parEstimationLBode: Perform parameter estimation using a genetic algorithm...
In CNORode: ODE add-on to CellNOptR

Description Usage Arguments Value Author(s) See Also Examples

This function is an alias to the parEstimationLBode variants (parEstimationLBodeGA and parEstimationLBodeSSm)

1 2	parEstimationLBode(cnolist, model, method="ga", ode_parameters = NULL, indices = NULL, paramsGA=NULL, paramsSSm=NULL)

`cnolist`	A list containing the experimental design and data.
`model`	The logic model to be simulated.
`method`	Only "ga" or "essm" arguments are accepted.
`ode_parameters`	A list with the ODEs parameter information. Obtained with `createLBodeContPars`.
`indices`	Indices to map data in the model. Obtained with indexFinder function from CellNOptR.
`paramsGA`	A list of GA parameters. default is the list returned by `defaultParametersGA`.
`paramsSSm`	A list of SSm parameters. default is the list returned by`defaultParametersSSm`.

`LB_n`	A numeric value to be used as lower bound for all parameters of type n.
`LB_k`	A numeric value to be used as lower bound for all parameters of type k.
`LB_tau`	A numeric value to be used as lower bound for all parameters of type tau.
`UB_n`	A numeric value to be used as upper bound for all parameters of type n.
`UB_k`	A numeric value to be used as upper bound for all parameters of type k.
`UB_tau`	A numeric value to be used as upper bound for all parameters of type tau.
`default_n`	The default parameter to be used for every parameter of type n.
`default_k`	The default parameter to be used for every parameter of type k.
`default_tau`	The default parameter to be used for every parameter of type tau.
`LB_in`	An array with the the same length as ode_parameters$parValues with lower bounds for each specific parameter.
`UB_in`	An array with the the same length as ode_parameters$parValues with upper bounds for each specific parameter.
`opt_n`	Add all parameter n to the index of parameters to be fitted.
`opt_k`	Add all parameter k to the index of parameters to be fitted.
`opt_tau`	Add all parameter tau to the index of parameters to be fitted.
`random`	A logical value that determines that a random solution is for the parameters to be optimized.
`res`	A list containing the information provided by the solver.

David Henriques, Thomas Cokelaer

CellNOptR createLBodeContPars rbga

data("ToyCNOlist",package="CNORode");
data("ToyModel",package="CNORode");
data("ToyIndices",package="CNORode");
	
ode_parameters=createLBodeContPars(model,random=TRUE);
#Visualize initial solution
simulatedData=plotLBodeFitness(cnolistCNORodeExample, model,ode_parameters,indices=indices)
paramsGA = defaultParametersGA()
paramsGA$maxStepSize = 1
paramsGA$popSize = 10
paramsGA$iter = 10
paramsGA$transfer_function = 2
	
ode_parameters=parEstimationLBode(cnolistCNORodeExample,model,ode_parameters=ode_parameters,
	paramsGA=paramsGA)
#Visualize fitted solution
simulatedData=plotLBodeFitness(cnolistCNORodeExample, model,ode_parameters,indices=indices)