Here you will find code that is able to infer fitness effects of viral variants in the context of cellular coinfection. We implement deterministic and stochastic frameworks to accomplish this task.
Each of the main directories for the deterministic and stochastic models you see above contain two subdirectories. One contains code relevant to the production and analysis of the simulated datasets. The other contains code relevant to the analysis and inference applied to the Wilker H5N1 dataset.