CNORode (version 1.14.0)

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

Description

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

Usage

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

Arguments

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 bydefaultParametersSSm.

Value

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.

See Also

CellNOptR createLBodeContPars rbga

Examples

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)