clear;
saveDirectory='C:\Users\bacaer\Desktop\Nicolas\2010HIVTBarticles\Revise\';
saveDirectory2='C:\Users\bacaer\Desktop\Nicolas\2010Londres\Expose\';
loadDirectory='C:\Users\bacaer\Desktop\';
universal=0; //0 means no, 1 means yes
showassumptions=0; //same
savefig=0; //same
show='HIV';
//show='DEATH';
//show='PYRAMID';
//************** assumptions **********************
xmax=100;
ymax=xmax;
t0=1986;
liste=(20/1152)*[1152 1150 1147 1142 1136 1124 1109 1093 1074 1053 1031 1031 1030 1028 102
5 1022  1018 1013 1008 1004 1000 993 987 978 963 955 943 930 916 906 902 898 893 887 880 8
74 868 861 854  846 840 834 828 821 814 808 803 797 791 785 780 774 769 764 759]; //births
 between 1986 and 2020 (US Census Bureau)
function z=B(t)
  z=liste(t-t0+1)
endfunction
tmax=2020;
Sm=zeros(xmax,1); Im=zeros(xmax,ymax); Rm=zeros(xmax,ymax); SSm=zeros(xmax,1); IIm=zeros(x
max,ymax); RRm=zeros(xmax,ymax);  //males
Sf=zeros(xmax,1); If=zeros(xmax,ymax); Rf=zeros(xmax,ymax); SSf=zeros(xmax,1); IIf=zeros(x
max,ymax); RRf=zeros(xmax,ymax); //females
df=0.001*linear_interpn([1:xmax],[1 2 5 10:5:100],[40 2 1 0.5 0.6 2.0 2.5 3.1 3.9 4.5 5.0
7.5 10.0 15 22 29 36 43 50 57 64 71])';  //female death rate
dm=0.001*linear_interpn([1:xmax],[1 2 5 10:5:100],[50 2 1 0.6 0.7 2.3 3.5 4.2 5.0 6.5 8.5
12.0 17.0 26 37 48 59 70 81 92 103 114])';  //male death rate
debut=14;  //age of female sexual debut
choix=zeros(xmax,xmax); ym=zeros(1,xmax); yave=zeros(1,xmax); yM=zeros(1,xmax);
//choice of male sexual partner
for x=debut:xmax,
  ym(x)=linear_interpn(x,[debut 40 100],[debut 22 84]); //minimum
  yave(x)=linear_interpn(x,[debut 30 100],[debut+1 30 95]); //modal
  yM(x)=linear_interpn(x,[debut 30 100],[debut+15 65 100]); //maximum
  choix(x,ym(x):yM(x))=linear_interpn(ym(x):yM(x),[ym(x) yave(x) yM(x)],[0 1 0]);
  choix(x,ym(x):yM(x))=choix(x,ym(x):yM(x))/sum(choix(x,ym(x):yM(x))); //probability distr
ibution
end;
underreport=2; //underreporting of male sexual partners
rate=underreport*linear_interpn([1:xmax],[0 debut 15 25 35 45 60 100],[0 0 0.6 0.3 0.15 0.
05 0.025 0.02])'; //rate of change of sexual partner
pm=0.5; //transmission probability female to male per partnership
pf=0.85;  //male to female
overreport=1;  //overreporting of condom use
epsi=0.01; //relative infectivity on ART
AIDS=zeros(xmax,ymax);
//survivalAIDS=exp(-0.00494*([0:ymax].^2.25)); //median 9 years
survivalAIDS=exp(-0.0039*([0:ymax].^2.25)); //median 10 years
//survivalAIDS=exp(-0.00315*([0:ymax].^2.25)); //median 11 years
AIDSdeath=(survivalAIDS(1:ymax)-survivalAIDS(2:ymax+1))./survivalAIDS(1:ymax);
for x=1:xmax,
  if x