obj_alpha: Objective function to minimize certain elements of the local...
In dlill/MRAr: Functions to do MRA with

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.

1 2	obj_alpha(pars, fixed = NULL, perturbation_prediction, r_kept, obs_fun, p_fun, mypars, method = "simple", ...)

`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