SOSExperiment-class {rsbml} | R Documentation |
Implementation of Experiment
for
simulating SBML models using the SOS: (S)BML (O)DE (S)olver library.
The general workflow for running a simulation:
Model
.
Event
s.
SOSSubject
,
e.g. new("SOSSubject", model)
.
SOSDesign
for
running the experiment in batch over several sets of model parameter
settings.
SOSProtocol
for
specifying the time points and other parameters controlling the
simulation.
simulate
on the SOSExperiment
, optionally
specifying the number of iterations and the random seed.
SOSResult
, perhaps
starting by converting it to a time series with as.ts
and
making some plots.
Objects can be created by calls of the form new("SOSExperiment", ...)
.
protocol
:SOSProtocol
, where
the simulation parameters are specified.design
:SOSDesign
,
specifying model parameters for each run of a batch experiment.subject
:SOSSubject
,
containing the Model
to be simulated.result
:SOSResult
containing the result of the simulation.
Class Experiment
, directly.
signature(object = "SOSExperiment")
:
simulate(object, nsim = 10, seed, ...)
: Simulates
the model in the subject
slot according to the
design points in design
and parameters in protocol
for nsim
iterations, using seed
as the random
seed. Returns an instance of SOSExperiment
, which now
should include a SOSResult
for analysis.Michael Lawrence
See http://www.tbi.univie.ac.at/~raim/odeSolver/ for more information on the SBML ODE Solver library.
The simulate
method on SBMLDocument
is a
shortcut, but most users will probably find the above approach most
useful.