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simVax2.m
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% Accepts end year of analysis, number of tests, and population vector from
% calibrated model as inputs
% function simVax(lastYear , nTests, testParams , currPop)
close all; clear all; clc
lastYear = 2100;
disp('Start up')
% load population
popIn = load('H:\HHCoM_Results\kCC_Cin3_0.5Mult.mat');
currPop = popIn.popLast;
% load variables
load('general');
load('settings');
load('mixInfectIndices')
load('vlAdvancer')
load('fertMat')
load('hivFertMats')
load('deathMat')
load('circMat')
load('vaxer')
load('mixInfectParams');
load('hpvData')
load('popData')
load('HIVParams')
load('hivIndices')
load('hpvIndices')
load('ager')
load('vlBeta')
load('hpvTreatIndices')
load('vaxInds')
%%%%%%%
load('calibParams')
w = ones(4 , 1) ./ 4;
kCC_Cin3_Orig = kCC_Cin3;
kCin2_Cin3_Orig = kCin2_Cin3;
kCin2_Cin1_Orig = kCin2_Cin1;
kCin1_Cin2_Orig = kCin1_Cin2;
kCin3_Cin2_Orig = kCin3_Cin2;
rNormal_Inf_Orig = rNormal_Inf;
for i = 1 : 3
rNormal_Inf(: , i) = conv(rNormal_Inf_Orig(: , i) , w , 'same');
rNormal_Inf(end - 1 : end , i) = conv(rNormal_Inf_Orig(end - 1 : end , i) , w , 'same');
kCC_Cin3(: , i) = conv(kCC_Cin3_Orig(: , i) , w , 'same');
kCC_Cin3(end - 1 : end , i) = kCC_Cin3_Orig(end - 1 : end , i);
% kCin2_Cin3(: , i) = conv(kCin2_Cin3_Orig(: , i) , w , 'same');
% kCin2_Cin3(end - 1 : end , i) = kCin3_Cin2_Orig(end - 1 : end , i);
kCin3_Cin2(: , i) = conv(kCin3_Cin2_Orig(: , i) , w , 'same');
kCin3_Cin2(end - 1 : end , i) = kCin3_Cin2_Orig(end - 1 : end , i);
kCin1_Cin2(: , i) = conv(kCin1_Cin2_Orig(: , i) , w , 'same');
kCin1_Cin2(end - 1 : end , i) = kCin1_Cin2_Orig(end - 1 : end , i);
kCin2_Cin1(: , i) = conv(kCin2_Cin1_Orig(: , i) , w , 'same');
kCin2_Cin1(end - 1 : end , i) = kCin2_Cin1_Orig(end - 1 : end , i);
end
% rNormal_Inf(: , 1) = rNormal_Inf(: , 1) .* 1.2;
% rNormal_Inf(: , 2) = rNormal_Inf(: , 2) .* 0.8;
% rNormal_Inf(: , 3) = rNormal_Inf(: , 3) .* 0.9;
rNormal_Inf = rNormal_Inf .* 0.85;
% c2c1Mults = 1.5 .* c2c1Mults;
% kCin1_Cin2(1 : end , :) = 1.2 * kCin1_Cin2(1 : end , :);
kCin2_Cin1(6 : end , :) = 1.25 * kCin2_Cin1(6 : end , :);
kCin3_Cin2(10 : end , :) = 2.8 * kCin3_Cin2(10 : end , :);
kCin2_Cin3 = 0.5 .* kCin2_Cin3;
kCC_Cin3(7 : end , :) = 4 .* kCC_Cin3(7 : end , :);
muCC = min(muCC .* 12 , 0.99); % convert cervical cancer mortality rate from yearly to monthly
% fImm(4 : age) = 1; % RR(0.75; 0.5 , 0.92) fraction fully protected by immunity based on RR of natural immunity (Beachler, 2017)
artHpvMult = hpv_hivMult(1 , :) * 0.25;
perPartnerHpv = 0.1; % high risk HPV transmission risk per month
rImmuneHiv = 3 ./ hpv_hivClear;
fImm(1 : age) = 1; % all infected individuals who clear HPV get natural immunity
