Index

B

bootstrap_count_data_to_summary_stats() (memocell.data.Data method) bootstrapping_covariance() (memocell.data.Data static method)

bootstrapping_mean() (memocell.data.Data static method) bootstrapping_variance() (memocell.data.Data static method)

C

compute_bayesian_information_criterion() (memocell.estimation.Estimation static method) compute_bestfit_simulation() (memocell.estimation.Estimation method) compute_initial_moment_first() (memocell.simulation_lib.sim_moments.MomentsSim static method) compute_initial_moment_second_factorial() (memocell.simulation_lib.sim_moments.MomentsSim static method) compute_initial_moment_second_mixed_ii() (memocell.simulation_lib.sim_moments.MomentsSim static method) compute_initial_moment_second_mixed_ik() (memocell.simulation_lib.sim_moments.MomentsSim static method) compute_log_evidence_from_bic() (memocell.estimation.Estimation static method) compute_log_likelihood_norm() (memocell.estimation.Estimation static method) compute_model_bayes_factors() (in module memocell.selection) compute_model_bayes_factors_from_log_evidences() (in module memocell.selection) compute_model_probabilities() (in module memocell.selection) compute_model_probabilities_from_log_evidences() (in module memocell.selection) compute_simulation_credible_band() (memocell.estimation.Estimation method) convert_none_data_to_empty_array() (memocell.data.Data static method) count_net_hidden_nodes() (memocell.network.Network static method)

count_net_main_nodes() (memocell.network.Network static method) create_data_variable_order() (memocell.data.Data static method) create_module_nodes() (memocell.network.Network static method) create_module_reaction_types() (memocell.network.Network static method) create_net_modules_and_identifiers() (memocell.network.Network method) create_node_identifiers() (memocell.network.Network static method) create_node_order() (memocell.network.Network static method) create_node_state_update_str() (memocell.simulation_lib.sim_gillespie.GillespieSim static method) create_node_summation_indices() (memocell.simulation_lib.sim_gillespie.GillespieSim static method) create_propensities_update_str() (memocell.simulation_lib.sim_gillespie.GillespieSim static method) create_rate_identifiers() (memocell.network.Network static method) create_theta_numeric_exec() (memocell.simulation_lib.sim_gillespie.GillespieSim static method) create_theta_order() (memocell.network.Network static method) create_variables_identifiers() (memocell.simulation.Simulation static method) create_variables_order() (memocell.simulation.Simulation static method) create_variables_summation_indices() (memocell.simulation_lib.sim_gillespie.GillespieSim static method)

D

Data (class in memocell.data) data_covariance_plot() (in module memocell.plots) data_hist_variables_plot() (in module memocell.plots) data_hist_waiting_times_plot() (in module memocell.plots) data_mean_plot() (in module memocell.plots) data_variable_scatter_plot() (in module memocell.plots)

data_variance_plot() (in module memocell.plots) define_gill_fct() (memocell.simulation_lib.sim_gillespie.GillespieSim static method) derive_moment_eqs() (memocell.simulation_lib.sim_moments.MomentsSim static method) derive_moment_order_hidden() (memocell.simulation_lib.sim_moments.MomentsSim static method) derive_moment_order_main() (memocell.simulation_lib.sim_moments.MomentsSim static method) derive_moment_pde() (memocell.simulation_lib.sim_moments.MomentsSim method)

E

est_bestfit_covariance_plot() (in module memocell.plots) est_bestfit_mean_plot() (in module memocell.plots) est_bestfit_variance_plot() (in module memocell.plots) est_chains_plot() (in module memocell.plots) est_corner_kernel_plot() (in module memocell.plots) est_corner_plot() (in module memocell.plots) est_corner_weight_plot() (in module memocell.plots) est_parameter_plot() (in module memocell.plots) est_runplot() (in module memocell.plots) est_traceplot() (in module memocell.plots)

estimate() (memocell.estimation.Estimation method) Estimation (class in memocell.estimation) event_find_first_cell_count_increase() (memocell.data.Data method) event_find_first_cell_count_increase_after_cell_type_conversion() (memocell.data.Data method) event_find_first_cell_type_conversion() (memocell.data.Data method) event_find_first_change_from_inital_conditions() (memocell.data.Data method) event_find_second_cell_count_increase_after_first_cell_count_increase_after_cell_type_conversion() (memocell.data.Data method) event_find_third_cell_count_increase_after_first_and_second_cell_count_increase_after_cell_type_conversion() (memocell.data.Data method) events_find_all() (memocell.data.Data method) exact_interpolation() (memocell.simulation_lib.sim_gillespie.GillespieSim static method)

