simulate: Simulate value signals a CNO list With Logic-Based ODEs.
In CNORode: ODE add-on to CellNOptR

Description Usage Arguments Details Value Author(s) See Also Examples

This function receives a set of inputs, namely the cnolist and the model and returns a list with the same size of the cnolist$valueSignals.

	simulate(cnolist, model, ode_parameters=NULL, indices=NULL,
	adjMatrix=NULL, time=1, verbose=0, transfer_function=3,
	reltol=1e-04, atol=0.001, maxStepSize=Inf, maxNumSteps=1e+05, 
	maxErrTestsFails=50)

`cnolist`	A list containing the experimental design and data.
`model`	A list with the ODEs parameter information. Obtained with `createLBodeContPars`.
`ode_parameters`	A list with the ODEs parameter information. Obtained with makeParameterList function.
`indices`	Indices to map data in the model. Obtained with indexFinder function from CellNOptR.
`adjMatrix`	The adjacency matrix. Recomputed if not provided
`time`	An integer with the index of the time point to start the simulation. Default is 1.
`verbose`	A logical value that triggers a set of comments.
`transfer_function`	The type of used transfer. Use 1 for no transfer function, 2 for Hill function and 3 for normalized Hill function.
`reltol`	Relative Tolerance for numerical integration.
`atol`	Absolute tolerance for numerical integration.
`maxStepSize`	The maximum step size allowed to ODE solver.
`maxNumSteps`	The maximum number of internal steps between two points being sampled before the solver fails.
`maxErrTestsFails`	Specifies the maximum number of error test failures permitted in attempting one step.

Check CellNOptR for details about the cnolist and the model format. For more details in the configuration of the ODE solver check the CVODES manual.

Returns a list with simulated data that has the same structure as the cnolist$valueSignals. One matrix for each time-point.

David Henriques, Thomas Cokelaer

CellNOptR parEstimationLBode parEstimationLBodeSSm

library(CNORode)
data("ToyCNOlist",package="CNORode");
data("ToyModel",package="CNORode");
data("ToyIndices",package="CNORode");
dataSimulation = simulate(cnolistCNORodeExample, model,indices=indices);