File tree

• cpp
  • CMakeLists.txt
  • benchmarks
    • 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
    • adapt_rk_test.cpp
    • data_dir.h.in
    • euler_test.cpp
    • graph.cpp
    • graph_stochastic_mobility.cpp
    • ide_secir.cpp
    • ide_seir.cpp
    • ode_secir.cpp
    • ode_secir_ageres.cpp
    • ode_secir_parameter_sampling.cpp
    • ode_secir_parameter_study.cpp
    • ode_secir_read_graph.cpp
    • ode_secir_save_results.cpp
    • ode_secirvvs.cpp
    • ode_seir.cpp
    • ode_seir_flows.cpp
    • ode_sir.cpp
    • serialize.cpp
    • twitter_migration.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
      • 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
      • epi_data.cpp
      • epi_data.h
      • hdf5_cpp.h
      • history.h
      • io.cpp
      • io.h
      • json_serializer.cpp
      • json_serializer.h
      • 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
    • 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
      • parameter_distributions.h
      • parameter_set.cpp
      • parameter_set.h
      • pointer_dereferencing_iterator.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
    • ide_secir
      • infection_state.h
      • model.cpp
      • model.h
      • parameters.h
      • simulation.cpp
      • simulation.h
    • ide_seir
      • infection_state.h
      • model.cpp
      • model.h
      • parameters.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
  • simulations
    • 2020_npis_sarscov2_wildtype_germany.cpp
    • 2021_vaccination_sarscov2_delta_germany.cpp
  • tests
    • actions.h
    • distributions_helpers.cpp
    • distributions_helpers.h
    • load_test_data.h
    • matchers.h
    • temp_file_register.h
    • 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_graph.cpp
    • test_graph_simulation.cpp
    • test_ide_secir.cpp
    • test_ide_seir.cpp
    • test_io_cli.cpp
    • test_io_framework.cpp
    • test_matrix_shape.cpp
    • test_metaprogramming.cpp
    • test_mobility.cpp
    • test_mobility_io.cpp
    • test_model.cpp
    • test_numericalIntegration.cpp
    • test_odesecir.cpp
    • test_odesecir_ageres.cpp
    • test_odesecirvvs.cpp
    • test_odeseir.cpp
    • test_odesir.cpp
    • test_parameter_set.cpp
    • test_parameter_studies.cpp
    • test_populations.cpp
    • test_regions.cpp
    • test_save_parameters.cpp
    • test_save_results.cpp
    • test_smoother.cpp
    • test_state_age_function.cpp
    • test_stl_util.cpp
    • test_time_series.cpp
    • test_type_safe.cpp
    • test_uncertain.cpp
    • test_utils.cpp
• pycode
  • examples
    • epidata
      • PlotCaseData.py
      • PlotGermanData.py
      • ProgressIndicator.py
    • plot
      • plotResultsMapGermany.py
    • simulation
      • migration.py
      • migration_parameter_study.py
      • oseir_simple.py
      • osir_simple.py
      • parameter_studies.py
      • secir_groups.py
      • secir_simple.py
  • memilio-epidata
    • memilio
      • __init__.py
      • epidata_test
        • test_epidata_cleandata.py
        • test_epidata_customPlot.py
        • test_epidata_defaultDict.py
        • test_epidata_geoModificationGermany.py
        • test_epidata_getCaseData.py
        • test_epidata_getCaseDatawithEstimations.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
        • getCaseDatawithEstimations.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
    • setup.py
  • memilio-generation/memilio
    • __init__.py
    • generation_test
      • __init__.py
      • test_data
        • test_oseir.cpp.txt
        • test_oseir.py.txt
      • test_oseir_generation.py
    • generation
      • __init__.py
      • generator.py
      • intermediate_representation.py
      • scanner.py
      • scanner_config.py
      • template
        • __init__.py
        • template_cpp.txt
        • template_py.txt
        • template_string.py
      • utility.py
    • tools
      • example_oseir.py
  • memilio-plot
    • memilio
      • __init__.py
      • plot_test
        • test_plot_plotMap.py
      • plot
        • __init__.py
        • plotMap.py
    • setup.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_migration.py
        • test_oseir.py
        • test_osir.py
        • test_parameter_study.py
        • test_regions.py
        • test_secir.py
        • test_time_series.py
        • test_uncertain_matrix.py
        • test_uncertain_value.py
      • simulation
        • __init__.py
        • abm.cpp
        • abm.py
        • compartments
          • compartmentalmodel.h
          • simulation.h
        • epidemiology
          • contact_matrix.h
          • damping.h
          • damping_sampling.cpp
          • damping_sampling.h
          • populations.h
          • uncertain_matrix.cpp
          • uncertain_matrix.h
        • mobility
          • graph_simulation.h
          • metapopulation_mobility_instant.cpp
          • metapopulation_mobility_instant.h
        • oseir.cpp
        • oseir.py
        • osir.cpp
        • osir.py
        • pickle_serializer.h
        • pybind_util.h
        • secir.cpp
        • secir.py
        • 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
    • setup.py
  • memilio-surrogatemodel
    • memilio
      • __init__.py
      • surrogatemodel_test
        • test_surrogatemodel_ode_secir_simple.py
      • surrogatemodel
        • __init__.py
        • ode_secir_simple
          • __init__.py
          • data_generation.py
          • model.py
          • network_architectures.py
    • setup.py