Epidemic forecasting in Python
Welcome to the epifx documentation. This package uses a bootstrap particle filter (pypfilt) to generate forecasts of infectious disease epidemics.
Note
This documentation assumes that you are already familiar with the pypfilt package. If this is not the case, please read the pypfilt Getting Started tutorial before proceeding.
The epifx package provides a number of new components and features on top of those provided by the pypfilt package, including:
Compartmental models of infectious diseases epidemics;
Observation models for case counts and sentinel surveillance data;
Summary tables for epidemic simulations;
Example scenarios of epidemic forecasting;
A command-line program (
epifx-forecast
) for running estimation and forecast simulations; andAn accept-reject sampler for sampling from arbitrary target distributions.
Installation
You can install epifx using pip
, preferably in a
virtual environment:
pip install epifx
See the pypfilt documentation for further details about installation.
License
The code is distributed under the terms of the BSD 3-Clause license (see
LICENSE
), and the documentation is distributed under the terms of the
Creative Commons BY-SA 4.0 license.
User Documentation
Development
- Contributing to epifx
- Testing with nox
- Release process
- Editable installs
- Change Log
- 0.8.1 (2023-10-13)
- 0.8.0 (2022-11-03)
- 0.7.1 (2022-05-30)
- 0.7.0 (2022-04-20)
- 0.6.1 (2020-10-20)
- 0.6.0 (2020-08-13)
- 0.5.8 (2020-04-03)
- 0.5.7 (2020-03-28)
- 0.5.6 (2018-06-07)
- 0.5.5 (2017-10-26)
- 0.5.4 (2017-08-17)
- 0.5.3 (2017-08-16)
- 0.5.2 (2017-08-16)
- 0.5.1 (2017-06-15)
- 0.5.0 (2017-05-10)
- 0.4.3 (2016-09-16)
- 0.4.2 (2016-06-16)
- 0.4.1 (2016-04-22)
- 0.4.0 (2016-04-22)
- 0.3.1 (2016-02-25)
- 0.3.0 (2016-02-23)
- 0.2.0 (2015-11-17)
- 0.1.10 (2015-07-09)
- 0.1.9 (2015-07-06)
- 0.1.8 (2015-06-18)
- 0.1.7 (2015-06-18)
- 0.1.6 (2015-06-08)
- 0.1.5 (2015-06-04)
- 0.1.4 (2015-06-03)
- 0.1.3 (2015-06-01)
- 0.1.2 (2015-06-01)
- 0.1.1 (2015-05-29)
- 0.1.0 (2015-05-29)