gerstung-lab / sarscov2-b117

Spatiotemporal analysis of strain-specific B.1.1.7 SARS-CoV-2 infection dynamics

Spatio-temporal analysis of B.1.1.7 infection dynamics

This repository contains code to analyse strain-specific infection dynamics based on generic PCR test and B.1.1.7 genomic prevalence data across 382 British lower tier local authorities (LTLAs).

The code was developed by Harald Vöhringer and amended by Moritz Gerstung.

Data is from publicly available sources and COG-UK.

The analysis is implemented in python and uses numpyro for stochastic variation inference of the underlying model.

You can install the necessary python packages using (tested with pip version 20.2.3):

$ pip install -r requirements.txt

Additionally install numpyro with the --no-deps flag.

pip install -r requirements-no-deps.txt --no-deps

Depending on your installation you may need to install libspatialindex using

$ brew install spatialindex

or

$ conda install -c conda-forge libspatialindex

The main notebook is sarscov2-b117.ipynb