parEstimationLBode {CNORode} | R Documentation |
This function is an alias to the parEstimationLBode variants
(parEstimationLBodeGA
and parEstimationLBodeSSm
)
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 |
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 |
paramsSSm |
A list of SSm parameters. default is the list returned by |
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)