lambdaMultImm(1 : 4) = 1 - 0.01;
lambdaMultImm(5 : 10) = 1 - logspace(log10(0.01) , log10(0.1) , 6);
lambdaMultImm(11 : age) = lambdaMultImm(10);
lambdaMultVax = ones(age , 2);
%%%%%
% load('HPV_calib.dat')
% kCin2_Cin3(: , 1) = HPV_calib(1 : age);
% kCin3_Cin2(: , 1) = HPV_calib(age + 1 : 2 * age);
% kCC_Cin3(: , 1) = HPV_calib(2 * age + 1 : 3 * age);
% kCin2_Cin3(: , 2) = HPV_calib(3 * age + 1 : 4 * age);
% kCin3_Cin2(: , 2) = HPV_calib(4 * age + 1 : 5 * age);
% kCC_Cin3(: , 2) = HPV_calib(5 * age + 1 : 6 * age);
% kCin2_Cin3(: , 3) = HPV_calib(6 * age + 1 : 7 * age);
% kCin3_Cin2(: , 3) = HPV_calib(7 * age + 1 : 8 * age);
% kCC_Cin3(: , 3) = HPV_calib(8 * age + 1 : 9 * age);
% rImmuneHiv = HPV_calib(9 * age + 1 : 9 * age + 1 + 3);
% c3c2Mults = HPV_calib(9 * age + 5 : 9 * age + 8);
% c2c1Mults = HPV_calib(9 * age + 9 : 9 * age + 12);
% artHpvMult = HPV_calib(9 * age + 13);
% perPartnerHpv = HPV_calib(9 * age + 14);
load('calibInitParams')
load('HPV_calib3.dat')
for i = 1 : 3
kCin2_Cin3(: , i) = HPV_calib3(i) .* kCin2_Cin3(: , i);
kCin3_Cin2(: , i) = HPV_calib3(3 + i) .* kCin3_Cin2(: , i);
kCC_Cin3(: , i) = HPV_calib3(6 + i) .* kCC_Cin3(: , i);
end
rImmuneHiv = HPV_calib3(10 : 13);
c3c2Mults = HPV_calib3(14 : 17);
c2c1Mults = HPV_calib3(18 : 21);
artHpvMult = HPV_calib3(22);
perPartnerHpv= HPV_calib3(23);
lambdaMultImm = HPV_calib3(24 : 39);
%%%%%
c = fix(clock);
currYear = c(1); % get the current year
vaxEff = 0.8;
t_linearWane = 20; % pick a multiple of 5
k_wane = - vaxEff / t_linearWane;
lambdaMultVax_Arr = {zeros(age , 2) , zeros(age , 2) , zeros(age , 2) , ...
zeros(age , 2)};
% 20 year waning
lambdaMultVax_Arr{1}(3 : 6 , 1) = vaxEff;
lambdaMultVax_Arr{1}(7 : 10 , 1) = vaxEff + k_wane * (5 : 5 : t_linearWane);
% 15 year waning
lambdaMultVax_Arr{2}(3 : 5 , 1) = vaxEff;
lambdaMultVax_Arr{2}(6 : 9 , 1) = vaxEff + k_wane * (5 : 5 : t_linearWane);
% 10 year waning
lambdaMultVax_Arr{3}(3 : 4 , 1) = vaxEff;
lambdaMultVax_Arr{3}(5 : 8 , 1) = vaxEff + k_wane * (5 : 5 : t_linearWane);
% 0 year waning
lambdaMultVax_Arr{4}(3 : age , 1) = vaxEff;
k_wane_d = [20 , 15 , 10 , 0];
vaxCover = [0 , 0.5 , 0.7, 0.9];
testParams = allcomb(vaxCover , 1 : length(lambdaMultVax_Arr));
% titles = {'noVax' , 'vax50' , 'vax70' , 'vax90'};
nTests = size(testParams , 1);
%%%%%%%
dim = [disease , viral , hpvTypes , hpvStates , periods , gender , age ,risk];
% run analyses
stepsPerYear = 6;
c = fix(clock);
currYear = c(1); % get the current year
% Initialize vectors
timeStep = 1 / stepsPerYear;
years = lastYear - currYear;
s = 1 : timeStep : years + 1;
hivOn = 1;
hpvOn = 1;
% Intervention start years
circStartYear = 1990;
vaxStartYear = 2017;
disp(['Simulating period from ' num2str(currYear) ' to ' num2str(lastYear) ...
