ODE add-on to CellNOptR

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Documentation for package ‘CNORode’ version 1.44.0

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

Help Pages

cnodata	A cnodata from CellNoptR
cnolist	A cnolist from CellNoptR
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
crossvalidateODE	Crossvalidate ODE model
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.
pknmodel	A pknmodel from CellNoptR
plotLBodeFitness	Plot data against simulated values.
plotLBodeModelSim	Simulate the model and plot the obtained with the different experimental conditions.
runCNORode	runCNORode
simdata2cnolist	converts output of getLBodeModelSim to cnolist
simulate	Simulate value signals a CNO list With Logic-Based ODEs.