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hivSimResultsGenAge.m
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% Total HIV positive
hivInds = toInd(allcomb(2 : 6 , 1 : viral , 1 : hpvTypes , 1 : hpvStates, ...
1 : periods , 1 : gender , 4 : 10 , 1 : risk));
hivPopAge = sum(artAge.popVec(: , hivInds) , 2);
hivPopMed = sum(artMed.popVec(: , hivInds) , 2);
hivPopHigh = sum(artHigh.popVec(: , hivInds) , 2);
hivPopMH = sum(artMH.popVec(: , hivInds) , 2);
artInds = toInd(allcomb(10 , 6 , 1 : hpvTypes , 1 : hpvStates, ...
1 : periods , 1 : gender , 4 : 10 , 1 : risk));
artPopAge = sum(artAge.popVec(: , artInds) , 2);
artPopMed = sum(artMed.popVec(: , artInds) , 2);
artPopHigh = sum(artHigh.popVec(: , artInds) , 2);
artPopMH = sum(artMH.popVec(: , artInds) , 2);
% Compared to Africa Center data
overallHivPrev_KZN_AC(1 , :) = 1990 : 2009;
overallHivPrev_KZN_AC(2 , :) = [0.464072571
0.985438052
1.506803533
5.576509907
8.126044402
13.04177608
12.54905705
16.61876343
19.50632609
19.52064932
22.2391979
20.22439723
22.09787539
22.78825495
25.16877536
26.19622822
25.36548102
27.2380043
27.42134161
28.44974934];
figure()
totInds = toInd(allcomb(1 : disease , 1 : viral , 1 : hpvTypes , 1 : hpvStates , 1 : periods , ...
1 : gender , 4 : 10, 1 : risk));
agePopTot = artAge.popVec(: , totInds);
medPopTot = artMed.popVec(: , totInds);
highPopTot = artHigh.popVec(: , totInds);
mhPopTot = artMH.popVec(: , totInds);
agePrev = 100 * (hivPopAge + artPopAge) ./ sum(agePopTot , 2);
medPrev = 100 * (hivPopMed + artPopMed) ./ sum(medPopTot , 2);
highPrev = 100 * (hivPopHigh + artPopHigh) ./ sum(highPopTot , 2);
mhPrev = 100 * (hivPopMH + artPopMH) ./ sum(mhPopTot , 2);
plot(tVec , medPrev , tVec , mhPrev , tVec , highPrev , tVec , agePrev)
hold on
plot(overallHivPrev_KZN_AC(1 , :) , overallHivPrev_KZN_AC(2 , :) , '*')
xlabel('Year'); ylabel('Proportion of Population (%)'); title('HIV Prevalence (Ages 15-49)')
xlim([tVec(1) , tVec(end)])
legend('65% Both' , 'M:65%, F:80%' , '80% Both' , 'Age & Gender Dependent' , 'KZN Actual (Africa Center Data)')
%% Change in HIV incidence
susInds = toInd(allcomb(1 , 1 : viral , 1 : hpvTypes , 1 : hpvStates , 1 : periods , ...
1 : gender , 4 : 10, 1 : risk));
% population at risk (use midpoint)
agePopSus = (sum(artAge.popVec(1 : end - 1 , susInds) , 2) + ...
sum(artAge.popVec(2 : end , susInds) , 2)) ./ 2;
medPopSus =(sum(artMed.popVec(1 : end - 1 , susInds) , 2) + ...
sum(artMed.popVec(2 : end , susInds) , 2)) ./ 2;
highPopSus = (sum(artHigh.popVec(1 : end - 1 , susInds) , 2) + ...
sum(artHigh.popVec(2 : end , susInds) , 2)) ./ 2;
mhPopSus = (sum(artMH.popVec(1 : end - 1 , susInds) , 2) + ...
sum(artHigh.popVec(2 : end , susInds) , 2)) ./ 2;
fac = 10 ^ 5;
artInc = sum(sum(sum(artAge.newHiv(2 : end , 1 : gender , 4 : 10 , 1 : risk), 2), 3 ), 4)...
./ agePopSus * fac;
medInc =sum(sum(sum(artMed.newHiv(2 : end , 1 : gender , 4 : 10 , 1 : risk), 2), 3 ), 4)...
./ medPopSus * fac;
highInc = sum(sum(sum(artHigh.newHiv(2 : end , 1 : gender , 4 : 10 , 1 : risk), 2), 3 ), 4)...
./ highPopSus * fac;
mhInc = sum(sum(sum(artMH.newHiv(2 : end , 1 : gender , 4 : 10 , 1 : risk), 2), 3 ), 4)...
./ highPopSus * fac;
figure()
plot(tVec(2 : end) , medInc , tVec(2 : end ) , mhInc , ...
tVec( 2 : end) , highInc , tVec(2 : end) , artInc);
xlim([tVec(1) , tVec(end)])
xlabel('Year'); ylabel('Incidence per 100,000');
title('HIV Incidence')
legend('65% Both' , 'M:65%, F:80%' , '80% Both' , 'Age & Gender Dependent')
deltaMed = (medInc - artInc) ./ artInc * 100;
deltaHigh = (highInc - artInc) ./ artInc * 100;
deltaMH = (mhInc - artInc) ./ artInc * 100;
figure()
plot(tVec(2 : end) , deltaMed , tVec(2 : end) , deltaMH , ...
