Control Options for SAEM
saemControl(seed = 99, nBurn = 200, nEm = 300, nmc = 3, nu = c(2,
2, 2), atol = 1e-06, rtol = 1e-04, stiff = TRUE,
transitAbs = FALSE, print = 1, trace = 0, covMethod = c("fim",
"r,s", "r", "s"), logLik = FALSE, optExpression = TRUE, ...)Random Seed for SAEM step. (Needs to be set for reproducibility.) By default this is 99.
Number of iterations in the Stochastic Approximation
(SA), or burn-in step. This is equivalent to Monolix's K_0 or K_b.
Number of iterations in the Expectation-Maximization
(EM) Step. This is equivalent to Monolix's K_1.
Number of Markov Chains. By default this is 3. When
you increase the number of chains the numerical integration by
MC method will be more accurate at the cost of more
computation. In Monolix this is equivalent to L
This is a vector of 3 integers. They represent the
numbers of transitions of the three different kernels used in
the Hasting-Metropolis algorithm. The default value is c(2,2,2),
representing 40 for each transition initially (each value is
multiplied by 20).
The first value represents the initial number of multi-variate Gibbs samples are taken from a normal distribution.
The second value represents the number of uni-variate, or multi- dimensional random walk Gibbs samples are taken.
The third value represents the number of bootstrap/reshuffling or uni-dimensional random samples are taken.
a numeric absolute tolerance (1e-8 by default) used by the ODE solver to determine if a good solution has been achieved; This is also used in the solved linear model to check if prior doses do not add anything to the solution.
a numeric relative tolerance (1e-6 by default) used by the ODE solver to determine if a good solution has been achieved. This is also used in the solved linear model to check if prior doses do not add anything to the solution.
a logical (TRUE by default) indicating whether
the ODE system is stiff or not.
For stiff ODE sytems (stiff = TRUE), RxODE uses the
LSODA (Livermore Solver for Ordinary Differential Equations)
Fortran package, which implements an automatic method switching
for stiff and non-stiff problems along the integration
interval, authored by Hindmarsh and Petzold (2003).
For non-stiff systems (stiff = FALSE), RxODE uses
DOP853, an explicit Runge-Kutta method of order 8(5, 3) of
Dormand and Prince as implemented in C by Hairer and Wanner
(1993).
boolean indicating if this is a transit compartment absorption
The number it iterations that are completed before anything is printed to the console. By default, this is 1.
An integer indicating if you want to trace(1) the SAEM algorithm process. Useful for debugging, but not for typical fitting.
Method for calculating covariance. In this discussion, R is the Hessian matrix of the objective function. The S matrix is the sum of each individual's gradient cross-product (evaluated at the individual empirical Bayes estimates).
"fim" Use the SAEM-calculated Fisher Information Matrix to calculate the covariance.
"r,s" Uses the sandwich matrix to calculate the covariance, that is: \(R^-1 \times S \times R^-1\)
"r" Uses the Hessian matrix to calculate the covariance as \(2\times R^-1\)
"s" Uses the crossproduct matrix to calculate the covariance as \(4\times S^-1\)
"" Does not calculate the covariance step.
boolean indicating that log-likelihood should be calculate by Gaussian quadrature.
Optimize the RxODE expression to speed up calculation. By default this is turned on.
Other arguments to control SAEM.
List of options to be used in nlmixr fit for
SAEM.