%  PLOT_SID.m
%
%   analyze and plot the model results

LW=2;FS=16;FW='demi';

% Figure 1: 3 subplots S,I, D 
figure
  
subplot(2,2,1)

plot(t,S,'b-','LineWidth',LW)
title('Susceptible','FontSize',FS,'FontWeight',FW)
xlabel('Time (days)','FontSize',FS,'FontWeight',FW)
ylabel('Individuals m^{-2}','FontSize',FS,'FontWeight',FW)
set(gca,'LineWidth',LW,'FontSize',FS,'FontWeight',FW)  
  
subplot(2,2,2)
  
plot(t,I,'g-','LineWidth',LW)
title('Infected','FontSize',FS,'FontWeight',FW)
xlabel('Time (days)','FontSize',FS,'FontWeight',FW)
ylabel('Individuals m^{-2}','FontSize',FS,'FontWeight',FW)
set(gca,'LineWidth',LW,'FontSize',FS,'FontWeight',FW)

subplot(2,2,3)
 
plot(t,D,'k-','LineWidth',LW)
title('Dead','FontSize',FS,'FontWeight',FW)
xlabel('Time (days)','FontSize',FS,'FontWeight',FW)
ylabel('Individuals m^{-2}','FontSize',FS,'FontWeight',FW)
set(gca,'LineWidth',LW,'FontSize',FS,'FontWeight',FW)
  

  
 %xlim([0 100])

   % print and sent  plot to a folder
  %print('-dpng',['/Users/gorka/Documents/1-EHU/Master Projects/OSASUNA/matlab code/' PAR.case 'Num.png'])


 % Figure 2:  Infection rate by contact 
 
figure
N=2199711;
infI=PAR.Dinfect  .*  D .* S;
plot(t,infI,'r-','LineWidth',LW)
 title('Infection rate','FontSize',FS,'FontWeight',FW)
 xlabel('Time (days)','FontSize',FS,'FontWeight',FW)
 ylabel('Infection rate (individuals m^{-2} day^{-1}','FontSize',FS,'FontWeight',FW)
 set(gca,'LineWidth',LW,'FontSize',FS,'FontWeight',FW)
% print('-dpng',['Figures/Ab' PAR.case 'InfRate.png'])


% Figure 3 for Susceptible, Infected, Dead together

figure


plot(t,S,'b-',t,I,'r-',t,D,'k-','LineWidth',LW)
 %title(' Susceptible, Infected, Dead','FontSize',FS,'FontWeight',FW)
legend({'Susceptible','Infected','Dead'},'Location','northeast','FontSize',16)
xlabel('Time (days)','FontSize',FS,'FontWeight',FW)
 ylabel('Individuals m^{-2}','FontSize',FS,'FontWeight',FW)
 set(gca,'LineWidth',LW,'FontSize',FS,'FontWeight',FW)
% print('-dpng',['Figures/Ab' PAR.case 'InfRate.png'])

 %xlim([0 100])




%%% COMENT UNCOMMENT

% % import excel real cases
% 
% % Figure 5: for Real Cases of basque country and model predictions
% 
% figure
% 
% %d=[0.0;2.0;9.0;14.0;19.0;20.0;21.0;22.0;24.0;26.0;27.0;28.0;32.0;51.0;62.0;62.5;63.0;63.0;63.5;64.0;64.5;65.0;65.0;68.0;71.5;80.0;82.5;83;83.5;84.0;84.5;85.0;85.5;86.0;87.0]';
% 
% z=(0:1:350);
% %z=(0:1:100);
% %plot(z,Cases,'r-','LineWidth',2)
% plot(z,Cases,'w--s','LineWidth',1,'MarkerEdgeColor','k','MarkerFaceColor','r','MarkerSize',3);
% 
% 
% hold on 
% 
% N=2199711;
% tspan=[0 350];
% % %tspan=[0 100];
% [t,y]=ode45(@RHS_SID,tspan,y0);
% %fitted nodel 
% 
% %Iday=(PAR.Iinfect.*S.*I)/N;
% Iday=(PAR.Iinfect.*S.*I);
% plot(t,Iday,'r-','LineWidth',3) % orange color
% %title('Model Fit','FontSize',20)
% 
% % xlabel('Time (days)','FontSize',15)
% % ylabel('Mortality (%)','FontSize',15)
%  
% 
% 
% set(gca,'FontSize',16,'LineWidth',1)
% h=legend(' Real cases',' Simulation 1');
% set(h,'Location','NorthWest','box','off','FontSize',11);
% 
% Hx=xlabel('Time (days)');
% set(Hx,'FontSize',16)
% Hy=ylabel('Cases');
% set(Hy,'FontSize',16)
% %ylim([-2 1800])
% xlim([0 350])
% 
% print('-dpdf','Model_validation_cases.pdf')
% 
%