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CNORode (version 1.14.0)

ODE add-on to CellNOptR

Description

ODE add-on to CellNOptR

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Version

Version

1.14.0

License

GPL-2

Maintainer

David Henriques

Last Published

February 15th, 2017

Functions in CNORode (1.14.0)

getLBodeContObjFunction

Returns the objective function to perform parameter estimation.
parEstimationLBode

Perform parameter estimation using a genetic algorithm (package genalg) or ssm (if package essm available).
parEstimationLBodeSSm

Perform parameter estimation using essR.
getLBodeModelSim

Simulate the logic-based ODE model
minlpLBodeSSm

Search for the best combination of continuous parameters and logic gates.
incidence2Adjacency

Convert an incidence matrix into an adjacency matrix.
plotLBodeModelSim

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

Get the objective function to evaluate the fitness of a given model structure and set of parameters.
cnolistCNORodeExample

A cnolist from CellNoptR
defaultParametersSSm

Create default options to perform parameter estimation with scatter search meta-heuristic.
simdata2cnolist

converts output of getLBodeModelSim to cnolist
model

A model from CellNoptR
getLBodeSimFunction

Get a function to simulate a logic based ODE model.
plotLBodeFitness

Plot data against simulated values.
simulate

Simulate value signals a CNO list With Logic-Based ODEs.
parEstimationLBodeGA

Perform parameter estimation using a genetic algorithm (package genalg).
CNORode

Logic based ODE extension for CellNOptR
createLBodeContPars

Create a list with ODE parameter information needed to perform parameter estimation
getLBodeDataSim

Simulate value signals a CNO list With Logic-Based ODEs.
defaultParametersGA

Create default options to perform parameter estimation with a genetic algorithm.
getStates

Find which species in the model are states.
indices

Indices that relate cnolist to model