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Creates and returns an instance of a SimulationBatch that can be used to efficiently vary parameters and initial values in a simulation

Source: R/utilities-simulation.R
createSimulationBatch.Rd

Creates and returns an instance of a SimulationBatch that can be used to efficiently vary parameters and initial values in a simulation

Usage

createSimulationBatch(
  simulation,
  parametersOrPaths = NULL,
  moleculesOrPaths = NULL
)

Arguments

simulation

Instance of a Simulation to simulate in a batch mode

parametersOrPaths

Parameter instances (element or vector) typically retrieved using getAllParametersMatching or parameter path (element or vector of strings) that will be varied in the simulation. (optional) When providing the paths, only absolute full paths are supported (i.e., no matching with '*' possible). If parametersOrPaths is NULL, you will not be able to set parameter values during batch run.

moleculesOrPaths

Molecule instances (element or vector) typically retrieved using getAllMoleculesMatching or molecule path (element or vector of strings) that will be varied in the simulation. (optional) When providing the paths, only absolute full paths are supported (i.e., no matching with '*' possible). If moleculesOrPaths is NULL, you will not be able to set molecule initial values during batch run.

Value

SimulationBatch that can be used to vary parameter values or molecule initial values and run simulation in an optimized manner

Examples

simPath <- system.file("extdata", "simple.pkml", package = "ospsuite")
sim <- loadSimulation(simPath)

# Create a simulation batch that will allow batch run for one parameter value
simulationBatch <- createSimulationBatch(sim, "Organism|Liver|Volume")

# Create a simulation batch that will allow batch run for multiple parameter
# values and initial values
simulationBatch <- createSimulationBatch(
  sim,
  c("Organism|Liver|Volume", "R1|k1"),
  c("Organism|Liver|A")
)