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 nlm 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 in nlm, passed as the rel.tolerance argument to the function (see documentation on nlm). Default is 1e-7.

msScale

scale function passed as the scale argument to the nlm function (see documentation on that function). Default is lmeScale.

msVerbose

a logical value passed as the trace argument to nlm (see documentation on that function). 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 nlm optimization. This option is only available when the correlation structure (corStruct

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 since (R2.2.0) or optim (the previous
   default).

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

`Value`

a list with components for each of the possible arguments.

`See Also`

lme, nlm, optim,
  lmeScale

`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)
Run the code above in your browser using DataLab