lmeControl: Control Values for lme Fit

Description

The values supplied in the function call replace the defaults and a list with all possible arguments is returned. The returned list is used as the control argument to the lme function.

Usage

lmeControl(maxIter, msMaxIter, tolerance, niterEM, msMaxEval, msTol,
           msScale, msVerbose, returnObject, gradHess, apVar,
           .relStep, minAbsParApVar, nlmStepMax,
           opt = c("nlminb", "optim"), optimMethod,
           natural, ...)

Arguments

maxIter

maximum number of iterations for the lme optimization algorithm. Default is 50.

msMaxIter

maximum number of iterations for the optimization step inside the lme optimization. Default is 50.

tolerance

tolerance for the convergence criterion in the lme algorithm. Default is 1e-6.

niterEM

number of iterations for the EM algorithm used to refine the initial estimates of the random effects variance-covariance coefficients. Default is 25.

msMaxEval

maximum number of evaluations of the objective function permitted for nlminb. Default is 200.

msTol

tolerance for the convergence criterion the first iteration. Default is 1e-7.

msScale

No longer used.

msVerbose

a logical value passed as the trace argument to nlminb or optim. Default is FALSE.

returnObject

a logical value indicating whether the fitted object should be returned when the maximum number of iterations is reached without convergence of the algorithm. Default is FALSE.

gradHess

a logical value indicating whether numerical gradient vectors and Hessian matrices of the log-likelihood function should be used in the internal optimization. This option is only available when the correlation structure (corStruct) a

apVar

a logical value indicating whether the approximate covariance matrix of the variance-covariance parameters should be calculated. Default is TRUE.

.relStep

relative step for numerical derivatives calculations. Default is .Machine$double.eps^(1/3).

nlmStepMax

stepmax value to be passed to nlm. See nlm for details. Default is 100.0

opt

the optimizer to be used, either "nlminb" (the default) or "optim".

optimMethod

character - the optimization method to be used with the optim optimizer. The default is "BFGS". An alternative is "L-BFGS-B".

minAbsParApVar

numeric value - minimum absolute parameter value in the approximate variance calculation. The default is 0.05.

natural

a logical value indicating whether the pdNatural parametrization should be used for general positive-definite matrices (pdSymm) in reStruct, when the approximate covariance matrix of the estimators is calcul

...

Further named control arguments to be passed to nlminb (those from abs.tol down) or optim (those except trace and maxit

Value

a list with components for each of the possible arguments.

Examples

Run this code

# decrease the maximum number iterations in the ms call and
# request that information on the evolution of the ms iterations be printed
lmeControl(msMaxIter = 20, msVerbose = TRUE)

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