CNORode                 Logic based ODE extension for CellNOptR
cnolistCNORodeExample   A cnolist from 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.