G

gamma_compute_bin_probabilities() (memocell.data.Data method) gamma_fit_binned_waiting_times() (memocell.data.Data method) gamma_negative_multinomial_log_likelihood() (memocell.data.Data method) get_credible_interval() (memocell.estimation.Estimation static method) get_indices_for_moment_readout() (memocell.simulation_lib.sim_moments.MomentsSim static method) get_indices_for_solution_readout() (memocell.simulation_lib.sim_moments.MomentsSim static method)

get_maximal_log_likelihood() (memocell.estimation.Estimation static method) get_model_evidence() (memocell.estimation.Estimation static method) get_number_data_points() (memocell.data.Data static method) get_posterior_samples() (memocell.estimation.Estimation static method) gillespie_simulation() (memocell.simulation_lib.sim_gillespie.GillespieSim method) GillespieSim (class in memocell.simulation_lib.sim_gillespie)

I

initialise_estimation() (memocell.estimation.Estimation method) initialise_net_theta_bounds() (memocell.estimation.Estimation static method)

initialise_time_values() (memocell.estimation.Estimation static method) introduce_basic_sigma() (memocell.data.Data static method)

L

load() (memocell.data.Data method)

log_likelihood() (memocell.estimation.Estimation method)

M

match_data_to_network() (memocell.estimation.Estimation static method) memocell.data module memocell.estimation module memocell.network module memocell.plots module memocell.selection module memocell.simulation module memocell.simulation_lib.sim_gillespie module

memocell.simulation_lib.sim_moments module memocell.utils module module memocell.data memocell.estimation memocell.network memocell.plots memocell.selection memocell.simulation memocell.simulation_lib.sim_gillespie memocell.simulation_lib.sim_moments memocell.utils moment_simulation() (memocell.simulation_lib.sim_moments.MomentsSim method) MomentsSim (class in memocell.simulation_lib.sim_moments)

N

net_estimation() (in module memocell.selection) net_hidden_plot() (in module memocell.plots)

net_main_plot() (in module memocell.plots) Network (class in memocell.network)

P

phase_type_from_erlang() (in module memocell.utils) phase_type_from_parallel_erlang2() (in module memocell.utils) phase_type_from_parallel_erlang3() (in module memocell.utils) phase_type_pdf() (in module memocell.utils) prepare_gillespie_simulation() (memocell.simulation_lib.sim_gillespie.GillespieSim method) prepare_moment_simulation() (memocell.simulation_lib.sim_moments.MomentsSim method) prepare_simulation() (memocell.simulation.Simulation method) prepare_simulation_variables() (memocell.simulation.Simulation method) prepare_theta_values() (memocell.simulation.Simulation method) prepare_time_values() (memocell.simulation.Simulation method)

prior_transform() (memocell.estimation.Estimation method) process_initial_values() (memocell.simulation_lib.sim_gillespie.GillespieSim method) (memocell.simulation_lib.sim_moments.MomentsSim method) process_initial_values_synchronous() (memocell.simulation_lib.sim_gillespie.GillespieSim static method) (memocell.simulation_lib.sim_moments.MomentsSim method) process_initial_values_uniform() (memocell.simulation_lib.sim_gillespie.GillespieSim static method) (memocell.simulation_lib.sim_moments.MomentsSim method) process_mean_exist_only() (memocell.data.Data static method) process_sim_mean_only() (memocell.simulation.Simulation static method) process_theta_values() (memocell.simulation.Simulation static method)

R

reac_type_start_to() (memocell.simulation_lib.sim_moments.MomentsSim static method) reac_type_start_to_end() (memocell.simulation_lib.sim_moments.MomentsSim static method) reac_type_start_to_end1_end2() (memocell.simulation_lib.sim_moments.MomentsSim static method) reac_type_start_to_end_end() (memocell.simulation_lib.sim_moments.MomentsSim static method) reac_type_start_to_start_end() (memocell.simulation_lib.sim_moments.MomentsSim static method)

reac_type_start_to_start_start() (memocell.simulation_lib.sim_moments.MomentsSim static method) reac_type_to_end() (memocell.simulation_lib.sim_moments.MomentsSim static method) run_estimation() (memocell.estimation.Estimation method) run_gillespie_first_reaction_method() (memocell.simulation_lib.sim_gillespie.GillespieSim static method) run_moment_ode_system() (memocell.simulation_lib.sim_moments.MomentsSim method)

S

select_models() (in module memocell.selection) selection_plot() (in module memocell.plots) set_moment_eqs_from_template_after_reset() (memocell.simulation_lib.sim_moments.MomentsSim method) setup_executable_moment_eqs_template() (memocell.simulation_lib.sim_moments.MomentsSim method) sim_counts_plot() (in module memocell.plots) sim_covariance_plot() (in module memocell.plots) sim_mean_plot() (in module memocell.plots)

sim_variance_plot() (in module memocell.plots) simulate() (memocell.simulation.Simulation method) Simulation (class in memocell.simulation) structure() (memocell.network.Network method) structure_net_hidden() (memocell.network.Network method) structure_net_main() (memocell.network.Network method) summation_main_nodes() (memocell.simulation_lib.sim_gillespie.GillespieSim static method) summation_simulation_variables() (memocell.simulation_lib.sim_gillespie.GillespieSim static method)