This repo contains simulation scripts for modelling the spread of the covid variants omicron and delta in society, modelled as a Markov jump process. Three different situations are modelled: societal spread without any measures implemented, societal spread with quarantine measures, and societal spread in a vaccinated population.

To run the simulations clone the repo and start a Julia session in the base of the repo. Then run

include("<script>.jl")

where the script is either of baseline.jl, quarantine.jl or vaccine.jl. Then run the simulation for a given starting state by entering

sims = runsim(population_size, I1, I2, endtime, number_of_sims)

If you allow Julia several threads, the function will run several simulations in parallel.

To plot the mean and standard deviation of the simulation, run

bandplot(sims, number_of_samples)

and to plot the evolution of all simulated states run

plotter(sims, number_of_samples)