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Specify engine parameters for model execution

engineParams.Rd

Use to define extra engine parameters for model execution.

Usage

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
)

Arguments

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"`, `"Higham"`, `"DVERK"`, `"DOPRI5"`, `"AutoDetect"`, `"Stiff"`. See Details section.

rtolODE

Numeric; Specifying relative tolerance for the numerical ODE solver.

atolODE

Numeric; Specifying absolute tolerance for the numerical 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.

Details

Both `"DVERK"` and `"DOPRI5"` are non-stiff solvers. `"Higham"` is a matrix exponent based ODE solver which could be useful when overscaling issue should be avoided, i.e. the ratio between observed values and doses is too high or too low. `"AutoDetect"` represents LSODA solver implemenation, which solves the initial value problem for stiff or nonstiff systems of first order ordinary differential equations. `"Stiff"` is a LSODE (Livermore solver). It is best suited for stiff problems.