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

Ensure that pypfilt is already installed, then clone the epifx repository and install it a Virtual Environment (here, called venv-pypfilt):

# Activate the virtual environment.
source venv-pypfilt/bin/activate
# Clone the epifx repository.
git clone https://bitbucket.org/robmoss/epidemic-forecasting-for-python.git
cd epidemic-forecasting-for-python
# Install epifx in the virtual environment.
python setup.py install

If you are not using a virtual environment, and you don’t have permission to install epifx system-wide, you can install the package locally:

# Clone the epifx repository.
git clone https://bitbucket.org/robmoss/epidemic-forecasting-for-python.git
cd epidemic-forecasting-for-python
# Install epifx in the user's "site-packages" directory.
python setup.py install --user