SOSProtocol-class {rsbml} | R Documentation

## SOSProtocol

### Description

Holds the parameters controlling the execution of the simulation using the SBML ODE Solver library.

### Details

Most users will probably set only the `times` slot, either directly or through the `timeStep` slot and the `nsim` parameter to `simulate`.

### Objects from the Class

Objects can be created by calls of the form `new("SOSProtocol", ...)`. Each argument in `...` should correspond to one of the slots described below.

### Slots

`times`:
  A `"numeric"` vector indicating the time points at which to evaluate the model. Defaults to `tail(seq(0, by = timeStep, length.out = nsim + 1), -1)`. The model is always evaluated at t = 0. This slot is ignored when `indefinite` (below) is `TRUE`.
`timeStep`:
  A scalar `"numeric"` value, giving the length in time between model evaluations. This is used when calculating the default value of `times`, above, but is otherwise only relevant when the `indefinite` slot, below, is `TRUE`. Defaults to 1.
`indefinite`:
  A scalar `"logical"`, indicating whether the simulation should run indefinitely, i.e. until one of the stopping conditions is met. See `haltOnEvent` and `haltOnSteadyState` below. Defaults to `FALSE`.
`atol`:
  Scalar `"numeric"`, the absolute tolerance in integration error. Defaults to `1e-18`.
`rtol`:
  Scalar `"numeric"`, the relative tolerance in integration error. Defaults to `1e-10`.
`maxStep`:
  Sclar `"numeric"`, the maximum number of steps for integration. Not to be confused with `timeStep`, etc, above, which control the simulation time points. Defaults to `10000`.
`odeMethod`:
  Scalar `"character"` naming the method for solving ODEs. Either `"bdf"` (the default) or `"adams-moulton"`.
`iterMethod`:
  Scalar `"character"`, naming the iteration method used by the ODE solver, either `"newton"` (the default) or `"functional"`.
`maxOrder`:
  Scalar `"numeric"` indicating maximum order for the ODE solver. Defaults to `5`.
`sensMethod`:
  Scalar `"character"` naming the method for sensitivity analysis. One of `"none"` (the default and currently the only valid option), `"simultaneous"`, `"staggered"` or `"staggered1"`.
`haltOnEvent`:
  Scalar `"logical"` indicating whether the simulation should halt when the model emits an `Event`. This allows the model to stop the simulation when some state is reached. Defaults to `FALSE`.
`haltOnSteadyState`:
  Scalar `"logical"`, indicating whether to halt when a steady state is detected. Defaults to `FALSE`.
`useJacobian`:
  Scalar `"logical"` indicating whether to use Jacobian ASTs (`TRUE`, the default) or the internal approximation in the CVODES library.
`storeResults`:
  Scalar `"logical"` indicating whether to store the entire time course (`TRUE`, the default) or just the last time point. Just for performance.

### Extends

Class `"ExperimentProtocol"`, directly.

### Methods

No methods defined with class "SOSProtocol" in the signature.

### Author(s)

Michael Lawrence

### References

See http://www.tbi.univie.ac.at/~raim/odeSolver/ for more information on the SBML ODE Solver library.

### See Also

The `SOSExperiment` class, which contains a `SOSProtocol` instance, for setting up and running a simulation.

[Package rsbml version 2.2.1 Index]