File tree

• cpp
  • benchmarks
    • abm.cpp
    • flow_simulation_ode_secirvvs.cpp
    • flow_simulation_ode_secirvvs.h
    • flow_simulation_ode_seir.cpp
    • graph_simulation.cpp
    • graph_simulation.h
    • integrator_step.cpp
    • integrator_step.h
    • secir_ageres_setups.h
    • simulation.cpp
    • simulation.h
  • examples
    • abm_history_object.cpp
    • abm_minimal.cpp
    • ad_odeint_example.cpp
    • ad_square_example.cpp
    • adapt_rk_test.cpp
    • cli.cpp
    • data_dir.h.in
    • euler_test.cpp
    • glct_secir.cpp
    • graph_stochastic_mobility.cpp
    • history.cpp
    • ide_initialization.cpp
    • ide_secir.cpp
    • ide_secir_ageres.cpp
    • ide_seir.cpp
    • lct_secir.cpp
    • ode_seair.cpp
    • ode_seair_optimization.cpp
    • ode_secir.cpp
    • ode_secir_ageres.cpp
    • ode_secir_contact_changes.cpp
    • ode_secir_graph.cpp
    • ode_secir_parameter_sampling.cpp
    • ode_secir_parameter_study.cpp
    • ode_secir_parameter_study_graph.cpp
    • ode_secir_read_graph.cpp
    • ode_secir_save_results.cpp
    • ode_secirts.cpp
    • ode_secirvvs.cpp
    • ode_seir.cpp
    • ode_seir_ageres.cpp
    • ode_seir_flows.cpp
    • ode_sir.cpp
    • ode_sir_ageres.cpp
    • sde_seirvv.cpp
    • sde_sir.cpp
    • sde_sirs.cpp
    • serialize.cpp
    • twitter_mobility.cpp
  • memilio
    • compartments
      • compartmentalmodel.h
      • flow_model.h
      • flow_simulation.h
      • parameter_studies.h
      • simulation.h
    • config.h
    • config_internal.h.in
    • data
      • analyze_result.cpp
      • analyze_result.h
    • epidemiology
      • age_group.h
      • contact_matrix.cpp
      • contact_matrix.h
      • damping.cpp
      • damping.h
      • damping_sampling.cpp
      • damping_sampling.h
      • dynamic_npis.cpp
      • dynamic_npis.h
      • lct_infection_state.h
      • lct_populations.h
      • populations.h
      • simulation_day.h
      • state_age_function.cpp
      • state_age_function.h
      • uncertain_matrix.cpp
      • uncertain_matrix.h
    • geography
      • holiday_data.ipp
      • regions.cpp
      • regions.h
    • io
      • binary_serializer.cpp
      • binary_serializer.h
      • cli.h
      • default_serialize.cpp
      • default_serialize.h
      • epi_data.cpp
      • epi_data.h
      • hdf5_cpp.h
      • history.h
      • io.cpp
      • io.h
      • json_serializer.cpp
      • json_serializer.h
      • mobility_io.cpp
      • mobility_io.h
      • result_io.cpp
      • result_io.h
      • serializer_base.cpp
      • serializer_base.h
    • math
      • adapt_rk.cpp
      • adapt_rk.h
      • eigen.h
      • eigen_util.h
      • euler.cpp
      • euler.h
      • floating_point.h
      • integrator.cpp
      • integrator.h
      • interpolation.cpp
      • interpolation.h
      • matrix_shape.cpp
      • matrix_shape.h
      • smoother.h
      • stepper_wrapper.cpp
      • stepper_wrapper.h
      • time_series_functor.cpp
      • time_series_functor.h
    • mobility
      • graph.cpp
      • graph.h
      • graph_simulation.cpp
      • graph_simulation.h
      • metapopulation_mobility_instant.cpp
      • metapopulation_mobility_instant.h
      • metapopulation_mobility_stochastic.cpp
      • metapopulation_mobility_stochastic.h
    • utils
      • compiler_diagnostics.h
      • custom_index_array.h
      • date.cpp
      • date.h
      • flow.h
      • index.h
      • index_range.h
      • logging.h
      • memory.h
      • metaprogramming.h
      • miompi.cpp
      • miompi.h
      • mioomp.h
      • parameter_distributions.h
      • parameter_set.cpp
      • parameter_set.h
      • pointer_dereferencing_iterator.h
      • profiler.h
