API for lme4
Linear Mixed-Effects Models using 'Eigen' and S4

Global functions
.get.checkingOpts	Source code
.hasScale	Source code
.isDiagonal.sq.matrix	Source code
.makeCC	Man page Source code
.merMod.msgs	Source code
.minimalOptinfo	Source code
.modelMatrixDrop	Source code
.onLoad	Source code
.onUnload	Source code
.optinfo	Source code
.prt.VC	Man page Source code
.prt.aictab	Man page Source code
.prt.call	Man page
.prt.family	Man page
.prt.grps	Man page Source code
.prt.methTit	Man page Man page
.prt.resids	Man page
.prt.warn	Man page Source code
.simpleCap	Source code
.simulateFun	Man page
Arabidopsis	Man page
Covariance-class	Man page
Covariance.ar1-class	Man page
Covariance.cs-class	Man page
Covariance.diag-class	Man page
Covariance.us-class	Man page
Cv_to_Sv	Man page Source code
Cv_to_Vv	Man page Source code
Dyestuff	Man page
Dyestuff2	Man page
GHrule	Man page
GQN	Man page
GQdk	Man page Source code
InstEval	Man page
NelderMead	Man page
NelderMead-class	Man page
Nelder_Mead	Man page Source code
Pastes	Man page
Penicillin	Man page
REMLcrit	Man page Source code
RHSForm	Source code
RglmerWrkIter	Source code
Sv_to_Cv	Man page Source code
VarCorr	Man page
VarCorr.merMod	Man page Source code
VerbAgg	Man page
Vv_to_Cv	Man page Source code
`%i%`	Source code
`RHSForm<-`	Source code
abbrDeparse	Source code
ad	Source code
all0	Source code
allFit	Man page Source code
allVarsRec	Source code
anova.merMod	Man page
anovaLmer	Source code
anyStructured	Man page
arrange.condVar	Source code
array_to_bdiag	Source code
as.data.frame.VarCorr.merMod	Man page Source code
as.data.frame.bootMer	Source code
as.data.frame.ranef.mer	Man page Source code
as.data.frame.thpr	Man page Source code
as.function.merMod	Man page Source code
asDf0	Source code
augment.RE	Source code
barnames	Source code
bdiag_to_array	Source code
bdiag_to_mlist	Source code
bootMer	Man page Source code
cake	Man page
cbpp	Man page
cbpp2	Man page
chck1	Source code
checkArgs	Source code
checkConv	Man page Source code
checkCtrlLevels	Source code
checkFormulaData	Source code
checkHess	Source code
checkNlevels	Source code
checkResponse	Source code
checkScaleX	Source code
checkZdims	Source code
checkZrank	Source code
check_dep_version	Source code
chk.cconv	Source code
chk.convOpt	Source code
chkRank.drop.cols	Source code
coef.lmList4	Source code
coef.merMod	Man page
coefMer	Source code
colSort	Source code
combineLists	Source code
condVar	Source code
confint.bootMer	Source code
confint.lmList4	Source code
confint.merMod	Man page Source code
confint.thpr	Man page Source code
cont	Source code
convergence	Man page
cooks.distance.influence.merMod	Man page Source code
cooks.distance.merMod	Man page Source code
cov2sdcor	Man page Source code
culcitalogreg	Man page
culcitalvolume	Man page
dens	Source code
densityplot.thpr	Man page Source code
deriv12	Source code
devCrit	Source code
devcomp	Man page Source code
devfun2	Man page Source code
deviance.merMod	Man page Source code
df.residual.merMod	Man page Source code
dfbeta.influence.merMod	Man page Source code
dfbetas.influence.merMod	Man page Source code
diagnostic.plots	Man page
diagnosticPlots	Man page
diagnostic_plots	Man page
diagnostics	Man page
dim.merMod	Source code
doCheck	Source code
dotplot.coef.mer	Source code
dotplot.ranef.mer	Man page Source code
drop1.merMod	Man page Source code
dropOffset	Source code
dummy	Man page Source code
est_theta	Source code
expandDoubleVerts	Man page
extractAIC.merMod	Man page Source code
factorize	Man page Source code
family.glmResp	Source code
family.lmResp	Source code
family.merMod	Man page Source code
family.nlsResp	Source code
family2char	Source code
findbars	Man page
fitted.merMod	Man page Source code
fixed.effects	Man page Source code
