Index

A

ABCSampler (class in epydemix.calibration) (class in epydemix.calibration.abc) add_compartments() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) add_contact_matrix() (epydemix.population.Population method) (epydemix.population.population.Population method) add_intervention() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) add_outcome() (in module epydemix.model.predefined_models) add_parameter() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) add_population() (epydemix.population.Population method) (epydemix.population.population.Population method)

add_transition() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) add_vaccination() (in module epydemix.model.predefined_models) add_waning_immunity() (in module epydemix.model.predefined_models) ae() (in module epydemix.calibration) (in module epydemix.calibration.metrics) aggregate_demographic() (in module epydemix.population.population) aggregate_matrix() (in module epydemix.population.population) apply_initial_conditions() (in module epydemix.utils.utils) apply_intervention() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) apply_overrides() (in module epydemix.utils.utils)

C

calibrate() (epydemix.calibration.abc.ABCSampler method) (epydemix.calibration.ABCSampler method) calibration_params (epydemix.calibration.calibration_results.CalibrationResults attribute), [1] (epydemix.calibration.CalibrationResults attribute), [1] calibration_strategy (epydemix.calibration.calibration_results.CalibrationResults attribute), [1] (epydemix.calibration.CalibrationResults attribute), [1] CalibrationResults (class in epydemix.calibration) (class in epydemix.calibration.calibration_results) clear_compartments() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) clear_interventions() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) clear_overrides() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) clear_parameters() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) clear_transitions() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) combine_simulation_outputs() (in module epydemix.utils) (in module epydemix.utils.utils)

compartment_idx (epydemix.model.simulation_output.Trajectory attribute), [1] (epydemix.model.simulation_results.SimulationResults property) (epydemix.model.SimulationResults property) compartments (epydemix.model.simulation_output.Trajectory attribute), [1] compute_contact_reductions() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) compute_days() (in module epydemix.utils) (in module epydemix.utils.utils) compute_effective_sample_size() (in module epydemix.utils) (in module epydemix.utils.abc_smc_utils) compute_mediated_transition_rate() (in module epydemix.model.epimodel) compute_simulation_dates() (in module epydemix.utils) (in module epydemix.utils.utils) compute_spontaneous_transition_rate() (in module epydemix.model.epimodel) convert_to_2Darray() (in module epydemix.utils) (in module epydemix.utils.utils) create_default_initial_conditions() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) create_definitions() (in module epydemix.utils.utils) create_seiar() (in module epydemix.model.predefined_models) create_seir() (in module epydemix.model.predefined_models) create_sir() (in module epydemix.model.predefined_models) create_sis() (in module epydemix.model.predefined_models)

D

dates (epydemix.model.simulation_output.Trajectory attribute), [1] (epydemix.model.simulation_results.SimulationResults property) (epydemix.model.SimulationResults property) DefaultPerturbationContinuous (class in epydemix.utils) (class in epydemix.utils.abc_smc_utils) DefaultPerturbationDiscrete (class in epydemix.utils) (class in epydemix.utils.abc_smc_utils)

delete_override() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) delete_parameter() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) distances (epydemix.calibration.calibration_results.CalibrationResults attribute), [1] (epydemix.calibration.CalibrationResults attribute), [1]

E

EpiModel (class in epydemix) (class in epydemix.model) (class in epydemix.model.epimodel) epydemix module epydemix.calibration module epydemix.calibration.abc module epydemix.calibration.calibration_results module epydemix.calibration.metrics module epydemix.model module epydemix.model.epimodel module epydemix.model.predefined_models module epydemix.model.simulation_output module

epydemix.model.simulation_results module epydemix.model.transition module epydemix.population module epydemix.population.population module epydemix.utils module epydemix.utils.abc_smc_utils module epydemix.utils.utils module epydemix.visualization module epydemix.visualization.plotting module evaluate() (in module epydemix.utils.utils)

F

fast_normal_pdf() (in module epydemix.utils.abc_smc_utils)

format_simulation_output() (in module epydemix.utils.utils)

