%This file runs the routines needed to produce the plots in the
%Atkeson-Kissler 2024 BPEA paper and the model plots in the online Appendix

%Each file starts with clear all and close all. Plots are output as PDF
%files

%This first file makes the plots for Figures 1 and 3 left and right panels in the main paper
% These plots are output in files
%Figure1.pdf, Figure3Left.pdf, Figure3Right.pdf
%It also produced the plots for Appendix Figure A1 left and right panels

Dataplotsmain

%This second file makes the left and right panels for Figures 2 and 4 in
%the maing paper. These plots are output in files
%Figure2Left.pdf, Figure2Right.pdf, Figure4Left.pdf, Figure4Right.pdf
%It also reports the number of cumulative deaths for this scenario as a
%printout in the command window

OmicronvBPEAbaseline

%This third file makes the left and right panels for Figure 5 and Figure 6
%in the main paper. The plots are output in files
%Figure5Left.pdf, Figure5Right.pdf, Figure6.pdf,
%It also reports the number of cumulative deaths for this scenario as a
%printout in the command window

OmicronvBPEAnovaccines

%This fourth file makes the left and right panels for Figure 7 
%in the main paper. The plots are output in files
%Figure7Left.pdf, Figure7Right.pdf,
%It also reports the number of cumulative deaths for this scenario as a
%printout in the command window

OmicronvBPEAnobehavior

%This fifth file makes the left and right panels for Figure A.5
%in the Appendix. The plots are output in files
%FigureA5Left.pdf and FigureA5Right.pdf
%It also reports the number of cumulative deaths for this scenario as a
%printout in the command window

OmicronvBPEAfastvaccines

%These sixth and seventh files makes the left and right panels of Figure B.14 in the Appendix
%The plots are output in files
%FigureB14Left.pdf and FigureB14Right.pdf
%They also report cumulative deaths with strong and weak behavior in the
%command window

OmicronvBPEAstrongbehavior

OmicronvBPEAweakbehavior


%These eight and ninth files makes the left and right panels of Figure B.15 in the Appendix
%The plots are output in files
%FigureB15Left.pdf and FigureB15Right.pdf
%They also report cumulative deaths with fast and slow  in the
%command window

OmicronvBPEAfasttransmission

OmicronvBPEAslowtransmission

%This tenth file makes the plots in Appendix Figure B7 Left and Right,
%Figure B9, and Figure B10 Left and Right

plotcumdeathbystate

%This eleventh file makes the plots in Appendix Figure A2, Figure B11 Left and Right,
% Figure B12 Left and Right, and Figure B13

Serology