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.