Perform parameter estimation using essR.

Share:

Description

This function uses essR to perform parameter estimation. The objective function is the same as the one provided by getLBodeContObjFunction.

Usage

1
2
3
4
5
	parEstimationLBodeSSm(cnolist, model, ode_parameters = NULL, indices = NULL, 
	maxeval = Inf, maxtime = 100, ndiverse = NULL, dim_refset = NULL, local_solver = NULL,
	time = 1, verbose = 0, transfer_function = 3, reltol = 1e-04, atol = 0.001, 
	maxStepSize = Inf, maxNumSteps = 1e+05, maxErrTestsFails = 50, nan_fac =1,
    useVariances=F,initial_state=0.1)

Arguments

cnolist

A list containing the experimental design and data.

model

The logic model to be simulated.

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.

maxeval

Maximum number of evaluation in the optimization procedure.

maxtime

Duration of the optimization procedure.

ndiverse

Number of diverse initial solutions.

dim_refset

Size of the reference set.

local_solver

Local solver to be used in SSm.

time

An integer with the index of the time point to start the simulation. Default is 1.

verbose

A logical value that triggers a set of comments.

transfer_function

The type of used transfer. Use 1 for no transfer function, 2 for Hill function and 3 for normalized Hill function.

reltol

Relative Tolerance for numerical integration.

atol

Absolute tolerance for numerical integration.

maxStepSize

The maximum step size allowed to ODE solver.

maxNumSteps

The maximum number of internal steps between two points being sampled before the solver fails.

maxErrTestsFails

Specifies the maximum number of error test failures permitted in attempting one step.

nan_fac

A penalty for each data point the model is not able to simulate. We recommend higher than 0 and smaller that 1.

useVariances

Uses variance if any

initial_state

initial state of the dynamic nodes (non-measured) (Defaults to 0.1)

Details

Check CellNOptR for details about the cnolist and the model format. For more details in the configuration of the ODE solver check the CVODES manual.

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.

smm_results

A list containing the information provided by the nonlinear optimization solver.

Author(s)

David Henriques, Thomas Cokelaer

See Also

CellNOptR createLBodeContPars

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
## Not run: 
data("ToyCNOlist",package="CNORode");
data("ToyModel",package="CNORode");
data("ToyIndices",package="CNORode");

ode_parameters=createLBodeContPars(model,random=TRUE);

#Visualize intial simulation
simulatedData=plotLBodeFitness(cnolistCNORodeExample, model,ode_parameters,indices=indices)

ode_parameters=parEstimationLBodeSSm(cnolistCNORodeExample,model,ode_parameters,
indices=indices,maxtime=20,ndiverse=50,dim_refset=6);

#Visualize fitterd solution
simulatedData=plotLBodeFitness(cnolistCNORodeExample, model,indices=indices,ode_parameters=ode_parameters);

## End(Not run)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.