This repository contains the relevant code used to simulate the results in https://www.medrxiv.org/content/10.1101/2021.02.08.21251383v1. 3 Files can be found here. mutvacc_tools.py, which contains most of the functionality and the main class. The other two files, generate_graphs.py and generate_2D.py, contain utilities for running the main code multiple times and visualizing the results. While above publication deals with a single locus, the code is general enough to account for any number of targets and vaccines.
Contains, aside some auxillary functions, the main class and the function run-stochastic. This function simulates a population in our extended SIR model for a time period of time T. For details on the model, please see https://www.medrxiv.org/content/10.1101/2021.02.08.21251383v1. All relevant parameters can be accessed and modified before a simulation is run.
Prduces graphs of the infection numbers of wildtype strains and emergent strain over the course of a simulation. Other quantities, such as the number of vaccinated individuals, the number of recovered individuals, etc. can be accessed and plotted via the model.graphs dictionary.
Produces graphs of macrovariables, such as the total death count at the end of a simulation or the appearance of an emergent strain after a given time. These macrovariables can be studied as a function of all parameters of the model.