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

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Description

Creates a list with the continuous parameters to simulate the model, upper and lower bounds for the parameter estimation, parameters names, indices of the parameters and other information.

Usage

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	createLBodeContPars(model, LB_n = 1, LB_k = 0.1, LB_tau = 0.01, 
	UB_n = 5, UB_k = 0.9, UB_tau = 10, default_n = 3, default_k = 0.5,
	default_tau = 1, LB_in = c(), UB_in = c(), opt_n = TRUE, opt_k = TRUE,
	opt_tau = TRUE, random = FALSE)

Arguments

model

The logic model to be simulated.

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

logical value that determines that a random solution is for the parameters to be optimized.

Value

parNames

An array containing the names of the parameters.

parValues

An array containing the values of the parameters, in the same order as the names.

index_opt_pars

An array containing the indexes for the parameters to be fitted.

index_n

An array containing the indexes of the parameters of type n.

index_k

An array containing the indexes of the parameters of type k.

index_tau

An array containing the indexes of the parameters of type tau.

LB

An array containing the lower bound for each parameter.

UB

An array containing the upper bound for each parameter.

Author(s)

David Henriques, Thomas Cokelaer

Examples

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	library(CNORode)
	data("ToyCNOlist",package="CNORode");
	data("ToyModel",package="CNORode");
	data("ToyIndices",package="CNORode");
	ode_parameters=createLBodeContPars(model, opt_n=FALSE,default_n=2,
	random=TRUE,LB_k=0.25,UB_k=0.8,LB_tau=0.01,UB_tau=10);

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