getLBodeSimFunction {CNORode} | R Documentation |
This function is internally used by CNORode to configure the simulation function with default arguments.
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)
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 |
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. |
A function that returns a simulated model.
This function is for CNORode internal use.
David Henriques, Thomas Cokelaer