r_kept_fun: Which elements to keep in the optimization procedure?
In dlill/MRAr: Functions to do MRA with

Description Usage Arguments

This function compares the connection coefficient in the local response matrices when either only free active kinases are measured or when the complexes are switched on. All free parameters a_ij are increased simultaneously

1 2	r_kept_fun(pars_opt, perturbation_prediction, obs_fun, p_fun, pars, alpha = -log(0 + .Machine$double.eps))

`pars_opt`	Free parameters a_ij to control the influence of the complexes
`perturbation_prediction`	Simulated steady state perturbation data
`obs_fun`	Observation function which returns the communicating species
`p_fun`	Parameter transformation which returns different conditions
`pars`	Parameters of the ODE model
`alpha`	Compares r(pars_opt) with r(pars_opt + alpha). Since pars_opt_0 defaults to log(0+.Machine$double.eps), I chose its negative value as the default. This is basically the same as comparing r(0) with r(1)