# Simulate the model and plot the obtained with the different experimental conditions.

### Description

Plots the simulated values of the logic based ODE model. Only dynamic states are plotted, i.e. those that are not inputs. a blue line. Additionally this functions returns the the simulated values.

### Usage

1 2 3 4 |

### 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. |

`adjMatrix` |
Model representation in the form of an adjacency matrix. When not provided will be automatically computed based in the model. |

`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 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. |

`large` |
Boolean variable defining if the plot should split into several subplots. |

`nsplit` |
In case the large plot options is selected define how many subplots will exist. Default is 4. |

`show` |
show the error (defaults to TRUE) |

### Value

Returns a list with simulated Model values. One matrix of size number of species by number of experimental conditions for each time-point.

### 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=plotLBodeModelSim(cnolistCNORodeExample, model,indices=indices);
``` |