Epidemic forecasting in Python

Welcome to the epifx documentation. This package uses a bootstrap particle filter to generate influenza epidemic forecasts from mechanistic infection models.

Installation

You can install epifx using pip:

# Install pypfilt (with plotting support) and epifx.
pip install pypfilt[plot] epifx

See the pypfilt documentation for further details.

User Documentation

• Home
• Getting Started
  • Simulation parameters
  • Temporal forcing
  • Infection models
  • Arbitrary model priors
  • Observation models
  • Forecast summaries
  • Generating forecasts
  • Comparing forecast outputs
• Observation Models
  • Observations from the entire population
  • Observations from population samples
  • The PopnCounts class
  • The SampleCounts class
  • Custom observation models
  • Reading observations from disk
• Commands
  • Local configuration
  • Observation model scans
  • Observation model performance
  • Live forecasting
  • Replay forecasts
  • Interactive forecast plots
  • Comparing simulation outputs
• Worked Example
  • Major decisions
  • Defining the forecast settings
  • Running the forecasts
  • Visualising the forecasts
  • Retrospective forecasts
  • Download the complete files
• Change Log
  • 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)

Development

• Contributing to epifx
  • Licensing
• Testing with tox
• Release process
  • Publishing to PyPI