• covid Python package
• model_spec.py defines the CovidUK model using tfp.JointDistributionNamed, plus helper functions
• inference.py demonstrates MCMC model fitting the model
• simulate.py demontrates simulating from the model
• example_config.yaml example configuration file containing data paths and MCMC settings
• data a directory containing example data (see below)
• environment.yaml conda description of the required environment. Create with conda create -f environment.yaml 8 summary.py python script to summarise MCMC results into a Geopkg file.

• data/example_cases.csv a file containing example case data for 43 local authorities in England collected and present of PHE's website
• data/example_population.csv a file containing local authority population data in the UK, taken from ONS prediction for December 2019
• data/example_mobility.csv inter local authority mobility matrix taken from UK Census 2011 commuting data
• data/example_traffic_flow a relative measure of traffic flow taken from mobility metrics from providers such as Google and Facebook. Data have been smoothed to represent a summary of the original data.

$ conda env create --prefix=./env -f environment.txt
$ conda activate ./env
$ python inference.py
$ python summary.py

Data contained in the data directory is all publicly available from UK government agencies or previous studies. No personally identifiable information is stored.

ONS: Office for National Statistics

PHE: Public Health England

UTLA: Upper Tier Local Authority

LAD: Local Authority District