merModclass  R Documentation 
A mixedeffects model is represented as a
merPredD
object and a response
module of a class that inherits from class
lmResp
. A model with a
lmerResp
response has class lmerMod
; a
glmResp
response has class glmerMod
; and a
nlsResp
response has class nlmerMod
.
## S3 method for class 'merMod' anova(object, ..., refit = TRUE, model.names=NULL) ## S3 method for class 'merMod' as.function(x, ...) ## S3 method for class 'merMod' coef(object, ...) ## S3 method for class 'merMod' deviance(object, REML = NULL, ...) REMLcrit(object) ## S3 method for class 'merMod' extractAIC(fit, scale = 0, k = 2, ...) ## S3 method for class 'merMod' family(object, ...) ## S3 method for class 'merMod' formula(x, fixed.only = FALSE, random.only = FALSE, ...) ## S3 method for class 'merMod' fitted(object, ...) ## S3 method for class 'merMod' logLik(object, REML = NULL, ...) ## S3 method for class 'merMod' nobs(object, ...) ## S3 method for class 'merMod' ngrps(object, ...) ## S3 method for class 'merMod' terms(x, fixed.only = TRUE, random.only = FALSE, ...) ## S3 method for class 'merMod' vcov(object, correlation = TRUE, sigm = sigma(object), use.hessian = NULL, ...) ## S3 method for class 'merMod' model.frame(formula, fixed.only = FALSE, ...) ## S3 method for class 'merMod' model.matrix(object, type = c("fixed", "random", "randomListRaw"), ...) ## S3 method for class 'merMod' print(x, digits = max(3, getOption("digits")  3), correlation = NULL, symbolic.cor = FALSE, signif.stars = getOption("show.signif.stars"), ranef.comp = "Std.Dev.", ...) ## S3 method for class 'merMod' summary(object, correlation = , use.hessian = NULL, ...) ## S3 method for class 'summary.merMod' print(x, digits = max(3, getOption("digits")  3), correlation = NULL, symbolic.cor = FALSE, signif.stars = getOption("show.signif.stars"), ranef.comp = c("Variance", "Std.Dev."), show.resids = TRUE, ...) ## S3 method for class 'merMod' update(object, formula., ..., evaluate = TRUE) ## S3 method for class 'merMod' weights(object, type = c("prior", "working"), ...)
object 
an R object of class 
x 
an R object of class 
fit 
an R object of class 
formula 
in the case of 
refit 
logical indicating if objects of class 
model.names 
character vectors of model names to be used in the anova table. 
scale 
Not currently used (see 
k 
see 
REML 
Logical. If 
fixed.only 
logical indicating if only the fixed effects components (terms or formula elements) are sought. If false, all components, including random ones, are returned. 
random.only 
complement of 
correlation 
(logical)
for 
use.hessian 
(logical) indicates whether to use the
finitedifference Hessian of the deviance function to compute
standard errors of the fixed effects, rather estimating
based on internal information about the inverse of
the model matrix (see

sigm 
the residual standard error; by default 
digits 
number of significant digits for printing 
symbolic.cor 
should a symbolic encoding of the fixedeffects correlation
matrix be printed? If so, the 
signif.stars 
(logical) should significance stars be used? 
ranef.comp 
character vector of length one or two, indicating if randomeffects parameters should be reported on the variance and/or standard deviation scale. 
show.resids 
should the quantiles of the scaled residuals be printed? 
formula. 
see 
evaluate 
see 
type 
For

