sbioensemblerun

Multiple stochastic ensemble runs of SimBiology model

Syntax

simdataObj = sbioensemblerun(modelObj, Numruns)
simdataObj = sbioensemblerun(modelObj, Numruns, Interpolation)
simdataObj = sbioensemblerun(modelObj, Numruns, configsetObj)
simdataObj = sbioensemblerun(modelObj, Numruns, configsetObj, Interpolation)
simdataObj = sbioensemblerun(modelObj, Numruns, variantObj)
simdataObj = sbioensemblerun(modelObj, Numruns, variantObj, Interpolation)
simdataObj = sbioensemblerun(modelObj, Numruns, configsetObj, variantObj)
simdataObj = sbioensemblerun(modelObj, Numruns, configsetObj, variantObj, Interpolation)


Arguments

simdataObj	An array of SimData objects containing simulation data generated by sbioensemblerun. All elements of simdataObj contain data for the same states in the same model.
modelObj	Model object to be simulated.
Numruns	Integer scalar representing the number of stochastic runs to make.
Interpolation	Character vector or string denoting the interpolation scheme to be used if data should be interpolated to get a consistent time vector. Valid values are 'linear' (linear interpolation), 'zoh' (zero-order hold), or 'off' (no interpolation). Default is 'off'. If interpolation is on, the data is interpolated to match the time vector with the smallest simulation stop time.
configsetObj	Specify the configuration set object to use in the ensemble simulation. For more information about configuration sets, see Configset object.
variantObj	Specify the variant object to apply to the model during the ensemble simulation. For more information about variant objects, see Variant object.

Description

simdataObj = sbioensemblerun(modelObj, Numruns) performs a stochastic ensemble run of the SimBiology^® model object (modelObj), and returns the results in simdataObj, an array of SimData objects. The active configset and the active variants are used during simulation and are saved in the output, SimData object (simdataObj).

sbioensemblerun uses the settings in the active configset on the model object (modelObj) to perform the repeated simulation runs. The SolverType property of the active configset must be set to one of the stochastic solvers: 'ssa', 'expltau', or 'impltau'. sbioensemblerun generates an error if the SolverType property is set to any of the deterministic (ODE) solvers.

simdataObj = sbioensemblerun(modelObj, Numruns, Interpolation) performs a stochastic ensemble run of a model object (modelObj), and interpolates the results of the ensemble run onto a common time vector using the interpolation scheme (Interpolation).

simdataObj = sbioensemblerun(modelObj, Numruns, configsetObj) performs an ensemble run of a model object (modelObj), using the specified configuration set (configsetObj).

simdataObj = sbioensemblerun(modelObj, Numruns, configsetObj, Interpolation) performs an ensemble run of a model object (modelObj), using the specified configuration set (configsetObj), and interpolates the results of the ensemble run onto a common time vector using the interpolation scheme (Interpolation).

simdataObj = sbioensemblerun(modelObj, Numruns, variantObj) performs an ensemble run of a model object (modelObj), using the variant object or array of variant objects (variantObj).

simdataObj = sbioensemblerun(modelObj, Numruns, variantObj, Interpolation) performs an ensemble run of a model object (modelObj), using the variant object or array of variant objects (variantObj), and interpolates the results of the ensemble run onto a common time vector using the interpolation scheme (Interpolation).

simdataObj = sbioensemblerun(modelObj, Numruns, configsetObj, variantObj) performs an ensemble run of a model object (modelObj), using the configuration set (configsetObj), and the variant object or array of variant objects (variantObj). If the configuration set object (configsetObj) is empty, the active configset on the model is used for simulation. If the variant object (variantObj) is empty, then no variant (not even the active variants in the model) is used for the simulation.

simdataObj = sbioensemblerun(modelObj, Numruns, configsetObj, variantObj, Interpolation) performs an ensemble run of a model object (modelObj), using the configuration set (configsetObj), and the variant object or array of variant objects (variantObj), and interpolates the results of the ensemble run onto a common time vector using the interpolation scheme (Interpolation).

Examples

Get Statistics from Ensemble Run of SimBiology Model

Load the radiodecay model.

sbioloadproject("radiodecay.sbproj");

Change the solver of the active configuration set to be ssa. Also, adjust the LogDecimation property on the SolverOptions property of the configuration set.

cs = getconfigset(m1,"active");
cs.SolverType = "ssa";
so = cs.SolverOptions;
so.LogDecimation = 10;

Perform an ensemble of 20 runs with no interpolation.

ensembleData = sbioensemblerun(m1,20);
sbioensembleplot(ensembleData, 'z', 1.0);

Create a 2-D distribution plot of the species z at time = 1.0.

sbioensembleplot(ensembleData,"z",1.0); 

Get ensemble statistics for all species using the default interpolation method.

[T,M,V] = sbioensemblestats(ensembleData);

Get ensemble statistics for a specific species using the default interpolation scheme.

[T2,M2,V2] = sbioensemblestats(ensembleData,"z");

Create a 3-D shaded plot of the species x and z.

sbioensembleplot(ensembleData,["x","z"]);

Version History

Introduced in R2006a