├── .coveragerc ├── .editorconfig ├── .flake8 ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── coverage-test.yml │ ├── cpp-coverage.yml │ ├── cpp-unit-tests-ubuntu.yml │ ├── doc-tests.yml │ ├── func-tests.yml │ ├── os-tests.yml │ ├── style-test.yml │ └── unit-tests.yml ├── .gitignore ├── .gitmodules ├── CITATION.cff ├── CONTRIBUTING.md ├── LICENSE.md ├── README.md ├── cEpiabm ├── CMakeLists.txt ├── README.rst ├── cmake │ ├── Catch.cmake │ ├── CatchAddTests.cmake │ ├── CompilerWarnings.cmake │ ├── FindSphinx.cmake │ ├── ProjectSettings.cmake │ ├── Sanitisers.cmake │ ├── StaticAnalysers.cmake │ └── epiabm-config.cmake ├── docs │ ├── .readthedocs.yaml │ ├── CMakeLists.txt │ ├── Doxyfile │ ├── Doxyfile.in │ ├── Makefile │ ├── conf.py │ ├── configuration.rst │ ├── dataclasses.rst │ ├── index.rst │ ├── make.bat │ ├── reporters.rst │ ├── requirements.txt │ ├── simulations.rst │ ├── sweeps.rst │ └── utilities.rst ├── examples │ ├── CMakeLists.txt │ └── basic_example │ │ ├── CMakeLists.txt │ │ └── main.cpp ├── src │ ├── CMakeLists.txt │ ├── configuration │ │ ├── config_factory_interface.hpp │ │ ├── host_progression_config.hpp │ │ ├── infection_config.hpp │ │ ├── json.hpp │ │ ├── json_factory.cpp │ │ ├── json_factory.hpp │ │ ├── population_config.hpp │ │ └── simulation_config.hpp │ ├── covidsim.cpp │ ├── covidsim.hpp │ ├── dataclasses │ │ ├── cell.cpp │ │ ├── cell.hpp │ │ ├── compartment_counter.cpp │ │ ├── compartment_counter.hpp │ │ ├── household.cpp │ │ ├── household.hpp │ │ ├── infection_status.hpp │ │ ├── microcell.cpp │ │ ├── microcell.hpp │ │ ├── person.cpp │ │ ├── person.hpp │ │ ├── place.cpp │ │ ├── place.hpp │ │ ├── population.cpp │ │ └── population.hpp │ ├── household_linker.cpp │ ├── household_linker.hpp │ ├── logfile.cpp │ ├── logfile.hpp │ ├── output_folder_handler.cpp │ ├── output_folder_handler.hpp │ ├── population_factory.cpp │ ├── population_factory.hpp │ ├── python_bindings │ │ ├── bind_configuration.hpp │ │ ├── bind_dataclasses.hpp │ │ ├── bind_logfile.hpp │ │ ├── bind_reporters.hpp │ │ ├── bind_simulation.hpp │ │ ├── bind_sweeps.hpp │ │ ├── bind_utilities.hpp │ │ └── bindings.cpp │ ├── reporters │ │ ├── age_stratified_new_cases_reporter.cpp │ │ ├── age_stratified_new_cases_reporter.hpp │ │ ├── age_stratified_population_reporter.cpp │ │ ├── age_stratified_population_reporter.hpp │ │ ├── cell_compartment_reporter.cpp │ │ ├── cell_compartment_reporter.hpp │ │ ├── new_cases_reporter.cpp │ │ ├── new_cases_reporter.hpp │ │ ├── percell_compartment_reporter.cpp │ │ ├── percell_compartment_reporter.hpp │ │ ├── population_compartment_reporter.cpp │ │ ├── population_compartment_reporter.hpp │ │ ├── timestep_reporter_interface.cpp │ │ └── timestep_reporter_interface.hpp │ ├── simulations │ │ ├── basic_simulation.cpp │ │ ├── basic_simulation.hpp │ │ ├── covid_sim.hpp │ │ ├── threaded_simulation.cpp │ │ └── threaded_simulation.hpp │ ├── sweeps │ │ ├── basic_host_progression_sweep.cpp │ │ ├── basic_host_progression_sweep.hpp │ │ ├── host_progression_sweep.cpp │ │ ├── host_progression_sweep.hpp │ │ ├── household_sweep.cpp │ │ ├── household_sweep.hpp │ │ ├── new_infection_sweep.cpp │ │ ├── new_infection_sweep.hpp │ │ ├── place_sweep.cpp │ │ ├── place_sweep.hpp │ │ ├── random_seed_sweep.cpp │ │ ├── random_seed_sweep.hpp │ │ ├── spatial_sweep.cpp │ │ ├── spatial_sweep.hpp │ │ ├── sweep_interface.cpp │ │ └── sweep_interface.hpp │ ├── toy_population_factory.cpp │ ├── toy_population_factory.hpp │ └── utilities │ │ ├── distance_metrics.cpp │ │ ├── distance_metrics.hpp │ │ ├── inverse_cdf.cpp │ │ ├── inverse_cdf.hpp │ │ ├── random_generator.hpp │ │ ├── random_manager.cpp │ │ ├── random_manager.hpp │ │ └── thread_pool.hpp └── test │ ├── CMakeLists.txt │ ├── catch │ └── catch.hpp │ ├── catch_main.cpp │ ├── configuration │ ├── helpers.hpp │ ├── test_host_progression_config.cpp │ ├── test_infection_config.cpp │ ├── test_json_factory.cpp │ ├── test_population_config.cpp │ └── test_simulation_config.cpp │ ├── dataclasses │ ├── test_cell.cpp │ ├── test_compartment_counter.cpp │ ├── test_distance_metrics.cpp │ ├── test_household.cpp │ ├── test_infection_status.cpp │ ├── test_microcell.cpp │ ├── test_person.cpp │ ├── test_place.cpp │ └── test_population.cpp │ ├── reporters │ ├── test_age_stratified_new_cases_reporter.cpp │ ├── test_age_stratified_population_reporter.cpp │ ├── test_cell_compartment_reporter.cpp │ ├── test_new_cases_reporter.cpp │ ├── test_percell_compartment_reporter.cpp │ └── test_population_compartment_reporter.cpp │ ├── sweeps │ ├── helpers.hpp │ ├── test_basic_host_progression_sweep.cpp │ ├── test_household_sweep.cpp │ ├── test_new_infection_sweep.cpp │ ├── test_place_sweep.cpp │ ├── test_random_seed_sweep.cpp │ └── test_spatial_sweep.cpp │ ├── test_basic_simulation.cpp │ ├── test_covidsim.cpp │ ├── test_log_file.cpp │ ├── test_output_file_handler.cpp │ ├── test_population_factory.cpp │ ├── test_toy_population_factory.cpp │ ├── testdata │ └── test_config.json │ └── utilities │ ├── test_distance_metrics.cpp │ ├── test_inverse_cdf.cpp │ ├── test_random_generator.cpp │ └── test_random_manager.cpp ├── images ├── Histograms │ ├── Withoutsim.png │ └── Withsim.png ├── covidsim_schema.png ├── diagram_covid_transition.jpg ├── distribution_covid_sim_rand.png ├── distribution_random_number.png ├── epiabm_logo_wide.png ├── epiabm_waning_immunity_diagram.png ├── infectiousness_dist_gamma11.png ├── infectiousness_dist_gamma251.png ├── infectiousness_progression │ ├── infectiousness_prog.png │ ├── infectiousness_prog_diff.png │ ├── infectiousness_prog_timestep1.png │ └── infectiousness_prog_timestep2.png ├── power_law_eqn.svg ├── transition_times_dist │ ├── asympt_to_recov_time.png │ ├── gp_to_dead_time.png │ ├── gp_to_hosp_time.png │ ├── gp_to_recov_time.png │ ├── hosp_to_dead_time.png │ ├── hosp_to_icu_time.png │ ├── hosp_to_recov_tume.png │ ├── icu_to_dead_time.png │ ├── icu_to_icurecov_time.png │ ├── icurecov_to_recov_time.png │ ├── latent_time.png │ ├── latent_time_exp.png │ ├── latent_time_noexp.png │ └── mild_to_recov_time.png └── workplace_dist.svg ├── pyEpiabm ├── README.rst ├── docs │ ├── .readthedocs.yaml │ ├── Makefile │ ├── make.bat │ └── source │ │ ├── conf.py │ │ ├── core.rst │ │ ├── index.rst │ │ ├── interventions.rst │ │ ├── outputs.rst │ │ ├── properties.rst │ │ ├── py2c.rst │ │ ├── routines.rst │ │ ├── sweeps.rst │ │ └── utility.rst ├── gibraltar_example │ └── gibraltar_rt_plots.py ├── pyEpiabm │ ├── __init__.py │ ├── core │ │ ├── __init__.py │ │ ├── _compartment_counter.py │ │ ├── cell.py │ │ ├── household.py │ │ ├── microcell.py │ │ ├── parameters.py │ │ ├── person.py │ │ ├── place.py │ │ └── population.py │ ├── intervention │ │ ├── __init__.py │ │ ├── abstract_intervention.py │ │ ├── case_isolation.py │ │ ├── disease_testing.py │ │ ├── household_quarantine.py │ │ ├── place_closure.py │ │ ├── social_distancing.py │ │ ├── travel_isolation.py │ │ └── vaccination.py │ ├── output │ │ ├── __init__.py │ │ ├── _csv_dict_writer.py │ │ ├── _csv_writer.py │ │ ├── abstract_reporter.py │ │ ├── age_stratified_new_cases_writer.py │ │ └── new_cases_writer.py │ ├── property │ │ ├── __init__.py │ │ ├── household_foi.py │ │ ├── infection_status.py │ │ ├── personal_foi.py │ │ ├── place_foi.py │ │ ├── place_type.py │ │ └── spatial_foi.py │ ├── py2c │ │ ├── __init__.py │ │ └── py2c_population.py │ ├── routine │ │ ├── __init__.py │ │ ├── abstract_population_config.py │ │ ├── file_population_config.py │ │ ├── simulation.py │ │ └── toy_population_config.py │ ├── sweep │ │ ├── __init__.py │ │ ├── abstract_sweep.py │ │ ├── host_progression_sweep.py │ │ ├── household_sweep.py │ │ ├── initial_demographics_sweep.py │ │ ├── initial_household_sweep.py │ │ ├── initial_infected_sweep.py │ │ ├── initial_place_sweep.py │ │ ├── initial_vaccine_sweep.py │ │ ├── intervention_sweep.py │ │ ├── place_sweep.py │ │ ├── queue_sweep.py │ │ ├── spatial_sweep.py │ │ ├── transition_matrices.py │ │ ├── travel_sweep.py │ │ └── update_place_sweep.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_func │ │ │ ├── __init__.py │ │ │ ├── functional_testing_class.py │ │ │ ├── helper_func.py │ │ │ ├── spatial_input.csv │ │ │ ├── test_closure_functional.py │ │ │ ├── test_distancing_functional.py │ │ │ ├── test_integration.py │ │ │ ├── test_isolation_functional.py │ │ │ ├── test_quarantine_functional.py │ │ │ ├── test_random_seeds.py │ │ │ └── test_sim_functional.py │ │ ├── test_unit │ │ │ ├── __init__.py │ │ │ ├── mocked_logging_tests.py │ │ │ ├── parameter_config_tests.py │ │ │ ├── test_core │ │ │ │ ├── __init__.py │ │ │ │ ├── test_cell.py │ │ │ │ ├── test_compartment_counter.py │ │ │ │ ├── test_household.py │ │ │ │ ├── test_microcell.py │ │ │ │ ├── test_parameters.py │ │ │ │ ├── test_person.py │ │ │ │ ├── test_place.py │ │ │ │ └── test_population.py │ │ │ ├── test_intervention │ │ │ │ ├── __init__.py │ │ │ │ ├── test_abstract_intervention.py │ │ │ │ ├── test_case_isolation.py │ │ │ │ ├── test_household_quarantine.py │ │ │ │ ├── test_place_closure.py │ │ │ │ ├── test_social_distancing.py │ │ │ │ ├── test_testing.py │ │ │ │ ├── test_travel_isolation.py │ │ │ │ └── test_vaccination.py │ │ │ ├── test_output │ │ │ │ ├── __init__.py │ │ │ │ ├── test_abstract_reporter.py │ │ │ │ ├── test_age_stratified_new_cases_writer.py │ │ │ │ ├── test_csv_dict_writer.py │ │ │ │ ├── test_csv_writer.py │ │ │ │ └── test_new_cases_writer.py │ │ │ ├── test_property │ │ │ │ ├── __init__.py │ │ │ │ ├── test_household_foi.py │ │ │ │ ├── test_infection_status.py │ │ │ │ ├── test_personal_foi.py │ │ │ │ ├── test_place_foi.py │ │ │ │ ├── test_place_type.py │ │ │ │ └── test_spatial_foi.py │ │ │ ├── test_py2c │ │ │ │ ├── __init__.py │ │ │ │ ├── test_py2c_population.py │ │ │ │ └── test_timer.py │ │ │ ├── test_routine │ │ │ │ ├── __init__.py │ │ │ │ ├── test_abstract_population_config.py │ │ │ │ ├── test_file_population_config.py │ │ │ │ ├── test_simulation.py │ │ │ │ └── test_toy_population_config.py │ │ │ ├── test_sweep │ │ │ │ ├── __init__.py │ │ │ │ ├── test_abstract_sweep.py │ │ │ │ ├── test_host_progression_sweep.py │ │ │ │ ├── test_household_sweep.py │ │ │ │ ├── test_initial_demographics_sweep.py │ │ │ │ ├── test_initial_household_sweep.py │ │ │ │ ├── test_initial_infected_sweep.py │ │ │ │ ├── test_initial_vaccine_sweep.py │ │ │ │ ├── test_initialise_place_sweep.py │ │ │ │ ├── test_intervention_sweep.py │ │ │ │ ├── test_place_sweep.py │ │ │ │ ├── test_queue_sweep.py │ │ │ │ ├── test_spatial_sweep.py │ │ │ │ ├── test_state_transition_matrix.py │ │ │ │ ├── test_transition_time_matrix.py │ │ │ │ ├── test_travel_sweep.py │ │ │ │ └── test_update_place_sweep.py │ │ │ └── test_utility │ │ │ │ ├── __init__.py │ │ │ │ ├── test_antibody_multiplier.py │ │ │ │ ├── test_covidsim_kernel.py │ │ │ │ ├── test_distance_metrics.py │ │ │ │ ├── test_exception_logger.py │ │ │ │ ├── test_inverse_cdf.py │ │ │ │ ├── test_random_methods.py │ │ │ │ └── test_rate_multiplier.py │ │ └── testing_parameters.json │ ├── utility │ │ ├── __init__.py │ │ ├── antibody_multiplier.py │ │ ├── covidsim_kernel.py │ │ ├── distance_metrics.py │ │ ├── exception_logger.py │ │ ├── inverse_cdf.py │ │ ├── random_methods.py │ │ └── rate_multiplier.py │ └── version_info.py ├── requirements.txt ├── run_tests.py └── setup.py └── python_examples ├── NI_example ├── NI_flow.py ├── NI_inputs │ └── NI_microcells.csv ├── NI_parameters.json └── README.md ├── NZ_example ├── NZ_flow.py ├── NewZealand_noInt_parameters.json ├── NewZealand_parameters.json └── NewZealand_parameters_relaxed.json ├── R0_inference ├── learn_R.ipynb └── si-covid.csv ├── README.md ├── age_stratified_example ├── age_hist │ ├── age_hist.py │ └── simulation_outputs │ │ └── output_gibraltar.csv ├── age_stratified_plot.py ├── simple_parameters_with_age.json ├── simulation_flow_with_age.py └── simulation_outputs │ ├── age_stratify.png │ ├── daily_cases.csv │ ├── gibraltar_cases.csv │ ├── output_with_age.csv │ └── simulation_flow_SIR_plot.png ├── antibody_igG_test ├── IgG_validation_graphs.png ├── Lumley_paper_igG_levels_graph.png └── antibody_igG_test_graph.py ├── basic_infection_history_simulation ├── simple_parameters.json ├── simulation_flow.py └── simulation_outputs │ ├── demographics.csv │ ├── inf_status_history.csv │ ├── infectiousness_history.csv │ └── output.csv ├── basic_simulation ├── simple_parameters.json ├── simulation_flow.py └── simulation_outputs │ ├── output.csv │ └── simulation_flow_SIR_plot.png ├── cEpiabm_example ├── icdf.ipynb ├── output │ └── population_results.csv ├── parameters.json ├── parameters_live.json ├── python_parameters.json ├── python_to_cpp_population_converter.ipynb ├── simulation.ipynb ├── threaded_output │ └── population_results.csv └── threaded_simulation.ipynb ├── gibraltar_example ├── README.md ├── covidsim_results │ ├── WeeklyIncidenceCasesbyAgeGroup.png │ ├── covidsim_daily_cases.csv │ ├── modified_age_severity.csv │ ├── plot_covidsim.py │ └── severity_age.csv ├── gibraltar_flow.py ├── gibraltar_inputs │ ├── gib_input.csv │ ├── microcell_conversion.py │ └── wpop_gib.txt ├── gibraltar_parameters.json ├── gibraltar_parameters_without_intervention.json └── simulation_outputs │ ├── with_intervention │ ├── age_stratify.png │ ├── gibraltar_weeky_cases.csv │ └── simulation_flow_SIR_plot.png │ └── without_intervention │ ├── age_stratify.png │ ├── gibraltar_weeky_cases.csv │ └── simulation_flow_SIR_plot.png ├── gibraltar_example_cpp ├── gibraltar_parameters_cpp.json ├── gibraltar_parameters_py.json ├── gibraltar_simulation_flow_cpp.py ├── output │ ├── age_stratified_new_cases.csv │ ├── age_stratified_population_results.csv │ ├── new_cases.csv │ └── population_results.csv └── plot.ipynb ├── intervention_example ├── README.md ├── case_isolation_parameters.json ├── case_isolation_simulation_flow.py ├── disease_testing_parameters.json ├── disease_testing_simulation_flow.py ├── household_quarantine_parameters.json ├── household_quarantine_simulation_flow.py ├── input.csv ├── intervention_outputs │ ├── case_isolation_Icurve_plot.png │ ├── case_isolation_via_testing_plot.png │ ├── household_quarantine_Icurve_plot.png │ ├── place_closure_closure_place_type_Icurve_plot.png │ ├── social_distancing_distancing_enhanced_prob_Icurve_plot.png │ ├── travel_isolation_Icurve_plot.png │ └── vaccination_Icurve_plot.png ├── place_closure_parameters.json ├── place_closure_simulation_flow.py ├── social_distancing_parameters.json ├── social_distancing_simulation_flow.py ├── travel_isolation_parameters.json ├── travel_isolation_simulation_flow.py ├── vaccination_flow.py └── vaccination_parameters.json ├── luxembourg_example ├── animation │ ├── population_output_intervention_simulation_1.gif │ ├── population_output_simulation_1.gif │ ├── population_output_simulation_1_grid.png │ └── pre_population_output_simulation_1.gif ├── luxembourg_flow.py ├── luxembourg_inputs │ ├── luxembourg_adapted_5_in_cell_input.csv │ ├── luxembourg_initial_infect.py │ └── luxembourg_input_file.csv ├── luxembourg_intervention_parameters.json ├── luxembourg_parameters.json ├── paper_plots │ ├── incidence_rural_vs_urban.png │ ├── post_day_40.png │ ├── pre_day_40.png │ ├── pre_post_raw.png │ └── pre_post_rural_vs_urban.png ├── rural_v_urban.ipynb └── simulation_outputs │ ├── all_post_summary.csv │ ├── all_pre_summary.csv │ ├── urban_rural_post_summary.csv │ ├── urban_rural_pre_summary.csv │ ├── urban_rural_summary.csv │ └── urban_rural_summary_interventions.csv ├── model_population_example ├── IntCI_params.json ├── IntMult_params.json ├── model_interventions.ipynb ├── model_population.ipynb ├── noInt_params.json ├── simulation_outputs │ ├── combined_summary.csv │ └── multi_interventions │ │ ├── summary_4x4_av5_CI+HQ+PC.csv │ │ ├── summary_4x4_av5_CI+HQ.csv │ │ ├── summary_4x4_av5_CI.csv │ │ └── summary_4x4_av5_No intervention.csv ├── toy_plotter.py └── uniform_inputs │ ├── input_12x12_av5_places.csv │ ├── input_15x15_av5_places.csv │ ├── input_4x4_av5_places.csv │ ├── input_6x6_av5_places.csv │ └── input_8x8_av5_places.csv ├── sim_speeds ├── Readme.md ├── Sim_Speeds.txt ├── basic_speed_plot.py ├── old_intervention_basic_speeds.csv ├── old_intervention_spatial_speeds.csv ├── sim_runner.py ├── sim_runner_spatial.py ├── sim_speeds.ipynb ├── sim_speeds_plots │ └── basic_sim_speed_from_file.png ├── simple_parameters.json └── spatial_parameters.json ├── spatial_example ├── input.csv ├── spatial_outputs │ ├── output.csv │ ├── spatial_flow_Icurve_plot.png │ ├── voronoi_animation.gif │ └── voronoi_grid_img.png ├── spatial_parameters.json ├── spatial_simulation_flow.py └── voronoi_plotting_example.py └── travel_example ├── input.csv ├── travel_simulation_flow.py ├── travelling_outputs ├── travelling_constant_introduce_cases_Icurve_plot.png └── travelling_ratio_introduce_cases_Icurve_plot.png └── 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