fixef	Man page
fixef.merMod	Man page Source code
forceCopy	Source code
forceNewMerMod	Man page
formatVC	Man page
formula.lmList4	Source code
formula.merMod	Man page Source code
fortify	Man page
fortify.merMod	Man page
get.which	Source code
getConv	Source code
getData	Man page
getData.merMod	Man page Source code
getDoublevertDefault	Man page Source code
getFixedFormula	Source code
getGroups.lmList4	Source code
getGroupsFormula	Source code
getGroupsFormula.merMod	Source code
getIDLabels	Source code
getL	Man page
getL,merMod-method	Man page
getLambda	Man page
getLambda,Covariance.ar1-method	Man page
getLambda,Covariance.cs-method	Man page
getLambda,Covariance.diag-method	Man page
getLambda,Covariance.us-method	Man page
getLambda,merMod-method	Man page
getLambdat.dp	Man page
getLambdat.dp,Covariance.ar1-method	Man page
getLambdat.dp,Covariance.cs-method	Man page
getLambdat.dp,Covariance.diag-method	Man page
getLambdat.dp,Covariance.us-method	Man page
getLambdat.i	Man page
getLambdat.i,Covariance.ar1-method	Man page
getLambdat.i,Covariance.cs-method	Man page
getLambdat.i,Covariance.diag-method	Man page
getLambdat.i,Covariance.us-method	Man page
getLower	Man page
getLower,Covariance.ar1-method	Man page
getLower,Covariance.cs-method	Man page
getLower,Covariance.diag-method	Man page
getLower,Covariance.us-method	Man page
getLower,merMod-method	Man page
getME	Man page Source code
getME.merMod	Man page Source code
getMsg	Source code
getNBdisp	Source code
getNBdisp.fam	Source code
getOptfun	Source code
getPar	Man page
getPar,Covariance-method	Man page
getPar,merMod-method	Man page
getParLength	Man page
getParLength,Covariance-method	Man page
getParLength,merMod-method	Man page
getParNames	Man page
getParNames,Covariance.ar1,character,character-method	Man page
getParNames,Covariance.cs,character,character-method	Man page
getParNames,Covariance.diag,character,character-method	Man page
getParNames,Covariance.us,character,character-method	Man page
getParNames,merMod,missing,missing-method	Man page
getProfLower	Man page
getProfLower,Covariance.ar1-method	Man page
getProfLower,Covariance.cs-method	Man page
getProfLower,Covariance.diag-method	Man page
getProfLower,Covariance.us-method	Man page
getProfLower,merMod-method	Man page
getProfPar	Man page
getProfPar,Covariance.ar1-method	Man page
getProfPar,Covariance.cs-method	Man page
getProfPar,Covariance.diag-method	Man page
getProfPar,Covariance.us-method	Man page
getProfPar,merMod-method	Man page
getProfUpper	Man page
getProfUpper,Covariance.ar1-method	Man page
getProfUpper,Covariance.cs-method	Man page
getProfUpper,Covariance.diag-method	Man page
getProfUpper,Covariance.us-method	Man page
getProfUpper,merMod-method	Man page
getReCovs	Man page
getResponseFormula	Source code
getSingTol	Man page Source code
getTheta	Man page
getTheta,Covariance.ar1-method	Man page
getTheta,Covariance.cs-method	Man page
getTheta,Covariance.diag-method	Man page
getTheta,Covariance.us-method	Man page
getTheta,merMod-method	Man page
getThetaIndex	Man page
getThetaIndex,Covariance.ar1-method	Man page
getThetaIndex,Covariance.cs-method	Man page
getThetaIndex,Covariance.diag-method	Man page
getThetaIndex,Covariance.us-method	Man page
getThetaIndexLength	Man page
getThetaIndexLength,Covariance.ar1-method	Man page
getThetaIndexLength,Covariance.cs-method	Man page
getThetaIndexLength,Covariance.diag-method	Man page
getThetaIndexLength,Covariance.us-method	Man page
getThetaLength	Man page
getThetaLength,Covariance.ar1-method	Man page
getThetaLength,Covariance.cs-method	Man page
getThetaLength,Covariance.diag-method	Man page
getThetaLength,Covariance.us-method	Man page
getThetaLength,merMod-method	Man page
getThetaNames	Man page
