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This project contains the Python code for the PhD thesis titled "Joint epidemic and spatio-temporal approach for modelling disease outbreaks" at Lancaster University supervised by Dr. Chris Jewell and Prof. Dr. Peter Neal.

It provides an extension to the Python probabilistic programming library PyMC3 with a sampler to effectively impute missing infection and removal time data. Furthermore, it integrates a mechanistic modeling approach into an epidemiological modeling setting.

Analysis of PHE covid19 data for weekly SPI-M reports

Repository containing the Covid19UK pipeline

This is the repository for the main InFER (Inference for Epidemic Risk) package.

sourceR R package to fit source attribution models

Add-on classes for Tensorflow Probability provided by GEM. This is a transitional repo, intended to be incorporated into GEM eventually.

This project has been migrated to https://gitlab.com/gem-epidemics/gemlib

Note on DataOps for CHICAS

GEM epidemic modelling software base -- https://gem.readthedocs.io/en/latest/

The DRUM agent-based model.