10.1.1.1.5. freeflux.analysis.stats

Define statistic functions.

10.1.1.1.5.1. Attributes

__author__

10.1.1.1.5.2. Functions

_chi2_test(obj_value, dof, confidence_level)

_normal_probability(resids, show_fig, output_dir)

_simulated_vs_measured_measurements(sim_meas, ...)

_simulated_vs_measured_MDVs(simulated_MDVs, ...)

_simulated_vs_measured_fluxes(simulated_fluxes, ...)

_confidence_intervals_le(res, irr, cov, dof, ...)

_confidence_intervals_mc(res_set, irr, confidence_level)

_MDV_kinetics(emuid, simulated_inst_MDVs, show_fig, ...)

_simulated_vs_measured_inst_MDVs(simulated_inst_MDVs, ...)

_contribution_matrix(cov, trans_mat, simulated_der, ...)

_sensitivity(cov, trans_mat, simulated_der, ...)

10.1.1.1.5.3. Module Contents

freeflux.analysis.stats.__author__ = 'Chao Wu'[source]
freeflux.analysis.stats._chi2_test(obj_value, dof, confidence_level)[source]
Parameters:

  • obj_value (float) – Objective value.

  • dof (int) – Degree of freedom.

  • confidence_level (float) – Confidence level, e.g., 0.95 as 95% confidence level.

freeflux.analysis.stats._normal_probability(resids, show_fig, output_dir)[source]
Parameters:

  • resids (array) – Residuals.

  • show_fig (bool) – Whether to show figure.

  • output_dir (str) – Output directory.

freeflux.analysis.stats._simulated_vs_measured_measurements(sim_meas, exp_meas, exp_meas_err, xlabel, ylabel, xticklabels, filename, show_fig, output_dir)[source]
Parameters:

  • sim_meas (array or list) – Simulated measurements.

  • exp_meas (array or list) – Measured measurements.

  • exp_meas_err (array or list) – Errors of measured measurements.

  • xlabel (str) – Xlabel.

  • ylabel (str) – Ylabel.

  • xticklabels (array or list) – Xticklabels.

  • filename (str) – File name.

  • show_fig (bool) – Whether to show figure.

  • output_dir (str) – Output directory.

freeflux.analysis.stats._simulated_vs_measured_MDVs(simulated_MDVs, measured_MDVs, show_fig, output_dir)[source]
Parameters:

  • simulated_MDVs (dict) – EMU ID => simulated MDV.

  • measured_MDVs (dict) – EMU ID => [means, sds].

  • show_fig (bool) – Whether to show figure.

  • output_dir (str) – Output directory.

freeflux.analysis.stats._simulated_vs_measured_fluxes(simulated_fluxes, measured_fluxes, show_fig, output_dir)[source]
Parameters:

  • simulated_fluxes (dict) – Flux ID => simulated flux.

  • measured_fluxes (dict) – Flux ID => [mean, sd].

  • show_fig (bool) – Whether to show figure.

  • output_dir (str) – Output directory.

freeflux.analysis.stats._confidence_intervals_le(res, irr, cov, dof, confidence_level)[source]
Parameters:

  • res (ser) – Optimal results, e.g., net fluxes, total fluxes or concentrations.

  • irr (list) – Irreversible items. total fluxes and concentrations are all considered irreversible.

  • cov (array) – Corvariance matrix of free fluxes obtained from hessian at convergence.

  • dof (int) – Degree of freedom.

  • confidence_level (float) – Confidence level, e.g., 0.95 as 95% confidence level.

freeflux.analysis.stats._confidence_intervals_mc(res_set, irr, confidence_level)[source]
Parameters:

  • res_set (list of ser) – Set of optimal net fluxes. Total fluxes or concentrations.

  • irr (list) – Irreversible items. Total fluxes and concentrations are all considered irreversible.

  • confidence_level (float) – Confidence level, e.g., 0.95 as 95% confidence level.

freeflux.analysis.stats._MDV_kinetics(emuid, simulated_inst_MDVs, show_fig, output_dir)[source]
Parameters:

  • emuid (str) – EMU ID.

  • simulated_inst_MDVs (dict) – Timepoint => MDV.

  • show_fig (bool) – Whether to show figure.

  • output_dir (str) – Output directory.

freeflux.analysis.stats._simulated_vs_measured_inst_MDVs(simulated_inst_MDVs, measured_inst_MDVs, show_fig, output_dir)[source]
Parameters:

  • simulated_inst_MDVs (dict) – EMU ID => {t => simulated MDV}.

  • measured_inst_MDVs (dict) – EMU ID => {t => [means, sds]}.

  • show_fig (bool) – Whether to show figure.

  • output_dir (str) – Output directory.

freeflux.analysis.stats._contribution_matrix(cov, trans_mat, simulated_der, measured_cov)[source]
Parameters:

  • cov (array) – Corvariance matrix of free fluxes obtained from hessian at convergence.

  • trans_mat (array) – Transformation matrix from free flux to total flux or net flux, i.e., N to total flux, T@N to net flux.

  • simulated_der (array) – Derivative of simulated measurements w.r.t. free fluxes.

  • measured_cov (array) – Corvariance matrix of measurements.

freeflux.analysis.stats._sensitivity(cov, trans_mat, simulated_der, measured_inv_cov)[source]
Parameters:

  • cov (array) – Corvariance matrix of free fluxes obtained from hessian at convergence.

  • trans_mat (array) – Transformation matrix from free flux to total flux or net flux, i.e., N to total flux, T@N to net flux.

  • simulated_der (array) – Derivative of simulated measurements w.r.t. free fluxes.

  • measured_inv_cov (array) – Inversed corvariance matrix of measurements.