' with ' num2str(stepsPerYear), ' steps per year.'])
vaxerAgerArray = cell(3 , 1);
% for n = 1 : length(testParams)
% vaxer = speye(length(currPop));
% vaxRate = testParams(n);
% at = @(x , y) sort(prod(dim)*(y-1) + x);
% susFemale = toInd(allcomb(1 : disease , 1 : viral , 1 , 1 , 1 : periods , 2 , 3 , 1 : risk));
% vaxdFemale = toInd(allcomb(1 : disease , 1 : viral , 1 , 9 , 1 : periods , 2 , 3 , 1 : risk));
% vaxer(at(vaxdFemale , susFemale)) = 1/5 .* vaxRate;
% vaxer(at(susFemale , susFemale)) = 1 - vaxRate .* 1/5;
% vaxerArray{n} = vaxer;
% end
for n = 1 : size(testParams , 1)
vaxerAger = ager;
vaxRate = testParams(n , 1);
at = @(x , y) sort(prod(dim)*(y-1) + x);
fromAge = toInd(allcomb(1 : disease , 1 : viral , 1 , 1 , 1 : periods , ...
2 , 2 , 1 : risk));
toAge = toInd(allcomb(1 : disease , 1 : viral , 1 , 1 , 1 : periods , ...
2 , 3 , 1 : risk));
toAgeVaxd = toInd(allcomb(1 : disease , 1 : viral , 1 , 9 , 1 : periods , ...
2 , 3 , 1 : risk));
vaxerAger(at(toAge , fromAge)) = (1 - vaxRate) * ager(at(toAge , fromAge));
vaxerAger(at(toAgeVaxd , fromAge)) = vaxRate * ager(at(toAge , fromAge)) ;
% vaxer(at(toAge , fromAge)) = 1 - vaxRate;
vaxerAgerArray{n} = vaxerAger;
end
% for males (future version?)
% susMale = toInd(allcomb(1 : disease , 1 : viral , 1 , 1 , 1 : periods , 1 , a , 1 : risk));
% vaxdMale = toInd(allcomb(1 : disease , 1 : viral , 5 , 6 , 1 : periods , 1 , a , 1 : risk));
% vaxer(vaxdMale , susMale) = V(2 , a);
% vaxer(susMale , susMale) = -V(2 , a);
%%
kCC_Cin3_Orig = kCC_Cin3;
kCC_Cin3 = kCC_Cin3_Orig .*0.5;
parfor n = 1 : nTests
vaxerAger = vaxerAgerArray{n};
k_wane = k_wane_d(testParams(n , 2));
lambdaMultVax = 1 - lambdaMultVax_Arr{testParams(n , 2)};
vaxRate = testParams(n , 1);
popVec = spalloc(years / timeStep , prod(dim) , 10 ^ 8);
popIn = currPop; % initial population to "seed" model
newHiv = zeros(length(s) - 1 , gender , age , risk);
newHpv = zeros(length(s) - 1 , gender , disease , age , risk);
newImmHpv = newHpv;
newVaxHpv = newHpv;
newCC = zeros(length(s) - 1 , disease , viral , hpvTypes , age);
ccDeath = newCC;
hivDeaths = zeros(length(s) - 1 , age);
deaths = zeros(size(popVec));
artTreatTracker = zeros(length(s) - 1 , disease , viral , gender , age , risk);
popVec(1 , :) = popIn;
tVec = linspace(currYear , lastYear , size(popVec , 1));
k = cumprod([disease , viral , hpvTypes , hpvStates , periods , gender , age]);
artDist = zeros(disease , viral , gender , age , risk); % initial distribution of inidividuals on ART = 0
%%
for i = 2 : length(s) - 1
year = currYear + s(i) - 1;
currStep = round((s(i) + currYear) * stepsPerYear);
tspan = [s(i) , s(i + 1)]; % evaluate diff eqs over one time interval
popIn = popVec(i - 1 , :);
if hpvOn
hystOption = 'on';
[~ , pop , newCC(i , : , : , : , :) , ccDeath(i , : , : , : , :)] ...