G

generate_unique_string() (in module epydemix.utils.utils) get_available_locations() (in module epydemix.population) (in module epydemix.population.population) get_black_to_grey() (in module epydemix.visualization.plotting) get_calibration_quantiles() (epydemix.calibration.calibration_results.CalibrationResults method) (epydemix.calibration.CalibrationResults method) get_calibration_trajectories() (epydemix.calibration.calibration_results.CalibrationResults method) (epydemix.calibration.CalibrationResults method) get_distances() (epydemix.calibration.calibration_results.CalibrationResults method) (epydemix.calibration.CalibrationResults method) get_initial_conditions_dict() (in module epydemix.utils) (in module epydemix.utils.utils) get_parameter() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) get_posterior_distribution() (epydemix.calibration.calibration_results.CalibrationResults method) (epydemix.calibration.CalibrationResults method) get_primary_contacts_source() (in module epydemix.population.population)

get_projection_quantiles() (epydemix.calibration.calibration_results.CalibrationResults method) (epydemix.calibration.CalibrationResults method) get_projection_trajectories() (epydemix.calibration.calibration_results.CalibrationResults method) (epydemix.calibration.CalibrationResults method) get_quantiles() (epydemix.model.simulation_results.SimulationResults method) (epydemix.model.SimulationResults method) get_quantiles_compartments() (epydemix.model.simulation_results.SimulationResults method) (epydemix.model.SimulationResults method) get_quantiles_transitions() (epydemix.model.simulation_results.SimulationResults method) (epydemix.model.SimulationResults method) get_selected_trajectories() (epydemix.calibration.calibration_results.CalibrationResults method) (epydemix.calibration.CalibrationResults method) get_stacked_compartments() (epydemix.model.simulation_results.SimulationResults method) (epydemix.model.SimulationResults method) get_stacked_transitions() (epydemix.model.simulation_results.SimulationResults method) (epydemix.model.SimulationResults method) get_timeseries_data() (in module epydemix.visualization.plotting) get_weights() (epydemix.calibration.calibration_results.CalibrationResults method) (epydemix.calibration.CalibrationResults method)

I

import_epydemix_population() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method)

is_iterable() (in module epydemix.utils.utils) is_scalar() (in module epydemix.utils.utils)

K

kind (epydemix.model.Transition attribute) (epydemix.model.transition.Transition attribute)

L

layers (epydemix.population.Population property) (epydemix.population.population.Population property) load_epydemix_population() (in module epydemix.population) (in module epydemix.population.population)

load_predefined_model() (in module epydemix) (in module epydemix.model) (in module epydemix.model.predefined_models)

M

mae() (in module epydemix.calibration) (in module epydemix.calibration.metrics) map_age_groups_to_idx() (in module epydemix.population.population) mape() (in module epydemix.calibration) (in module epydemix.calibration.metrics) mean_contacts (epydemix.population.Population property) (epydemix.population.population.Population property) module epydemix epydemix.calibration epydemix.calibration.abc epydemix.calibration.calibration_results epydemix.calibration.metrics epydemix.model epydemix.model.epimodel epydemix.model.predefined_models epydemix.model.simulation_output epydemix.model.simulation_results epydemix.model.transition epydemix.population epydemix.population.population epydemix.utils epydemix.utils.abc_smc_utils epydemix.utils.utils epydemix.visualization epydemix.visualization.plotting

multinomial() (in module epydemix.utils.utils)

N

n_compartments (epydemix.EpiModel property) (epydemix.model.EpiModel property) (epydemix.model.epimodel.EpiModel property) n_transitions (epydemix.EpiModel property) (epydemix.model.EpiModel property) (epydemix.model.epimodel.EpiModel property)

njit() (in module epydemix.utils.utils) Nsim (epydemix.model.simulation_results.SimulationResults property) (epydemix.model.SimulationResults property) num_groups (epydemix.population.Population property) (epydemix.population.population.Population property)

O

observed_data (epydemix.calibration.calibration_results.CalibrationResults attribute), [1] (epydemix.calibration.CalibrationResults attribute), [1]

override_parameter() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method)

P

parameters (epydemix.model.simulation_output.Trajectory attribute), [1] (epydemix.model.simulation_results.SimulationResults attribute), [1] (epydemix.model.SimulationResults attribute), [1] params (epydemix.model.Transition attribute) (epydemix.model.transition.Transition attribute) pdf() (epydemix.utils.abc_smc_utils.DefaultPerturbationContinuous method) (epydemix.utils.abc_smc_utils.DefaultPerturbationDiscrete method) (epydemix.utils.abc_smc_utils.Perturbation method) (epydemix.utils.DefaultPerturbationContinuous method) (epydemix.utils.DefaultPerturbationDiscrete method) (epydemix.utils.Perturbation method) Perturbation (class in epydemix.utils) (class in epydemix.utils.abc_smc_utils) plot_contact_matrix() (in module epydemix.visualization) (in module epydemix.visualization.plotting) plot_distance_distribution() (in module epydemix.visualization) (in module epydemix.visualization.plotting) plot_population() (in module epydemix.visualization) (in module epydemix.visualization.plotting) plot_posterior_distribution() (in module epydemix.visualization) (in module epydemix.visualization.plotting) plot_posterior_distribution_2d() (in module epydemix.visualization) (in module epydemix.visualization.plotting)

