# summer2: compartmental disease modelling in Python
[](https://github.com/monash-emu/summer2/actions/workflows/tests.yml)
summer2 is a Python-based framework for the creation and execution of [compartmental](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology) (or "state-based") epidemiological models of infectious disease transmission.
It provides a range of structures for easily implementing compartmental models, including structure for some of the most common features added to basic compartmental frameworks, including:
- A variety of inter-compartmental flows (infections, transitions, births, deaths, imports)
- Force of infection multipliers (frequency, density)
- Post-processing of compartment sizes into derived outputs
- Stratification of compartments, including:
- Adjustments to flow rates based on strata
- Adjustments to infectiousness based on strata
- Heterogeneous mixing between strata
- Multiple disease strains
Some helpful links to learn more:
- **[Documentation](https://summer2.readthedocs.io/)** with [code examples](https://summer2.readthedocs.io/en/latest/examples/index.html)
- [Available on PyPi](https://pypi.org/project/summerepi2/) as `summerepi2`.
## Installation and Quickstart
This project requires at least Python 3.10
Set up and activate an appropriate virtual environment, then install the `summerepi2` package from PyPI
```bash
pip install summerepi2
```
You can now use the library to build and run models. See [here](https://summer2.readthedocs.io/en/latest/examples/index.html) for some code examples.
## Optional (recommended) extras
Summer has advanced interactive plotting tools built in - but they are greatly improved with the
addition of the pygraphviz library.
If you are using conda, the simplest method of installation is as follows:
```bash
conda install --channel conda-forge pygraphviz
```
For other install methods, see
https://pygraphviz.github.io/documentation/stable/install.html
## Development
[Poetry](https://python-poetry.org/) is used for packaging and dependency management.
## Releases
Releases are numbered using [Semantic Versioning](https://semver.org/)
- 1.0.0/1:
- Initial release
- 1.2.1
- Dropped support for Python 3.7. Variety of bugfixes and expanded features, see documentation
- 1.2.2
- Added capture utils
- Removed inner jit in model building to improve debugging
- 1.2.4
- CompartmentValues not functioning previously; include more comprehensive check in graph split
- 1.2.5
- Previous issue was not resolved correctly; bugfix-bugfix release
- 1.2.6
- Make full (comparment) outputs optional for jax runners
- 1.2.8
- Improve time varying functions (allow GraphObjects in x values)
- 1.2.9
- Derived output functions matching pandas.Series functionality (rolling, diff)
- 1.3.0
- Support initializing whole population via GraphObject
- 1.3.1
- Enforce jax minimum version in requirements
- 1.3.2
- Fix parameter bug in test models
- 1.3.3
- Fix issue with binary search for piecewise functions
- 1.3.4
- Update import in ode.py for changed jax API
- 1.3.5
- Force specific jax (0.4.24) to stop breaking changes
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"description": "# summer2: compartmental disease modelling in Python\n\n[](https://github.com/monash-emu/summer2/actions/workflows/tests.yml)\n\nsummer2 is a Python-based framework for the creation and execution of [compartmental](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology) (or \"state-based\") epidemiological models of infectious disease transmission.\n\nIt provides a range of structures for easily implementing compartmental models, including structure for some of the most common features added to basic compartmental frameworks, including:\n\n- A variety of inter-compartmental flows (infections, transitions, births, deaths, imports)\n- Force of infection multipliers (frequency, density)\n- Post-processing of compartment sizes into derived outputs\n- Stratification of compartments, including:\n - Adjustments to flow rates based on strata\n - Adjustments to infectiousness based on strata\n - Heterogeneous mixing between strata\n - Multiple disease strains\n\nSome helpful links to learn more:\n\n- **[Documentation](https://summer2.readthedocs.io/)** with [code examples](https://summer2.readthedocs.io/en/latest/examples/index.html)\n- [Available on PyPi](https://pypi.org/project/summerepi2/) as `summerepi2`.\n\n## Installation and Quickstart\n\nThis project requires at least Python 3.10\n\nSet up and activate an appropriate virtual environment, then install the `summerepi2` package from PyPI\n\n```bash\npip install summerepi2\n```\n\nYou can now use the library to build and run models. See [here](https://summer2.readthedocs.io/en/latest/examples/index.html) for some code examples.\n\n## Optional (recommended) extras\n\nSummer has advanced interactive plotting tools built in - but they are greatly improved with the\naddition of the pygraphviz library.\n\nIf you are using conda, the simplest method of installation is as follows:\n\n```bash\nconda install --channel conda-forge pygraphviz\n```\n\nFor other install methods, see\nhttps://pygraphviz.github.io/documentation/stable/install.html\n\n## Development\n\n[Poetry](https://python-poetry.org/) is used for packaging and dependency management.\n\n## Releases\n\nReleases are numbered using [Semantic Versioning](https://semver.org/)\n\n- 1.0.0/1:\n - Initial release\n- 1.2.1\n - Dropped support for Python 3.7. Variety of bugfixes and expanded features, see documentation\n- 1.2.2\n - Added capture utils\n - Removed inner jit in model building to improve debugging\n- 1.2.4\n - CompartmentValues not functioning previously; include more comprehensive check in graph split\n- 1.2.5\n - Previous issue was not resolved correctly; bugfix-bugfix release\n- 1.2.6\n - Make full (comparment) outputs optional for jax runners\n- 1.2.8\n - Improve time varying functions (allow GraphObjects in x values)\n- 1.2.9\n - Derived output functions matching pandas.Series functionality (rolling, diff)\n- 1.3.0\n - Support initializing whole population via GraphObject\n- 1.3.1\n - Enforce jax minimum version in requirements\n- 1.3.2\n - Fix parameter bug in test models\n- 1.3.3\n - Fix issue with binary search for piecewise functions\n- 1.3.4\n - Update import in ode.py for changed jax API\n- 1.3.5\n - Force specific jax (0.4.24) to stop breaking changes\n",
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