obj_alpha: Objective function to minimize certain elements of the local...

Description Usage Arguments

Description

This function squares all elements that flip sign once the complexes are added to the observation. This can then be used to minimize the values.

Usage

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obj_alpha(pars, fixed = NULL, perturbation_prediction, r_kept, obs_fun,
  p_fun, mypars, method = "simple", ...)

Arguments

pars

Free parameters a_ij to control the influence of the complexes

fixed

Fixed parameters are parameters for which no derivative is calculated

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

method

method for taking the derivative wrt pars_opt.

...

not needed except for throwing away an unnecessary input when applying the new mstrust


dlill/MRAr documentation built on May 16, 2019, 7:24 a.m.