= ode4xtra(@(t , pop) ...
hpv(t , pop , immuneInds , infInds , cin1Inds , ...
cin2Inds , cin3Inds , normalInds , ccInds , ccRegInds , ccDistInds , ...
kInf_Cin1 , kCin1_Cin2 , kCin2_Cin3 , ...
kCin2_Cin1 , kCin3_Cin2 , kCC_Cin3 , kCin1_Inf ,...
rNormal_Inf , hpv_hivClear , c3c2Mults , ...
c2c1Mults , fImm , kRL , kDR , muCC , disease , viral , age , hpvTypes , ...
rImmuneHiv , vaccinated , hystOption) , tspan , popIn);
popIn = pop(end , :);
if any(pop(end , :) < 0)
disp('After hpv')
break
end
% [~ , pop] = ode4x(@(t , pop) hpvTreat(t , pop , disease , viral , hpvTypes , age , ...
% periods , detCC , hivCC , muCC , ccRInds , ccSusInds , ...
% hystPopInds , screenFreq , screenCover , hpvSens , ccTreat , ...
% cytoSens , cin1Inds , cin2Inds , cin3Inds , normalInds , getHystPopInds ,...
% OMEGA , leep , hystOption , year) , tspan , pop(end , :));
end
[~ , pop , newHpv(i , : , : , : , :) , newImmHpv(i , : , : , : , :) , ...
newVaxHpv(i , : , : , : , :) , newHiv(i , : , : , :)] = ...
ode4xtra(@(t , pop) mixInfect(t , pop , currStep , ...
gar , perPartnerHpv , lambdaMultImm , lambdaMultVax , artHpvMult , epsA_vec , epsR_vec , yr , modelYr1 , ...
circProtect , condProtect , condUse , actsPer , partnersM , partnersF , ...
hpv_hivMult , hpvSus , hpvImm , toHpv_Imm , hpvVaxd , hpvVaxd2 , toHpv , toHpv_ImmVax , ...
hivSus , toHiv , mCurr , fCurr , mCurrArt , fCurrArt , ...
betaHIVF2M , betaHIVM2F , disease , viral , gender , age , risk , hpvStates , hpvTypes , ...
hrInds , lrInds , hrlrInds , periods , startYear , stepsPerYear , year) , tspan , popIn);
popIn = pop(end , :); % for next mixing and infection module
if any(pop(end , :) < 0)
disp('After mixInfect')
break
end
if hivOn
[~ , pop , hivDeaths(i , :) , artTreat] =...
ode4xtra(@(t , pop) hiv(t , pop , vlAdvancer , artDist , muHIV , ...
kCD4 , disease , viral , gender , age , risk , k , hivInds , ...
stepsPerYear , year) , tspan , pop(end , :));
artTreatTracker(i , : , : , : , : ,:) = artTreat;
if any(pop(end , :) < 0)
disp('After hiv')
break
end
% [~ , artTreat] = ode4x(@(t , artDist) treatDist(t , popCopy(end , :) , year) , tspan , artDist);
% if size(artDistList) >= 20
% artDistList.remove(); % remove earlier artDist matrix more than "20 time steps old"
% else
% artDistList.add(artTreat);
% end
% artDist = calcDist(artDistList);
end
[~ , pop , deaths(i , :)] = ode4xtra(@(t , pop) bornAgeDie(t , pop , ...
ager , year , currStep , age , fertility , fertMat , hivFertPosBirth ,...
hivFertNegBirth , deathMat , circMat , vaxerAger , MTCTRate , circStartYear , ...
vaxStartYear , vaxRate , startYear , endYear , stepsPerYear) , tspan , pop(end , :));
if any(pop(end , :) < 0)
disp('After bornAgeDie')
break
end
% add results to population vector
popVec(i , :) = pop(end , :);
end
popLast = popVec(end , :);
popVec = sparse(popVec); % compress population vectors
filename = ['0.5 CIN3_CC' , 'Vax_' , num2str(vaxRate) , '_wane_' , ...
num2str(k_wane) , '.mat']; %sprintf('test_output%d.mat' , n);
parsave(filename , tVec , popVec , newHiv ,...
newImmHpv , newVaxHpv , newHpv , deaths , hivDeaths , ccDeath , ...
newCC , artTreatTracker , currYear , lastYear , popLast);
% savdir = 'H:\HHCoM Results';
% parsave(fullfile(savdir , 'resultsVax50') , 'tVec' , 'popVec' , 'newHiv' ,...
% 'newImmHpv' , 'newVaxHpv' , 'newHpv' , 'hivDeaths' , 'vaxRate' ,...
% 'newCC' , 'artTreatTracker' , 'startYear' , 'endYear' , 'popLast');
end
disp('Done')
%%
simVaxResultOut()