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
16 Dec 2021
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.txtMany 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).