priesemann-group / covid19_variants_chile

Early mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants in Chile

This is the code repository to reproduce the figures and analysis from our "Mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants" publication.

Reproducing figures

The figures from our publication can be reproduced using the notebooks/create_plots.ipynb notebook. Before you can do that you have to run the analysis by having a look into the notebooks/Model.ipynb or the src/run_model.py script.

We advice you start with the notebooks/Model.ipynb notebook and than take a look into the src/run_model.py once necessary.

We also supply a small trace in the data folder which can be loaded if you don't want to run the time consuming sampling.

Notes

The herein presented code highly relies on our toolbox for Bayesian python toolbox for inference and forecast of the spread of the Coronavirus. If you want to run our code make sure to install the toolbox or to initialize the github submodule.

git submodule update --init