nskinetics.doe.fim.get_sensitivities

nskinetics.doe.fim.get_sensitivities(rxn_sys, t_eval, y0, param_inds, epsilon=0.0001, spikes=None, output_idx=None)

Compute finite-difference sensitivities of ReactionSystem outputs with respect to kinetic parameters.

Parameters:

• rxn_sys (ReactionSystem) – The reaction system to be evaluated.

• t_eval (array-like) – Time points at which to evaluate the solution.

• y0 (array-like) – Initial concentrations of all species.

• param_inds (list of str) – List of parameter indices to compute sensitivities for.

• epsilon (float, optional) – Relative perturbation size for finite difference (default is 1e-4).

• spikes (dict or None, optional) – Dictionary specifying species and corresponding spike amounts (optional).

• output_idx (list of int or None, optional) – Indices of species whose concentrations are observed/measured. If None, all are used.

Returns:

sensitivities – Flattened sensitivity matrix, where n_obs = len(t_eval) * len(output_idx), and n_params = len(param_inds).

Return type:

ndarray of shape (n_obs, n_params)