Mixed-model Markov chain Monte Carlo results

Description

Objects of class "merMCMC" are Markov chain Monte Carlo samples from the distribution of the parameters of a fitted mixed-effects model.

Objects from the Class

Objects can be created by calls of the form new("merMCMC", ...) or, more commonly, via the mer method for the generic mcmcsamp function.

Slots

Gp:

a copy of the Gp slot of the original mer object

ST:

matrix of samples from the parameters determining the ST slot of the mer object

call:

Matched call from the original mer object

deviance:

vector of samples of the (ML) deviance

dims:

a copy of the dims slot of the original mer object

fixef:

matrix of samples of the fixed-effects parameters

nc:

Integer vector of length dims["nf"]. The number of columns of random effects in each term.

ranef:

matrix of samples of the random effects. This matrix has zero columns unless saveb = TRUE is specified in the call to mcmcsamp. Consider the size of this matrix, which could be very large, before setting saveb = TRUE.

sigma:

vector of samples of the common scale parameter or numeric(0) if dims["useSc"] is FALSE.

Methods

HPDinterval

signature(object = "merMCMC"): use the chain to calculate Highest Posterior Density (HPD) intervals of a given empirical probability content for the model parameters. See HPDinterval.

VarCorr

signature(x = "merMCMC"): transform the ST and sigma slots to some combination of variances, covariances, standard deviations and correlations. See VarCorr for details.

as.data.frame

signature(x = "merMCMC"): returns the fixef-effects and variance-covariance parameters from the chain in the form of a data frame. The type argument for the VarCorr method can be passed to this method to select the type of variance-covariance parameters returned.

as.matrix

signature(x = "merMCMC"): Same as the as.data.frame method described above but returning a matrix.

coerce

signature(from = "merMCMC", to = "data.frame"): Same as the as.data.frame method.

densityplot

signature(object = "merMCMC"): plot empirical densities for the parameters from the chain. See also densityplot.

qqmath

signature(object = "merMCMC"): plot quantile-quantile plots for the parameters from the sample in the chain. See also qqmath.

xyplot

signature(object = "merMCMC"): plot traces of the parameter samples in the chain.

See Also

mcmcsamp produces these objects, lmer, glmer and nlmer produce the mer objects.

Examples

showClass("merMCMC")