getThetaNames,Covariance.ar1,character,character-method	Man page
getThetaNames,Covariance.cs,character,character-method	Man page
getThetaNames,Covariance.diag,character,character-method	Man page
getThetaNames,Covariance.us,character,character-method	Man page
getThetaNames,merMod,missing,missing-method	Man page
getUpper	Man page
getUpper,Covariance.ar1-method	Man page
getUpper,Covariance.cs-method	Man page
getUpper,Covariance.diag-method	Man page
getUpper,Covariance.us-method	Man page
getUpper,merMod-method	Man page
getVC	Man page
getVC,Covariance.ar1-method	Man page
getVC,Covariance.cs-method	Man page
getVC,Covariance.diag-method	Man page
getVC,Covariance.us-method	Man page
getVCNames	Man page
getVCNames,Covariance.ar1,character,character-method	Man page
getVCNames,Covariance.cs,character,character-method	Man page
getVCNames,Covariance.diag,character,character-method	Man page
getVCNames,Covariance.us,character,character-method	Man page
getVCNames,merMod,missing,missing-method	Man page
get_abi_version	Source code
get_clen	Source code
glFormula	Man page
glmFamily	Man page
glmFamily-class	Man page
glmResp	Man page
glmResp-class	Man page
glmer	Man page Source code
glmer.nb	Man page Source code
glmerControl	Man page
glmerLaplaceHandle	Man page Source code
glmerMod-class	Man page
glmerPwrssUpdate	Source code
golden	Man page
golden-class	Man page
gopherdat2	Man page
grouseticks	Man page
grouseticks_agg	Man page
grpfact	Source code
hasNoScale	Source code
hasScale	Source code
hatvalues.merMod	Man page
inForm	Source code
influence.merMod	Man page Source code
initialize,Covariance.ar1-method	Man page
initialize,Covariance.cs-method	Man page
initialize,Covariance.diag-method	Man page
initialize,Covariance.us-method	Man page
isFlexLambda	Source code
isGLMM	Man page Source code
isGLMM.merMod	Man page Source code
isGLMlist	Source code
isLMM	Man page Source code
isLMM.merMod	Man page Source code
isNBfamily	Source code
isNLMM	Man page Source code
isNLMM.merMod	Man page Source code
isNested	Man page
isNewMerMod	Man page
isRE	Source code
isREML	Man page Source code
isREML.merMod	Man page Source code
isSingular	Man page
isSingular,Covariance.ar1-method	Man page
isSingular,Covariance.cs-method	Man page
isSingular,Covariance.diag-method	Man page
isSingular,Covariance.us-method	Man page
isSingular,merMod-method	Man page
isSingular-methods	Man page
lFormula	Man page Source code
llikAIC	Man page
lmList	Man page Source code
lmList4-class	Man page
lmResp	Man page
lmResp-class	Man page
lme4	Man page
lme4-package	Man page
lme4_testlevel	Man page Source code
lmer	Man page Source code
lmerControl	Man page
lmerMod-class	Man page
lmerResp	Man page
lmerResp-class	Man page
log.thpr	Man page
logLik.merMod	Man page Source code
logProf	Man page
makeFac	Source code
mcmcsamp	Man page Source code
mcmcsamp.merMod	Source code
merControl	Source code
merMod	Man page
merMod-class	Man page
merPredD	Man page
merPredD-class	Man page
methTitle	Man page
mkBlist	Source code
mkDataTemplate	Man page Source code
mkGlmerDevfun	Man page
mkLmerDevfun	Man page
mkMerMod	Man page Source code
mkMinimalData	Source code
mkNewReTrms	Man page
mkParsTemplate	Man page Source code
mkPfun	Source code
mkReTrms	Man page
mkRespMod	Man page Source code
mkVarCorr	Man page Source code
mkWarnFun	Source code
mkdevfun	Source code
mlist2vec	Man page Source code
mlist_to_array	Source code
mmList	Source code
mmList.formula	Source code
mmList.merMod	Source code
model.frame.merMod	Man page Source code
model.matrix.merMod	Man page Source code
modelFormula	Source code
modular	Man page
my_reOnly	Source code
na.action.merMod	Source code
namedList	Man page Source code
negative.binomial	Man page
ngrps	Man page Source code
ngrps.default	Source code
ngrps.factor	Source code
