merMCMC-class {lme4} | R Documentation |
Objects of class "merMCMC"
are Markov chain Monte Carlo samples
from the distribution of the parameters of a fitted mixed-effects
model.
Objects can be created by calls of the form new("merMCMC", ...)
or, more commonly, via the mer
method for the generic
mcmcsamp
function.
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
.
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
.
signature(x = "merMCMC")
: transform the
ST
and sigma
slots to some combination of variances,
covariances, standard deviations and correlations. See
VarCorr
for details.
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.
signature(x = "merMCMC")
: Same as the
as.data.frame
method described above but returning a matrix.
signature(from = "merMCMC", to = "data.frame")
:
Same as the as.data.frame
method.
signature(object = "merMCMC")
: plot
empirical densities for the parameters from the chain. See also
densityplot
.
signature(object = "merMCMC")
: plot
quantile-quantile plots for the parameters from the sample in the
chain. See also qqmath
.
signature(object = "merMCMC")
: plot
traces of the parameter samples in the chain.
mcmcsamp
produces these objects,
lmer
, glmer
and nlmer
produce the mer
objects.
showClass("merMCMC")