# ODE add-on to CellNOptR

## Documentation for package ‘CNORode’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cnolistCNORodeExample | A cnolist from CellNoptR
CNORode | Logic based ODE extension for CellNOptR
createLBodeContPars | Create a list with ODE parameter information needed to perform parameter estimation
defaultParametersGA | Create default options to perform parameter estimation with a genetic algorithm.
defaultParametersSSm | Create default options to perform parameter estimation with scatter search meta-heuristic.
getLBodeContObjFunction | Returns the objective function to perform parameter estimation.
getLBodeDataSim | Simulate value signals a CNO list With Logic-Based ODEs.
getLBodeMINLPObjFunction | Get the objective function to evaluate the fitness of a given model structure and set of parameters.
getLBodeModelSim | Simulate the logic-based ODE model
getLBodeSimFunction | Get a function to simulate a logic based ODE model.
getStates | Find which species in the model are states.
incidence2Adjacency | Convert an incidence matrix into an adjacency matrix.
indices | Indices that relate cnolist to model
minlpLBodeSSm | Search for the best combination of continuous parameters and logic gates.
model | A model from CellNoptR
parEstimationLBode | Perform parameter estimation using a genetic algorithm (package genalg) or ssm (if package essm available).
parEstimationLBodeGA | Perform parameter estimation using a genetic algorithm (package genalg).
parEstimationLBodeSSm | Perform parameter estimation using essR.
plotLBodeFitness | Plot data against simulated values.
plotLBodeModelSim | Simulate the model and plot the obtained with the different experimental conditions.
simdata2cnolist | converts output of getLBodeModelSim to cnolist
simulate | Simulate value signals a CNO list With Logic-Based ODEs.