createLBodeContPars {CNORode} | R Documentation |
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.
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)
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. |
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. |
David Henriques, Thomas Cokelaer
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);