “theta” (Cholesky factor) scale

stderr

standard errors of fixed effect parameters

Arguments

fm

a fitted model inheriting from class "merMod".

useSc

(logical) indicating whether a scale parameter has been in the model or should be used.

scale

a character string indicating the scale of the argument of the deviance function.

...

arguments passed to the internal profnames function (signames=TRUE to use old-style .sigxx names, FALSE uses (sd_cor|xx); also prefix=c("sd","cor"))

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)))