# Simulate the logic-based ODE model

### Description

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.

### Usage

1 2 3 |

### Arguments

`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 |

`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. |

### Details

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.

### Value

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.

### Author(s)

David Henriques, Thomas Cokelaer

### See Also

`CellNOptR`

`createLBodeContPars`

### Examples

1 2 3 4 5 | ```
library(CNORode)
data('ToyCNOlist',package='CNORode');
data('ToyModel',package='CNORode');
data('ToyIndices',package='CNORode');
modelSimulation=getLBodeModelSim(cnolistCNORodeExample, model,indices=indices);
``` |