a two-sided linear formula object describing both the fixed-effects and random-effects parts of the model, with the response on the left of a ~ operator and the terms, separated by + operators, on the right. Random-effects terms are distinguished by vertical bars ("|") separating expressions for design matrices from grouping factors.

an optional data frame containing the variables named in formula. By default the variables are taken from the environment from which lmer is called. While data is optional, the package authors strongly recommend its use, especially when later applying methods such as update and drop1 to the fitted model (such methods are not guaranteed to work properly if data is omitted). If data is omitted, variables will be taken from the environment of formula (if specified as a formula) or from the parent frame (if specified as a character vector).

(logical) indicating to fit restricted maximum likelihood model.

an optional expression indicating the subset of the rows of data that should be used in the fit. This can be a logical vector, or a numeric vector indicating which observation numbers are to be included, or a character vector of the row names to be included. All observations are included by default.

an optional vector of ‘prior weights’ to be used in the fitting process. Should be NULL or a numeric vector.

a function that indicates what should happen when the data contain NAs. The default action (na.omit, inherited from the 'factory fresh' value of getOption("na.action")) strips any observations with any missing values in any variables.

this can be used to specify an a priori known component to be included in the linear predictor during fitting. This should be NULL or a numeric vector of length equal to the number of cases. One or more offset terms can be included in the formula instead or as well, and if more than one is specified their sum is used. See model.offset.

an optional list. See the contrasts.arg of model.matrix.default.

a list giving

for [g]lFormula:

all options for running the model, see lmerControl;

for mkLmerDevfun,mkGlmerDevfun:

options for the inner optimization step;

for optimizeLmer and optimizeGlmer:

control parameters for nonlinear optimizer (typically inherited from the ... argument to lmerControl).

A model frame containing the variables needed to create an lmerResp or glmResp instance.

fixed-effects design matrix

information on random effects structure (see mkReTrms).

starting values (see lmer; for glFormula, should be just a numeric vector of fixed-effect coefficients)

print output?

maximal number of Pwrss update iterations.

a deviance function, as generated by mkLmerDevfun

number of Gauss-Hermite quadrature points

optimization stage (1: nAGQ=0, optimize over theta only; 2: nAGQ possibly >0, optimize over theta and beta)

character - name of optimizing function(s). A character vector or list of functions: length 1 for lmer or glmer, possibly length 2 for glmer. The built-in optimizers are "Nelder_Mead" and "bobyqa" (from the minqa package). Any minimizing function that allows box constraints can be used provided that it

1. takes input parameters fn (function to be optimized), par (starting parameter values), lower (lower bounds) and control (control parameters, passed through from the control argument) and

2. returns a list with (at least) elements par (best-fit parameters), fval (best-fit function value), conv (convergence code) and (optionally) message (informational message, or explanation of convergence failure).

Special provisions are made for bobyqa, Nelder_Mead, and optimizers wrapped in the optimx package; to use optimx optimizers (including L-BFGS-B from base optim and nlminb), pass the method argument to optim in the control argument.

For glmer, if length(optimizer)==2, the first element will be used for the preliminary (random effects parameters only) optimization, while the second will be used for the final (random effects plus fixed effect parameters) phase. See modular for more information on these two phases.

see lmerControl

see lmerControl

a GLM family; see glm and family.

optional starting values on the scale of the conditional mean; see glm for details.

optional starting values on the scale of the unbounded predictor; see glm for details.

other potential arguments; for optimizeLmer and optimizeGlmer, these are passed to internal function optwrap, which has relevant parameters calc.derivs and use.last.params (see lmerControl).