      • random_number_generator.cpp
      • random_number_generator.h
      • span.cpp
      • span.h
      • stl_util.h
      • time_series.cpp
      • time_series.h
      • transform_iterator.h
      • type_list.h
      • type_safe.cpp
      • type_safe.h
      • uncertain_value.cpp
      • uncertain_value.h
      • visitor.h
  • models
    • abm
      • analyze_result.h
      • common_abm_loggers.h
      • config.h
      • household.cpp
      • household.h
      • infection.cpp
      • infection.h
      • infection_state.h
      • intervention_type.h
      • location.cpp
      • location.h
      • location_id.h
      • location_type.h
      • lockdown_rules.cpp
      • lockdown_rules.h
      • mask.cpp
      • mask.h
      • mask_type.h
      • mobility_data.h
      • mobility_rules.cpp
      • mobility_rules.h
      • model.cpp
      • model.h
      • model_functions.cpp
      • model_functions.h
      • parameters.cpp
      • parameters.h
      • person.cpp
      • person.h
      • person_id.h
      • personal_rng.cpp
      • personal_rng.h
      • protection_event.h
      • random_events.h
      • simulation.cpp
      • simulation.h
      • test_type.h
      • testing_strategy.cpp
      • testing_strategy.h
      • time.cpp
      • time.h
      • trip_list.cpp
      • trip_list.h
      • virus_variant.h
    • glct_secir
      • infection_state.h
      • model.cpp
      • model.h
      • parameters.h
    • ide_secir
      • infection_state.h
      • model.cpp
      • model.h
      • parameters.h
      • parameters_io.cpp
      • parameters_io.h
      • simulation.cpp
      • simulation.h
    • ide_seir
      • infection_state.h
      • model.cpp
      • model.h
      • parameters.h
    • lct_secir
      • infection_state.h
      • initializer_flows.h
      • model.cpp
      • model.h
      • parameters.h
      • parameters_io.h
    • ode_seair
      • infection_state.h
      • model.cpp
      • model.h
      • parameters.h
    • ode_secirts
      • analyze_result.cpp
      • analyze_result.h
      • infection_state.h
      • model.cpp
      • model.h
      • parameter_space.cpp
      • parameter_space.h
      • parameters.h
      • parameters_io.cpp
      • parameters_io.h
    • ode_secirvvs
      • analyze_result.cpp
      • analyze_result.h
      • infection_state.h
      • model.cpp
      • model.h
      • parameter_space.cpp
      • parameter_space.h
      • parameters.h
      • parameters_io.cpp
      • parameters_io.h
    • ode_secir
      • analyze_result.cpp
      • analyze_result.h
      • infection_state.h
      • model.cpp
      • model.h
      • parameter_space.cpp
      • parameter_space.h
      • parameters.h
      • parameters_io.cpp
      • parameters_io.h
    • ode_seir
      • infection_state.h
      • model.cpp
      • model.h
      • parameters.h
    • ode_sir
      • infection_state.h
      • model.cpp
      • model.h
      • parameters.h
    • sde_seirvv
      • infection_state.h
      • model.cpp
      • model.h
      • parameters.h
      • simulation.h
    • sde_sirs
      • infection_state.h
      • model.cpp
      • model.h
      • parameters.h
      • simulation.h
    • sde_sir
      • infection_state.h
      • model.cpp
      • model.h
      • parameters.h
      • simulation.h
  • simulations
    • 2020_npis_sarscov2_wildtype_germany.cpp
    • 2021_vaccination_sarscov2_delta_germany.cpp
    • abm.cpp
    • abm_braunschweig.cpp
    • munich_graph_sim.cpp
  • tests
    • abm_helpers.cpp
    • abm_helpers.h
    • actions.h
    • distributions_helpers.cpp
    • distributions_helpers.h
    • load_test_data.h
    • matchers.cpp
    • matchers.h
    • random_number_test.h