tVec(2 : end) , deltaHigh);
xlim([tVec(1) , tVec(end)])
xlabel('Year'); ylabel('Change (%)');
title('Change in Incidence')
legend('65% Both' , 'M:65%, F:80%' , '80% Both' , 'Age & Gender Dependent')
% Change in HIV-related mortality
fac = 10 ^ 5;
ageMort = sum(sum(artAge.hivDeaths(2 : end , 1 : gender , 1 : age), 2), 3) ./ agePopSus * fac;
medMort = sum(sum(artMed.hivDeaths(2 : end , 1 : gender , 1 : age) , 2), 3) ./ medPopSus * fac;
highMort = sum(sum(artHigh.hivDeaths(2 : end , 1 : gender , 1 : age) , 2), 3) ./ highPopSus * fac;
mhMort = sum(sum(artMH.hivDeaths(2 : end , 1 : gender , 1 : age) , 2), 3) ./ mhPopSus * fac;
figure()
plot(tVec(2 : end) , medMort , tVec(2 : end) , mhMort , ...
tVec( 2 : end) , highMort , tVec(2 : end) , ageMort);
xlim([tVec(1) , tVec(end)])
xlabel('Year'); ylabel('Mortality per 100,000');
title(['HIV Mortality'])
legend('65% Both' , 'M:65%, F:80%' , '80% Both' , 'Age & Gender Dependent')
deltaMortMed = (medMort - ageMort) ./ ageMort * 100;
deltaMortHigh = (highMort - ageMort) ./ ageMort * 100;
deltaMortMH = (mhMort - ageMort) ./ ageMort * 100;
figure()
plot(tVec(2 : end) , deltaMortMed , tVec(2 : end) , deltaMortMH , ...
tVec(2 : end) , deltaMortHigh);
xlim([tVec(1) , tVec(end)])
xlabel('Year'); ylabel('Change (%)');
title(['Change in Mortality'])
legend('65% Both' , 'M:65%, F:80%' , '80% Both' , 'Age & Gender Dependent')
%% Change in HIV incidence
figure()
for g = 1 : gender
susInds1 = toInd(allcomb(1 , 1 : viral , 1 : hpvTypes , 1 : hpvStates , 1 : periods , ...
g , 1 : 6 , 1 : risk));
susInds2 = toInd(allcomb(1 , 1 : viral , 1 : hpvTypes , 1 : hpvStates , 1 : periods , ...
g , 7 : age , 1 : risk));
% population at risk (use midpoint)
agePopSus1 =(sum(artAge.popVec(1 : end - 1 , susInds1) , 2) + ...
sum(artAge.popVec(2 : end , susInds1) , 2)) ./ 2;
agePopSus2 =(sum(artAge.popVec(1 : end - 1 , susInds2) , 2) + ...
sum(artAge.popVec(2 : end , susInds2) , 2)) ./ 2;
fac = 10 ^ 5;
ageInc1 =sum(sum(sum(artAge.newHiv(2 : end , g , 1 : 6 , 1 : risk), 2), 3 ), 4)...
./ agePopSus1 * fac;
ageInc2 =sum(sum(sum(artAge.newHiv(2 : end , g , 7 : age , 1 : risk), 2), 3 ), 4)...
./ agePopSus2 * fac;
plot(tVec(2 : end) , ageInc1 , tVec(2 : end) , ageInc2)
hold on
end
xlim([tVec(1) , tVec(end)])
xlabel('Year'); ylabel('Incidence per 100,000');
title('HIV Incidence by Age Group and Gender')
legend('Males: <30' , ' Males: 30+' , 'Females: <30' , 'Females: 30+')
%% summary table
yr_2030 = (2030 - startYear) * stepsPerYear;
yr_2040 = (2040 - startYear) * stepsPerYear;
yr_2050 = (2050 - startYear) * stepsPerYear - 1;
% Change in mortality
deltaM_Med = [deltaMortMed(yr_2030) ; deltaMortMed(yr_2040) ; ...
deltaMortMed(yr_2050)];
deltaM_High = [deltaMortHigh(yr_2030) ; deltaMortHigh(yr_2040) ; ...
deltaMortHigh(yr_2050)];
deltaM_MH = [deltaMortMH(yr_2030) ; deltaMortMH(yr_2040) ; ...
deltaMortMH(yr_2050)];
% Change in incidence
deltaIMed = [deltaMed(yr_2030) ; deltaMed(yr_2040) ; ...
deltaMed(yr_2050)];
deltaIHigh = [deltaHigh(yr_2030) ; deltaHigh(yr_2040) ; ...
deltaHigh(yr_2050)];
deltaIMH = [deltaMH(yr_2030) ; deltaMH(yr_2040) ; ...
deltaMH(yr_2050)];
ageP = [agePrev(yr_2030) ; agePrev(yr_2040) ; agePrev(yr_2050)];
medP = [medPrev(yr_2030) ; medPrev(yr_2040) ; medPrev(yr_2050)];
highP = [highPrev(yr_2030) ; highPrev(yr_2040) ; highPrev(yr_2050)];
mhP = [mhPrev(yr_2030) ; mhPrev(yr_2040) ; mhPrev(yr_2050)];
hivSumm = table({'2030' ; '2040' ; '2050'} , ageP , medP, mhP , highP ,...
deltaIMed , deltaIMH , deltaIHigh , deltaM_Med , deltaM_MH , deltaM_High);
hivSumm.Properties.VariableNames{1} = 'Year';
disp('Impact Summary for General Population')
disp(hivSumm)
filename = ['General_artCompare.xlsx'];
writetable(hivSumm , filename)
disp(['Results for general population written to ' , filename])