SOSProtocol-class: SOSProtocol

Description Details Objects from the Class Slots Extends Methods Author(s) References See Also


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


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.



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.


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.


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.


Scalar "numeric", the absolute tolerance in integration error. Defaults to 1e-18.


Scalar "numeric", the relative tolerance in integration error. Defaults to 1e-10.


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.


Scalar "character" naming the method for solving ODEs. Either "bdf" (the default) or "adams-moulton".


Scalar "character", naming the iteration method used by the ODE solver, either "newton" (the default) or "functional".


Scalar "numeric" indicating maximum order for the ODE solver. Defaults to 5.


Scalar "character" naming the method for sensitivity analysis. One of "none" (the default and currently the only valid option), "simultaneous", "staggered" or "staggered1".


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.


Scalar "logical", indicating whether to halt when a steady state is detected. Defaults to FALSE.


Scalar "logical" indicating whether to use Jacobian ASTs (TRUE, the default) or the internal approximation in the CVODES library.


Scalar "logical" indicating whether to store the entire time course (TRUE, the default) or just the last time point. Just for performance.


Class "ExperimentProtocol", directly.


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


Michael Lawrence


See 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.

rsbml documentation built on Nov. 8, 2020, 8:09 p.m.