    • temp_file_register.h
    • test_abm_household.cpp
    • test_abm_infection.cpp
    • test_abm_location.cpp
    • test_abm_lockdown_rules.cpp
    • test_abm_masks.cpp
    • test_abm_mobility_rules.cpp
    • test_abm_model.cpp
    • test_abm_person.cpp
    • test_abm_serialization.cpp
    • test_abm_simulation.cpp
    • test_abm_testing_strategy.cpp
    • test_ad.cpp
    • test_analyze_result.cpp
    • test_binary_serializer.cpp
    • test_compartmentsimulation.cpp
    • test_contact_matrix.cpp
    • test_custom_index_array.cpp
    • test_damping.cpp
    • test_damping_sampling.cpp
    • test_data_dir.h.in
    • test_date.cpp
    • test_dynamic_npis.cpp
    • test_eigen_util.cpp
    • test_epi_data_io.cpp
    • test_flows.cpp
    • test_glct_secir.cpp
    • test_graph.cpp
    • test_graph_simulation.cpp
    • test_history.cpp
    • test_ide_parameters_io.cpp
    • test_ide_secir.cpp
    • test_ide_secir_ageres.cpp
    • test_ide_seir.cpp
    • test_io_cli.cpp
    • test_io_framework.cpp
    • test_json_serializer.cpp
    • test_lct_initializer_flows.cpp
    • test_lct_parameters_io.cpp
    • test_lct_secir.cpp
    • test_math_floating_point.cpp
    • test_math_time_series_functor.cpp
    • test_matrix_shape.cpp
    • test_metaprogramming.cpp
    • test_mobility.cpp
    • test_mobility_io.cpp
    • test_model.cpp
    • test_numericalIntegration.cpp
    • test_odeseair.cpp
    • test_odesecir.cpp
    • test_odesecir_ageres.cpp
    • test_odesecirts.cpp
    • test_odesecirvvs.cpp
    • test_odeseir.cpp
    • test_odesir.cpp
    • test_parameter_set.cpp
    • test_parameter_studies.cpp
    • test_populations.cpp
    • test_random_number_generator.cpp
    • test_regions.cpp
    • test_save_parameters.cpp
    • test_save_results.cpp
    • test_sde_seirvv.cpp
    • test_sde_sir.cpp
    • test_sde_sirs.cpp
    • test_smoother.cpp
    • test_state_age_function.cpp
    • test_stl_util.cpp
    • test_time_series.cpp
    • test_transform_iterator.cpp
    • test_type_safe.cpp
    • test_uncertain.cpp
    • test_utils.cpp
    • testmain.cpp
• pycode
  • examples
    • epidata
      • PlotCaseData.py
      • PlotGermanData.py
      • ProgressIndicator.py
    • plot
      • plotResultsMapGermany.py
    • simulation
      • 2020_npis_sarscov2_wildtype_germany.py
      • 2021_vaccination_sarscov2_delta_germany.py
      • mobility_parameter_study.py
      • ode_secir_ageres.py
      • ode_secir_groups.py
      • ode_secir_mobility.py
      • ode_secir_parameter_study.py
      • ode_secir_simple.py
      • ode_secirvvs_simple.py
      • ode_seir_flows.py
      • ode_seir_simple.py
      • ode_sir_simple.py
  • memilio-epidata/memilio
    • __init__.py
    • epidata_test
      • __init__.py
      • test_epidata_cleandata.py
      • test_epidata_customPlot.py
      • test_epidata_defaultDict.py
      • test_epidata_geoModificationGermany.py
      • test_epidata_getCaseData.py
      • test_epidata_getCommuterMobility.py
      • test_epidata_getDataIntoPandasDataFrame.py
      • test_epidata_getHospitalizationData.py
      • test_epidata_getNPIData.py
      • test_epidata_get_divi_data.py
      • test_epidata_get_jh_data.py
      • test_epidata_get_population_data.py
      • test_epidata_get_simulation_data.py
      • test_epidata_get_vaccination_data.py
      • test_epidata_modifyDataframeSeries.py
      • test_epidata_progress_indicator.py
      • test_epidata_transform_mobility_data.py
    • epidata
      • __init__.py
      • cleanData.py
      • customPlot.py
      • defaultDict.py
      • geoModificationGermany.py
      • getCaseData.py
      • getCommuterMobility.py
      • getDIVIData.py
      • getDataIntoPandasDataFrame.py
