The values supplied in the `lmeControl()`

call replace the
defaults, and a `list`

with all settings (i.e., values for
all possible arguments) is returned. The returned list is
used as the `control`

argument to the `lme`

function.

```
lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, niterEM = 25,
msMaxEval = 200,
msTol = 1e-7, msVerbose = FALSE,
returnObject = FALSE, gradHess = TRUE, apVar = TRUE,
.relStep = .Machine$double.eps^(1/3), minAbsParApVar = 0.05,
opt = c("nlminb", "optim"),
optimMethod = "BFGS", natural = TRUE,
sigma = NULL,
allow.n.lt.q = FALSE,
...)
```

a list with components for each of the possible 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 on the first iteration when

`optim`

is used. Default is`1e-7`

.- 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 with a

`warning`

(instead of an error via`stop()`

) 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`

) and the variance function structure (`varFunc`

) have no "varying" parameters and the`pdMat`

classes used in the random effects structure are`pdSymm`

(general positive-definite),`pdDiag`

(diagonal),`pdIdent`

(multiple of the identity), or`pdCompSymm`

(compound symmetry). Default is`TRUE`

.- 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)`

.- 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 calculated. Default is`TRUE`

.- sigma
optionally a positive number to fix the residual error at. If

`NULL`

, as by default, or`0`

, sigma is estimated.- allow.n.lt.q
`logical`

indicating if it is ok to have less observations than random effects for each group. The default,`FALSE`

signals an error; if`NA`

, such a situation only gives a warning, as in nlme versions prior to 2019; if true, no message is given at all.

José Pinheiro and Douglas Bates bates@stat.wisc.edu; the
`sigma`

option: Siem Heisterkamp and Bert van Willigen.

```
# decrease the maximum number iterations in the ms call and
# request that information on the evolution of the ms iterations be printed
str(lCtr <- lmeControl(msMaxIter = 20, msVerbose = TRUE))
## This should always work:
do.call(lmeControl, lCtr)
```

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