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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.
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Repository containing the Covid19UK pipeline
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This is the repository for the main InFER (Inference for Epidemic Risk) package.
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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
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