I used this function to compare different optimizers. trust() was as fast as optim, but more reliable. All other methods like simulated annealing were not as reliable.
1 2 | obj_alpha_no_derivs(pars_opt, perturbation_prediction, r_kept, obs_fun,
p_fun, mypars)
|
perturbation_prediction |
Simulated steady state perturbation data |
r_kept |
elements kept in the minimization (=elements that describe sequestration connections) |
obs_fun |
Observation function which returns the communicating species |
p_fun |
Parameter transformation which returns different conditions |
mypars |
Parameters of the ODE model |
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