Get a function to simulate a logic based ODE model.

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Description

This function is internally used by CNORode to configure the simulation function with default arguments.

Usage

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	getLBodeSimFunction(cnolist1, model1, adjMatrix1, indices1, odeParameters1,
	time1 = 1, verbose1 = 0, transfer_function1 = 3, reltol1 = 1e-04, atol1 = 0.001,
	maxStepSize1 = Inf, maxNumSteps1 = 1e+05, maxErrTestsFails1 = 50,
initial_state1=0.1)

Arguments

cnolist1

A list containing the experimental design and data.

model1

The logic model to be simulated.

adjMatrix1

An adjacency matrix from the model.

indices1

Indices to map data in the model. Obtained with indexFinder function from CellNOptR.

odeParameters1

A list with the ODEs parameter information. Obtained with createLBodeContPars.

time1

An integer with the index of the time point to start the simulation. Default is 1.

verbose1

A logical value that triggers a set of comments.

transfer_function1

The type of used transfer. Use 1 for no transfer function, 2 for Hill function and 3 for normalized Hill function.

reltol1

Relative Tolerance for numerical integration.

atol1

Absolute tolerance for numerical integration.

maxStepSize1

The maximum step size allowed to ODE solver.

maxNumSteps1

The maximum number of internal steps between two points being sampled before the solver fails.

maxErrTestsFails1

Specifies the maximum number of error test failures permitted in attempting one step.

initial_state1

initial state of the dynamic nodes (non-measured) (Defaults to 0.1)

Value

A function that returns a simulated model.

Note

This function is for CNORode internal use.

Author(s)

David Henriques, Thomas Cokelaer

See Also

CellNOptR CNORode

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