... 
potentially further arguments passed from other methods. 
Objects of class merMod
are created by calls to
lmer
, glmer
or nlmer
.
The following S3 methods with arguments given above exist (this list is currently not complete):
anova
:returns the sequential decomposition of the contributions of
fixedeffects terms or, for multiple arguments, model comparison statistics.
For objects of class lmerMod
the default behavior is to refit the models
with ML if fitted with REML = TRUE
, this can be controlled via the
refit
argument. See also anova
.
as.function
:returns the deviance function, the same as
lmer(*, devFunOnly=TRUE)
, and mkLmerDevfun()
or mkGlmerDevfun()
, respectively.
coef
:Computes the sum of the random and fixed effects coefficients for each explanatory variable for each level of each grouping factor.
extractAIC
:Computes the (generalized) Akaike An
Information Criterion. If isREML(fit)
, then fit
is
refitted using maximum likelihood.
family
:family
of fitted
GLMM. (Warning: this accessor may not work properly with
customized families/link functions.)
fitted
:Fitted values, given the conditional modes of
the random effects. For more flexible access to fitted values, use
predict.merMod
.
logLik
:Loglikelihood at the fitted value of the
parameters. Note that for GLMMs, the returned value is only
proportional to the log probability density (or distribution) of the
response variable. See logLik
.
model.frame
:returns the frame
slot of merMod
.
model.matrix
:returns the fixed effects model matrix.
nobs
, ngrps
:Number of observations and vector of
the numbers of levels in each grouping factor. See ngrps
.
summary
:Computes and returns a list of summary statistics of the
fitted model, the amount of output can be controlled via the print
method,
see also summary
.
print.summary
:Controls the output for the summary method.
vcov
:Calculate variancecovariance matrix of the fixed
effect terms, see also vcov
.
update
:See update
.
One must be careful when defining the deviance of a GLM. For example, should the deviance be defined as minus twice the loglikelihood or does it involve subtracting the deviance for a saturated model? To distinguish these two possibilities we refer to absolute deviance (minus twice the loglikelihood) and relative deviance (relative to a saturated model, e.g. Section 2.3.1 in McCullagh and Nelder 1989).
With GLMMs however, there is an additional complication involving the
distinction between the likelihood and the conditional likelihood.
The latter is the likelihood obtained by conditioning on the estimates
of the conditional modes of the spherical random effects coefficients,
whereas the likelihood itself (i.e. the unconditional likelihood)
involves integrating out these coefficients. The following table
summarizes how to extract the various types of deviance for a
glmerMod
object:
conditional  unconditional  
relative  deviance(object)  NA in lme4 
absolute  object@resp$aic()  2*logLik(object)

This table requires two caveats:
If the link function involves a scale parameter
(e.g. Gamma
) then object@resp$aic()  2 * getME(object,
"devcomp")$dims["useSc"]
is required for the absoluteconditional
case.
If adaptive GaussHermite quadrature is used, then
logLik(object)
is currently only proportional to the
absoluteunconditional loglikelihood.
For more information about this topic see the misc/logLikGLMM
directory in the package source.
resp
:A reference class object for an lme4
response module (lmRespclass
).
Gp
:See getME
.
call
:The matched call.
frame
:The model frame containing all of the variables required to parse the model formula.
flist
:See getME
.
cnms
:See getME
.
lower
:See getME
.
theta
:Covariance parameter vector.
beta
:Fixed effects coefficients.
u
:Conditional model of spherical random effects coefficients.
devcomp
:See getME
.
pp
:A reference class object for an lme4
predictor module (merPredDclass
).
optinfo
:List containing information about the nonlinear optimization.
lmer
, glmer
,
nlmer
, merPredD
,
lmerResp
,
glmResp
,
nlsResp
Other methods for merMod
objects documented elsewhere include:
fortify.merMod
, drop1.merMod
,
isLMM.merMod
, isGLMM.merMod
,
isNLMM.merMod
, isREML.merMod
,
plot.merMod
, predict.merMod
,
profile.merMod
, ranef.merMod
,
refit.merMod
, refitML.merMod
,
residuals.merMod
, sigma.merMod
,
simulate.merMod
, summary.merMod
.
showClass("merMod") methods(class="merMod")## over 30 (S3) methods available ## > example(lmer) for an example of vcov.merMod()
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