Pathogen evolution across fitness valleys

Exploring pathogen evolution across fitness valleys using the Opqua evolutionary epidemiological modeling package. Check out the peer-reviewed preprint on biorXiv, now peer-reviewed.

Shows good examples of running parameter sweeps with Opqua.

Pablo Cárdenas, Vladimir Corredor, & Mauricio Santos-Vega

contact pablo at pcarden at mit . edu

tweet at pablo

16 Dec 2021

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Code required to generate figures in publication (preprint forthcoming).

Repository tracks one large zip file with data using Git LFS.

To run code, install requirements (including Opqua) using

pip install -r requirements.txt

Many of the scripts take 6 to 12 h to run on a decent laptop (parallelized across 16 processors on an 8-Core Intel Core i9).