/fitness_valleys_opqua

Exploring pathogen evolution across fitness valleys using Opqua.

Primary LanguagePythonMIT LicenseMIT

Pathogen evolution across fitness valleys

DOI

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


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).