├── .github └── workflows │ ├── ci.yml │ └── pypi-publish.yml ├── .gitignore ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── conf.py │ ├── epydemix.calibration.rst │ ├── epydemix.model.rst │ ├── epydemix.population.rst │ ├── epydemix.rst │ ├── epydemix.utils.rst │ ├── epydemix.visualization.rst │ ├── index.rst │ └── modules.rst ├── epydemix ├── __init__.py ├── calibration │ ├── __init__.py │ ├── abc.py │ ├── calibration_results.py │ └── metrics.py ├── model │ ├── __init__.py │ ├── epimodel.py │ ├── predefined_models.py │ ├── simulation_output.py │ ├── simulation_results.py │ └── transition.py ├── population │ ├── __init__.py │ └── population.py ├── utils │ ├── __init__.py │ ├── abc_smc_utils.py │ └── utils.py └── visualization │ ├── __init__.py │ └── plotting.py ├── pyproject.toml ├── pytest.ini ├── readthedocs.yml ├── requirements.txt ├── setup.py ├── tests ├── __init__.py ├── conftest.py ├── fixtures │ └── __init__.py ├── test_abc.py ├── test_epimodel.py ├── test_metrics.py ├── test_plotting.py ├── test_population.py ├── test_predefined_models.py ├── test_tutorial1.py ├── test_tutorial2.py ├── test_tutorial3.py ├── test_tutorial4.py ├── test_tutorial5.py └── test_tutorial6.py ├── tutorials ├── 01_Model_Definition_and_Simulation.ipynb ├── 02_Modeling_with_Population_Data.ipynb ├── 03_Modeling_Interventions.ipynb ├── 04_Model_Calibration_part1.ipynb ├── 05_Model_Calibration_part2.ipynb ├── 06_Advanced_Modeling_Features.ipynb ├── 07_Covid-19_Example.ipynb ├── 08_Multiple_Strains.ipynb ├── 09_Vaccinations.ipynb ├── 10_Multiprocessing.ipynb ├── colab_requirements.txt ├── data │ ├── incidence_data.csv │ └── massachusetts_data │ │ ├── MA_deaths.csv │ │ └── MA_google.csv └── img │ ├── behavioral_sir.png │ ├── epydemix-logo.png │ └── model_seird.png └── validation ├── compare_models.ipynb ├── compare_models_population.ipynb ├── compare_pyabc.ipynb └── models ├── stochastic_seir.py ├── 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