ngrps.merMod	Man page Source code
nlformula	Man page Source code
nlmer	Man page Source code
nlmerControl	Man page Source code
nlmerMod-class	Man page
nlminbwrap	Man page Source code
nloptwrap	Man page
nlsResp	Man page
nlsResp-class	Man page
nmkbw	Source code
noLHSform	Source code
nobars	Man page
nobs	Man page
nobs.merMod	Man page Source code
normalizeFamilyName	Source code
npar.merMod	Source code
optTheta	Source code
optimizeGlmer	Man page
optimizeLmer	Man page
optwrap	Source code
pad_Cmat	Source code
panel.thpr	Source code
plot.allFit	Source code
plot.coef.mer	Source code
plot.lmList	Man page
plot.lmList4.confint	Source code
plot.merMod	Man page Source code
plot.ranef.mer	Source code
pooledSD	Source code
predict.merMod	Man page
predy	Source code
print.VarCorr.merMod	Man page Source code
print.allFit	Source code
print.bootMer	Source code
print.bootWarnings	Source code
print.merMod	Man page Source code
print.ranef.mer	Source code
print.summary.merMod	Man page Source code
profile-methods	Man page
profile.merMod	Man page Source code
profnames	Source code
pvalues	Man page
qqmath.merMod	Man page
qqmath.ranef.mer	Man page Source code
qqplot	Man page
quad.tdiag	Source code
quickSimulate	Source code
random.effects	Source code
ranef	Man page
ranef.merMod	Man page Source code
reOnly	Man page Source code
rePCA	Man page Source code
rePCA.merMod	Source code
rePos	Man page
rePos-class	Man page
reexpr	Source code
refit	Man page Source code
refit.merMod	Man page Source code
refit2.merMod	Source code
refitML	Man page Source code
refitML.merMod	Man page
refitNB	Source code
replaceTerm	Source code
residuals.glmResp	Man page
residuals.lmResp	Man page
residuals.merMod	Man page
rstudent.glmerMod	Source code
sacos	Source code
safe_chol	Source code
safe_length	Source code
salamander	Man page
scale_vcov	Source code
schizophrenia	Man page
sdcor2cov	Man page Source code
setNBdisp	Source code
setPar	Man page
setPar,Covariance,numeric-method	Man page
setProfPar	Man page
setProfPar,Covariance.ar1,numeric-method	Man page
setProfPar,Covariance.cs,numeric-method	Man page
setProfPar,Covariance.diag,numeric-method	Man page
setProfPar,Covariance.us,numeric-method	Man page
setTheta	Man page
setTheta,Covariance.ar1,numeric-method	Man page
setTheta,Covariance.cs,numeric-method	Man page
setTheta,Covariance.diag,numeric-method	Man page
setTheta,Covariance.us,numeric-method	Man page
setVC	Man page
setVC,Covariance.ar1,numeric,numeric-method	Man page
setVC,Covariance.cs,numeric,numeric-method	Man page
setVC,Covariance.diag,numeric,numeric-method	Man page
setVC,Covariance.us,numeric,numeric-method	Man page
show,lmList4-method	Man page
show,merMod-method	Man page
show.merMod	Man page
show.summary.merMod	Man page
sigma	Man page
sigma.lmList4	Source code
sigma.merMod	Man page Source code
simulate.formula	Man page Source code
simulate.formula_lhs	Source code
simulate.merMod	Man page
sleepstudy	Man page
splitFormula	Source code
splom.thpr	Man page
stripExpr	Source code
subbars	Man page
subnms	Source code
summary	Man page
summary.allFit	Source code
summary.merMod	Man page Source code
summary.prcomplist	Source code
summary.summary.merMod	Source code
tauij	Source code
termnms	Source code
terms.merMod	Man page Source code
testLevel	Source code
toenail	Man page
troubleshooting	Man page
unscaledVar	Source code
update.lmList4	Source code
update.merMod	Man page Source code
updateGlmerDevfun	Man page
varianceProf	Man page Source code
vcconv	Man page
vcov.merMod	Man page Source code
vcov.summary.merMod	Man page Source code
vcov_full	Source code
vec2STlist	Man page Source code
vec2mlist	Man page Source code
weights.merMod	Man page Source code
wmsg	Source code
xyplot.thpr	Man page
zero_padding	Source code