`engineParams.Rd`

Use to define extra engine parameters for model execution.

```
engineParams(
model,
sort = NULL,
ODE = "MatrixExponent",
rtolODE = 1e-06,
atolODE = 1e-06,
maxStepsODE = 50000,
numIterations = 1000,
method = NULL,
stdErr = NULL,
isCentralDiffStdErr = TRUE,
stepSizeStdErr = NULL,
numIntegratePtsAGQ = 1,
numIterNonParametric = 0,
allowSyntheticGradient = FALSE,
numIterMAPNP = 0,
numRepPCWRES = 0,
stepSizeLinearize = 0.002,
numDigitLaplacian = 7,
numDigitBlup = 13,
mapAssist = 0,
iSample = 300,
iAcceptRatio = 0.1,
impDist = "Normal",
tDOF = 4,
numSampleSIR = 10,
numBurnIn = 0,
freezeOmega = FALSE,
MCPEM = FALSE,
runAllIterations = FALSE,
scramble = "Owen",
stepSizePartialDeriv = 1e-05,
numTimeStepPartialDeriv = 20
)
```

- model
Model object

- sort
Logical; Specifying whether or not to sort the input data by subject and time values.

If

`model@hasResetInfo = TRUE`

, then`sort`

must be set to`FALSE`

(default);Otherwise, the default value for

`sort`

is`TRUE`

.

- ODE
Character; Specifying the solver used to numerically solve Ordinary Differential Equations (ODEs). Options are

`"MatrixExponent"`

,`"DVERK"`

,`"DOPRI5"`

,`"AutoDetect"`

,`"Stiff"`

.Note: both

`"DVERK"`

and`"DOPRI5"`

are non-stiff solvers.- rtolODE
Numeric; Specifying relative tolerance for the ODE solver.

- atolODE
Numeric; Specifying absolute tolerance for the ODE solver.

- maxStepsODE
Numeric; Specifying maximum number of allowable steps or function evaluations for the ODE solver.

- numIterations
Numeric; Specifying maximum number of iterations for estimation.

- method
Character; Specifying engine method for estimation. For population models, options are

`"QRPEM"`

,`"IT2S-EM"`

,`"FOCE-LB"`

,`"FO"`

,`"FOCE-ELS"`

,`"Laplacian"`

,`"Naive-Pooled"`

. While, for individual models,`"Naive-Pooled"`

is the only option.Note: For population models, if

`model`

involves any discontinuous observed variable (e.g., count data) or BQL data, the default method is`"Laplacian"`

; otherwise, the default method is`"FOCE-ELS"`

.- stdErr
Character; Specifying method for standard error computations.

For individual models, options are

`"Hessian"`

(default) and`"None"`

;For population models with

`method = "QRPEM"`

, options are`"Fisher-Score"`

(default) and`"None"`

;For population models with

`method = "IT2s-EM"`

, the only option is`"None"`

;For population models with

`method`

set to either`"FOCE-LB"`

,`"FO"`

,`"FOCE-ELS"`

,`"Laplacian"`

, or`"Naive-Pooled"`

, options are`"Sandwich"`

(default),`"Hessian"`

,`"Fisher-Score"`

,`"Auto-Detect"`

, and`"None"`

.

Here

`"None"`

means that standard error calculations are not performed.- isCentralDiffStdErr
Logical; Default

`TRUE`

uses central difference for`stdErr`

calculations. Set to`FALSE`

for forward difference method.- stepSizeStdErr
Numeric; Specifying the step size used for

`stdErr`

calculations. If not specified, 0.01 is used for population models and 0.001 for individual models.- numIntegratePtsAGQ
Numeric; Specifying the number of integration points for adaptive Gaussian quadrature (AGQ) algorithm. Only applicable to population models with

`method`

set to either`"FOCE-ELS"`

or`"Laplacian"`

.- numIterNonParametric
Numeric; Specifying the number of iterations to perform non-parametric estimation. Only applicable to population models when

`method`

is not set to`Naive-Pooled`

.- allowSyntheticGradient
Logical, Set to

`TRUE`

to use synthetic gradient during the estimation process. Only applicable to population models when`method`

is not set to`Naive-Pooled`

.- numIterMAPNP
Numeric; Specifying the number of iterations to perform Maximum A Posterior (MAP) initial Naive Pooling (NP) run before estimation. Only applicable to population models when

`method`

is not set to`Naive-Pooled`

.- numRepPCWRES
Numeric; Specifying the number of replicates to generate the PCWRES after the simple estimation. Only applicable to population models when

`method`

is not set to`Naive-Pooled`

.- stepSizeLinearize
Numeric; Specifying the step size used for numerical differentiation when linearizing the model function during the estimation process.

- numDigitLaplacian
Numeric; Specifying the number of significant decimal digits for the Laplacian algorithm to use to reach convergence. Only applicable to population models.

- numDigitBlup
Numeric; Specifying the number of significant decimal digits for the individual estimation to use to reach convergence. Only applicable to population models.

- mapAssist
Numeric; Specifying the period used to perform MAP assistance (

`mapAssist = 0`

means that MAP assistance is not performed). Only applicable to population models with`method = "QRPEM"`

.- iSample
Numeric; Specifying the number of samples. Only applicable to population models with

`method = "QRPEM"`

.- iAcceptRatio
Numeric; Specifying the acceptance ratio. Only applicable to population models with

`method = "QRPEM"`

.- impDist
Character; Specifying the distribution used for important sampling, and options are

`"Normal"`

(default),`"DoubleExponential"`

,`"Direct"`

,`"T"`

,`"Mixture-2"`

,`Mixture-3`

. Only applicable to population models with`method = "QRPEM"`

.- tDOF
Numeric; Specifing the degree of freedom (allowed value is between 3 and 30) for T distribution. Only applicable to population models with

`method = "QRPEM"`

and`impDist = "T"`

.- numSampleSIR
Numeric; Specifying the number of samples per subject used in the Sampling Importance Re-Sampling (SIR) algorithm to determine the number of SIR samples taken from the empirical discrete distribution that approximates the target conditional distribution. Only applicable to population models with

`method = "QRPEM"`

.- numBurnIn
Numeric; Specifying the number of burn-in iterations to perform at startup to adjust certain internal parameters. Only applicable to population models with

`method = "QRPEM"`

.- freezeOmega
Logical; Set to

`TRUE`

to freeze Omega but not Theta for the number of iterations specified in the`numBurnIn`

. Only applicable to population models with`method = "QRPEM"`

.- MCPEM
Logical; Set to

`TRUE`

to use Monte-Carlo sampling instead of Quasi-Random. Only applicable to population models with`method = "QRPEM"`

.- runAllIterations
Logical; Set to

`TRUE`

to execute all requested iterations specified in`numIterations`

. Only applicable to population models with`method = "QRPEM"`

.- scramble
Character; Specifying the quasi-random scrambling method to use, and options are

`"Owen"`

,`"Tezuka-Faur"`

, or`"None"`

. Only applicable to population models with`method = "QRPEM"`

.- stepSizePartialDeriv
Numeric; Specifying the step size used to numerically calculate the partial derivatives of observed variables with respect to parameters. Only applicable to individual models.

- numTimeStepPartialDeriv
Numeric; Specifying the number of time steps used to output the partial derivatives of observed variables with respect to parameters. Only applicable to individual models.