Epidemics module¶

This module provides functions related to the simulation and measurement of epidemics.

class tacoma.epidemics.SIR_weighted(N, weighted_edge_tuples, infection_rate, recovery_rate, number_of_initially_infected)[source]¶

Bases: object

evaluate_rates()[source]¶

force_of_infection_on_node = []¶

infected = []¶

infection_event()[source]¶

node_status = []¶

rates¶

recovery_event()[source]¶

simulation(tmax)[source]¶

class tacoma.epidemics.SIS_weighted(N, weighted_edge_tuples, infection_rate, recovery_rate, number_of_initially_infected)[source]¶

Bases: object

evaluate_rates()[source]¶

force_of_infection_on_node = []¶

infected = []¶

infection_event()[source]¶

node_status = []¶

rates¶

recovery_event()[source]¶

simulation(tmax)[source]¶

tacoma.epidemics.get_SIS_critical_infection_rate(tn, recovery_rate, method='Powell', arpackmaxiter=10000, arpacktol=1e-09)[source]¶

tacoma.epidemics.get_SIS_critical_recovery_rate(tn, infection_rate, method='Powell', arpackmaxiter=10000, arpacktol=1e-09)[source]¶

tacoma.epidemics.get_SIS_max_eigenvalue(tn, infection_rate, recovery_rate, maxiter=10000, tol=1e-09)[source]¶

tacoma.epidemics.simulate_and_measure_i_inf(temporal_network_or_model, epidemic_object, t_equilibrate, is_static=False, verbose=False)[source]¶

Get the equilibrium ratio of infected.

Parameters:

temporal_network_or_model (_tacoma.edge_changes, _tacoma.edge_lists, _tacoma.edge_changes_with_histograms, _tacoma.edge_lists_with_histograms, or _tacoma.EdgeActivityModel.) – An instance of a temporal network or network model.
epidemic_object (_tacoma.SI, _tacoma.SIS, _tacoma.SIR, _tacoma.SIRS, _tacoma.node_based_SIS) – An initialized epidemic object.
t_equilibrate (float) – Time passed after t0 after which to start measuring.
is_static (bool, default : False) – The algorithm works a bit differently if it knows that the network is actually static. It works only with instances of _tacoma.edge_lists.
verbose (bool, optional) – Be chatty.

Returns:

i_inf (float) – Temporal average over the ratio of infected after equilibration.
i_inf_std (float) – RMSE of the ratio of infected.
R0 (float) – As measured after equilibration

tacoma.epidemics.simulate_quasi_stationary_SIS_on_model(model, qs_sis, verbose=False)[source]¶

tacoma.epidemics.simulate_quasi_stationary_SIS_on_static_network(network, qs_sis, verbose=False)[source]¶