A collection of multiple epidemiological models used in the modelling of cases observed during the COVID-19 pandemic. Amongst the models curated in this collection are:
- PHE & Cambridge: an official model used by the UK government for policy making.
- Roche: a model developed by F. Hoffmann-La Roche Ltd.
All features of our software are described in detail in our full API documentation.
More details on epidemiological models and inference can be found in these papers:
[1] Birrell, Paul and Blake, Joshua and van Leeuwen, Edwin and , and Gent, Nick and De Angelis, Daniela (2020). Real-time Nowcasting and Forecasting of COVID-19 Dynamics in England: the first wave?. In medRxiv.
[2] Lemenuel-Diot, Annabelle and Clinch, Barry and Hurt, Aeron C. and Boutry, Paul and Laurent, Johann and Leddin, Mathias and Frings, Stefan and Charoin, Jean Eric (2020). A COVID-19 transmission model informing medication development and supply chain needs. In medRxiv.
One way to install the module is to download the repositiory to your machine of choice and type the following commands in the terminal.
git clone https://github.com/I-Bouros/multi-epi-model-cross-analysis.git
cd ../path/to/the/fileA different method to install this is using pip:
pip install -e .import epimodels
# create a contact matrix using mobility data e.g. from a POLYMOD matrix
epimodels.ContactMatrix(age_groups, polymod_matrix)Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.
Please make sure to update tests as appropriate.