run simple_model_vs_SIR.m to plot figure1; run simple_model_herd_imm_thres_predic.m to plot figure2; run vaccine_coverage_calculation.m to plot figure3; run consider_mut_asymp_dose_age_geo2.m to plot figure4.A; run plot_movie.m to further generate the movie of epidemic over 4 cities. You can extract certain figures to generate the infection cases distribution at certain time point as shown in figure4.B.
Good Luck!