      • getHospitalizationData.py
      • getJHData.py
      • getNPIData.py
      • getPopulationData.py
      • getSimulationData.py
      • getTestingData.py
      • getVaccinationData.py
      • modifyDataframeSeries.py
      • progress_indicator.py
      • transformMobilityData.py
      • transformWeatherData.py
  • memilio-generation/memilio
    • __init__.py
    • generation_test
      • __init__.py
      • test_oseir_generation.py
    • generation
      • __init__.py
      • ast.py
      • generator.py
      • graph_visualization.py
      • intermediate_representation.py
      • scanner.py
      • scanner_config.py
      • template
        • __init__.py
        • template_string.py
      • utility.py
    • tools
      • example_oseir.py
  • memilio-plot/memilio
    • __init__.py
    • plot_test
      • __init__.py
      • test_plot_createGIF.py
      • test_plot_plotMap.py
    • plot
      • __init__.py
      • createGIF.py
      • plotMap.py
  • memilio-simulation
    • memilio
      • __init__.py
      • simulation_test
        • __init__.py
        • test_abm.py
        • test_analyze_result.py
        • test_custom_index_array.py
        • test_date.py
        • test_distributions.py
        • test_dynamic_npis.py
        • test_integrators.py
        • test_mobility.py
        • test_osecir.py
        • test_osecir_ageres.py
        • test_osecirvvs.py
        • test_oseir.py
        • test_osir.py
        • test_parameter_study.py
        • test_pickle.py
        • test_regions.py
        • test_time_series.py
        • test_uncertain_matrix.py
        • test_uncertain_value.py
      • simulation
        • __init__.py
        • abm.py
        • bindings
          • compartments
            • compartmentalmodel.h
            • flow_simulation.h
            • simulation.h
          • epidemiology
            • age_group.h
            • contact_matrix.h
            • damping.h
            • damping_sampling.cpp
            • damping_sampling.h
            • dynamic_npis.h
            • populations.h
            • simulation_day.h
            • uncertain_matrix.cpp
            • uncertain_matrix.h
          • io
            • mobility_io.h
            • result_io.h
          • math
            • integrator.h
          • mobility
            • graph_simulation.h
            • metapopulation_mobility_instant.cpp
            • metapopulation_mobility_instant.h
          • models
            • abm.cpp
            • osecir.cpp
            • osecirvvs.cpp
            • oseir.cpp
            • osir.cpp
          • pickle_serializer.h
          • pybind_util.h
          • simulation.cpp
          • utils
            • custom_index_array.h
            • date.cpp
            • date.h
            • index.h
            • logging.cpp
            • logging.h
            • parameter_distributions.cpp
            • parameter_distributions.h
            • parameter_set.h
            • time_series.cpp
            • time_series.h
            • uncertain_value.cpp
            • uncertain_value.h
        • osecir.py
        • osecirvvs.py
        • oseir.py
        • osir.py
    • tools
      • generate_stubs.py
  • memilio-surrogatemodel/memilio
    • __init__.py
    • surrogatemodel_test
      • __init__.py
      • test_surrogatemodel_ode_secir_groups.py
      • test_surrogatemodel_ode_secir_simple.py
    • surrogatemodel
      • __init__.py
      • ode_secir_groups
        • __init__.py
        • data_generation.py
        • model.py
        • network_architectures.py
      • ode_secir_simple
        • __init__.py
        • data_generation.py
        • model.py
        • network_architectures.py