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 object
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
.
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.
Numeric; Specifying relative tolerance for the ODE solver.
Numeric; Specifying absolute tolerance for the ODE solver.
Numeric; Specifying maximum number of allowable steps or function evaluations for the ODE solver.
Numeric; Specifying maximum number of iterations for estimation.
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"
.
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.
Logical; Default TRUE
uses central difference for stdErr
calculations.
Set to FALSE
for forward difference method.
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.
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"
.
Numeric; Specifying the number of iterations to perform non-parametric estimation.
Only applicable to population models when method
is not set to Naive-Pooled
.
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
.
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
.
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
.
Numeric; Specifying the step size used for numerical differentiation when linearizing the model function during the estimation process.
Numeric; Specifying the number of significant decimal digits for the Laplacian algorithm to use to reach convergence. Only applicable to population models.
Numeric; Specifying the number of significant decimal digits for the individual estimation to use to reach convergence. Only applicable to population models.
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"
.
Numeric; Specifying the number of samples. Only applicable to population models with method = "QRPEM"
.
Numeric; Specifying the acceptance ratio. Only applicable to population models with method = "QRPEM"
.
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"
.
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"
.
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"
.
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"
.
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"
.
Logical; Set to TRUE
to use Monte-Carlo sampling instead of Quasi-Random.
Only applicable to population models with method = "QRPEM"
.
Logical; Set to TRUE
to execute all requested iterations specified in numIterations
.
Only applicable to population models with method = "QRPEM"
.
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"
.
Numeric; Specifying the step size used to numerically calculate the partial derivatives of observed variables with respect to parameters. Only applicable to individual models.
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.