plot_quantiles() (in module epydemix.visualization) (in module epydemix.visualization.plotting) plot_selected_trajectories() (in module epydemix.visualization.plotting) plot_spectral_radius() (in module epydemix.visualization) (in module epydemix.visualization.plotting) plot_trajectories() (in module epydemix.visualization) (in module epydemix.visualization.plotting) Population (class in epydemix.population) (class in epydemix.population.population) posterior_distributions (epydemix.calibration.calibration_results.CalibrationResults attribute), [1] (epydemix.calibration.CalibrationResults attribute), [1] priors (epydemix.calibration.calibration_results.CalibrationResults attribute), [1] (epydemix.calibration.CalibrationResults attribute), [1] projection_parameters (epydemix.calibration.calibration_results.CalibrationResults attribute), [1] (epydemix.calibration.CalibrationResults attribute), [1] projections (epydemix.calibration.calibration_results.CalibrationResults attribute), [1] (epydemix.calibration.CalibrationResults attribute), [1] propose() (epydemix.utils.abc_smc_utils.DefaultPerturbationContinuous method) (epydemix.utils.abc_smc_utils.DefaultPerturbationDiscrete method) (epydemix.utils.abc_smc_utils.Perturbation method) (epydemix.utils.DefaultPerturbationContinuous method) (epydemix.utils.DefaultPerturbationDiscrete method) (epydemix.utils.Perturbation method)

R

register_transition_kind() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) resample() (epydemix.model.simulation_output.Trajectory method) (epydemix.model.simulation_results.SimulationResults method) (epydemix.model.SimulationResults method) resize_parameter() (in module epydemix.utils.utils) rmse() (in module epydemix.calibration) (in module epydemix.calibration.metrics) run_projections() (epydemix.calibration.abc.ABCSampler method) (epydemix.calibration.ABCSampler method)

run_rejection() (epydemix.calibration.abc.ABCSampler method) (epydemix.calibration.ABCSampler method) run_simulations() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) run_smc() (epydemix.calibration.abc.ABCSampler method) (epydemix.calibration.ABCSampler method) run_top_fraction() (epydemix.calibration.abc.ABCSampler method) (epydemix.calibration.ABCSampler method)

S

sample_prior() (in module epydemix.utils) (in module epydemix.utils.abc_smc_utils) selected_trajectories (epydemix.calibration.calibration_results.CalibrationResults attribute), [1] (epydemix.calibration.CalibrationResults attribute), [1] set_population() (epydemix.EpiModel method) (epydemix.model.EpiModel method) (epydemix.model.epimodel.EpiModel method) simulate() (in module epydemix) (in module epydemix.model) (in module epydemix.model.epimodel)

SimulationResults (class in epydemix.model) (class in epydemix.model.simulation_results) source (epydemix.model.Transition attribute) (epydemix.model.transition.Transition attribute) stochastic_simulation() (in module epydemix.model.epimodel) str_to_date() (in module epydemix.utils.utils)

T

target (epydemix.model.Transition attribute) (epydemix.model.transition.Transition attribute) total_contacts (epydemix.population.Population property) (epydemix.population.population.Population property) total_population (epydemix.population.Population property) (epydemix.population.population.Population property)

trajectories (epydemix.model.simulation_results.SimulationResults attribute), [1] (epydemix.model.SimulationResults attribute), [1] Trajectory (class in epydemix.model.simulation_output) Transition (class in epydemix.model) (class in epydemix.model.transition) transitions (epydemix.model.simulation_output.Trajectory attribute), [1] transitions_idx (epydemix.model.simulation_output.Trajectory attribute), [1]

U

update() (epydemix.utils.abc_smc_utils.DefaultPerturbationContinuous method) (epydemix.utils.abc_smc_utils.DefaultPerturbationDiscrete method) (epydemix.utils.abc_smc_utils.Perturbation method) (epydemix.utils.DefaultPerturbationContinuous method) (epydemix.utils.DefaultPerturbationDiscrete method) (epydemix.utils.Perturbation method)

V

validate() (epydemix.population.Population method) (epydemix.population.population.Population method) validate_age_group_mapping() (in module epydemix.population.population) validate_contacts_source() (in module epydemix.population.population)

validate_data() (in module epydemix.calibration.metrics) validate_parameter_shape() (in module epydemix.utils.utils) validate_population_name() (in module epydemix.population.population) validate_transition_function() (in module epydemix.model.epimodel)

W

weighted_quantile() (in module epydemix.utils) (in module epydemix.utils.abc_smc_utils) weights (epydemix.calibration.calibration_results.CalibrationResults attribute), [1] (epydemix.calibration.CalibrationResults attribute), [1]

wmape() (in module epydemix.calibration) (in module epydemix.calibration.metrics)