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Repository containing the Covid19UK pipeline

Analysis of PHE covid19 data for weekly SPI-M reports

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.