SimulationBatch: SimulationBatch

In Open-Systems-Pharmacology/OSPSuite-R: R package to manipulate OSPSuite Models

SimulationBatch

Description

An optimized simulation with faster loading. The corresponding .NET class is "OSPSuite.R.Services.ConcurrentRunSimulationBatch"

Super classes

rSharp::NetObject -> ospsuite::DotNetWrapper -> SimulationBatch

Active bindings

simulation

Underlying simulation used for the batch run. Read only.

runValuesIds

Ids of the run values that will be executed on next run

id

The id of the .NET wrapped object. (read-only)

Methods

Public methods

• SimulationBatch$new()

• SimulationBatch$addRunValues()

• SimulationBatch$getVariableParameters()

• SimulationBatch$getVariableMolecules()

• SimulationBatch$print()

Inherited methods

• rSharp::NetObject$call()
• rSharp::NetObject$finalize()
• rSharp::NetObject$get()
• rSharp::NetObject$getFields()
• rSharp::NetObject$getMemberSignature()
• rSharp::NetObject$getMethods()
• rSharp::NetObject$getProperties()
• rSharp::NetObject$getStaticFields()
• rSharp::NetObject$getStaticMethods()
• rSharp::NetObject$getStaticProperties()
• rSharp::NetObject$set()

---

Method new()

Initialize a new instance of the class

Usage

SimulationBatch$new(netObject, simulation)

Arguments

netObject

An rSharp::NetObject object.

simulation

Simulation used in the batch run

Returns

A new SimulationBatch object.

---

Method addRunValues()

Add a set of parameter and start values for next execution.

Usage

SimulationBatch$addRunValues(parameterValues = NULL, initialValues = NULL)

Arguments

parameterValues

Vector of parameter values to set in the simulation (default is NULL)

initialValues

Vector of initial values to set in the simulation (default is NULL)

Details

Intended for the use with runSimulationBatches. The simulation batch is executed with the sets of parameter and initial values that have been scheduled. The set of run values is cleared after successful run.

Returns

Id of the values set that can be used to get the correct result from runSimulationBatches.

Examples

\dontrun{
sim1 <- loadSimulation("sim1", loadFromCache = TRUE)
sim2 <- loadSimulation("sim2", loadFromCache = TRUE)
parameters <- c("Organism|Liver|Volume", "R1|k1")
molecules <- "Organism|Liver|A"
# Create two simulation batches.
simulationBatch1 <- createSimulationBatch(simulation = sim1,
parametersOrPaths = parameters,
moleculesOrPaths = molecules)
simulationBatch2 <- createSimulationBatch(simulation = sim2,
parametersOrPaths = parameters,
moleculesOrPaths = molecules)
#Ids of run values
ids <- c()
ids[[1]] <- simulationBatch1$addRunValues(parameterValues = c(1, 2), initialValues = 1)
ids[[2]] <- simulationBatch1$addRunValues(parameterValues = c(1.6, 2.4), initialValues = 3)
ids[[3]] <- simulationBatch2$addRunValues(parameterValues = c(4, 2), initialValues = 4)
ids[[4]] <- simulationBatch2$addRunValues(parameterValues = c(2.6, 4.4), initialValues = 5)
res <- runSimulationBatches(simulationBatches = list(simulationBatch1, simulationBatch2))
}

---

Method getVariableParameters()

Returns a list of parameter paths that are variable in this batch.

Usage

SimulationBatch$getVariableParameters()

Details

The order of parameters is the same as the order of parameter values added with ⁠$addRunValues()⁠ method.

Returns

List of parameter paths, or NULL if no parameter is variable.

---

Method getVariableMolecules()

Returns a list of molecules paths that are variable in this batch

Usage

SimulationBatch$getVariableMolecules()

Details

The order of molecules is the same as the order of molecule start values added with ⁠$addRunValues()⁠ method.

Returns

List of parameter paths, or NULL if no molecule is variable.

---

Method print()

Print the object to the console

Usage

SimulationBatch$print(...)

Arguments

...

Additional arguments.

Examples

## ------------------------------------------------
## Method `SimulationBatch$addRunValues`
## ------------------------------------------------

## Not run: 
sim1 <- loadSimulation("sim1", loadFromCache = TRUE)
sim2 <- loadSimulation("sim2", loadFromCache = TRUE)
parameters <- c("Organism|Liver|Volume", "R1|k1")
molecules <- "Organism|Liver|A"
# Create two simulation batches.
simulationBatch1 <- createSimulationBatch(simulation = sim1,
parametersOrPaths = parameters,
moleculesOrPaths = molecules)
simulationBatch2 <- createSimulationBatch(simulation = sim2,
parametersOrPaths = parameters,
moleculesOrPaths = molecules)
#Ids of run values
ids <- c()
ids[[1]] <- simulationBatch1$addRunValues(parameterValues = c(1, 2), initialValues = 1)
ids[[2]] <- simulationBatch1$addRunValues(parameterValues = c(1.6, 2.4), initialValues = 3)
ids[[3]] <- simulationBatch2$addRunValues(parameterValues = c(4, 2), initialValues = 4)
ids[[4]] <- simulationBatch2$addRunValues(parameterValues = c(2.6, 4.4), initialValues = 5)
res <- runSimulationBatches(simulationBatches = list(simulationBatch1, simulationBatch2))

## End(Not run)

Open-Systems-Pharmacology/OSPSuite-R documentation built on Feb. 14, 2025, 4:48 p.m.