getLBodeModelSim: Simulate the logic-based ODE model
In CNORode: ODE add-on to CellNOptR

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

This function simulates a logic-based ODE model and return a list with one matrix for each time point. The input species in the model are filled with NA values. If the simulation of a particular set of initial conditions fails the solver will fill the experience row with NA values.

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	getLBodeModelSim(cnolist, model, ode_parameters = NULL, indices = NULL, timeSignals=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`	The logic model to be simulated.
`ode_parameters`	A list with the ODEs parameter information. Obtained with `createLBodeContPars`.
`indices`	Indices to map data in the model. Obtained with indexFinder function from CellNOptR.
`timeSignals`	An array containing a different timeSignals. If you use this argument, it will also modify the dimensions from valueSignals.
`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 number of internal steps between two points being sampled before the solver fails.
`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 with similar structure to cnolist$valueSignals. Contains one matrix for each time-point. Each matrix contains one row per experiment and one columns per model species.

David Henriques, Thomas Cokelaer

CellNOptR createLBodeContPars

library(CNORode)
data('ToyCNOlist',package='CNORode');
data('ToyModel',package='CNORode');
data('ToyIndices',package='CNORode');
modelSimulation=getLBodeModelSim(cnolistCNORodeExample, model,indices=indices);