forked from ICRC-Models/HHCoM
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsimVaxCalib.m
203 lines (184 loc) · 8.91 KB
/
simVaxCalib.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
% 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 = 2081;
disp('Start up')
% load variables
paramDir = [pwd , '\Params\'];
load([paramDir, 'general'])
% load population
popIn = load('H:\HHCoM_Results\toNow');
currPop = popIn.popLast;
%%%%%%%
fImm(1 : age) = 1; % all infected individuals who clear HPV get natural immunity
%%%%%
%% use calibrated parameters
load([paramDir , 'General'])
load([paramDir , 'calibratedParams'])
maxRateM_vec = [0.45 , 0.45];% maxRateM_arr{sim};
maxRateF_vec = [0.6 , 0.6];% maxRateF_arr{sim};
maxRateM1 = 1 - exp(-maxRateM_vec(1));
maxRateM2 = 1 - exp(-maxRateM_vec(2));
maxRateF1 = 1 - exp(-maxRateF_vec(1));
maxRateF2 = 1 - exp(-maxRateF_vec(2));
%%%%%
% 90% efficacy against 70% of CC types, 100% efficacy against 70% of types, ...
% 100% efficacy against 90% of types
vaxEff = [0.9 * 0.7 , 0.7 , 0.9];
t_linearWane = 20; % pick a multiple of 5
k_wane = - vaxEff / t_linearWane;
vaxCover = [0 , 0.7 , 0.9];
testParams = allcomb(vaxCover , vaxEff);
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 = currYear;
disp(['Simulating period from ' num2str(currYear) ' to ' num2str(lastYear) ...
' with ' num2str(stepsPerYear), ' steps per year.'])
fromNonV = toInd(allcomb(1 : disease , 1 : viral , 1 , 1 , 1 , ...
2 , 3 , 1 : risk));
toV = toInd(allcomb(1 : disease , 1 : viral , 1 , 9 , 1 , ...
2 , 3 , 1 : risk));
import java.util.LinkedList
artDistList = LinkedList();
%%
parfor n = 1 : nTests
vaxerAger = ager;% vaxerAgerArray{n};
vaxMat = vaxMatArray{n};
vaxEff = testParams(n , 2);
lambdaMultVax = 1 - lambdaMultVaxMat(: , n);
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 , hpvTypes , age);
ccDeath = newCC;
ccTreated = zeros(length(s) - 1 , disease , hpvTypes , age , 3); % 3 cancer stages: local, regional, distant
hivDeaths = zeros(length(s) - 1 , gender , age);
deaths = zeros(size(popVec));
vaxd = zeros(length(s) - 1 , 1);
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) * 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 , : , : , :) , ...
ccTreated(i , : , : , : , :)] ...
= ode4xtra(@(t , pop) ...
hpv(t , pop , immuneInds , infInds , cin1Inds , ...
cin2Inds , cin3Inds , normalInds , ccInds , ccRegInds , ccDistInds , ...
ccTreatedInds , kInf_Cin1 , kCin1_Cin2 , kCin2_Cin3 , ...
kCin2_Cin1 , kCin3_Cin2 , kCC_Cin3 , kCin1_Inf ,...
rNormal_Inf , hpv_hivClear , c3c2Mults , ...
c2c1Mults , fImm , kRL , kDR , muCC , kCCDet , ...
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 , perPartnerHpv_lr , perPartnerHpv_nonV , ...
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 , ...
toHpv_ImmVaxNonV , 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) hiv2a(t , pop , vlAdvancer , artDist , muHIV , ...
kCD4 , maxRateM1 , maxRateM2 , maxRateF1 , maxRateF2 , disease , ...
viral , gender , age , risk , k , hivInds , ...
stepsPerYear , year) , tspan , pop(end , :));
artTreatTracker(i , : , : , : , : ,:) = artTreat;
artDistList.add(artTreat);
if size(artDist) >= stepsPerYear * 5
artDistList.remove(); % remove CD4 and VL distribution info for people initiating ART more than 5 years ago
end
artDist = calcDist(artDistList , disease , viral , gender , age , ...
risk);
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) ...
bornAgeDieRisk(t , pop , ager , year , currStep , gender , age , risk , fertility , ...
fertMat , fertMat2 , hivFertPosBirth ,hivFertNegBirth , hivFertPosBirth2 , ...
hivFertNegBirth2 , deathMat , circMat , ...
vaxerAger , vaxMat , MTCTRate , circStartYear , ageInd ,...
riskInd , riskDist , startYear , endYear, stepsPerYear) , tspan , pop(end , :));
if any(pop(end , :) < 0)
disp('After bornAgeDieRisk')
break
end
fracVaxd = sum(pop(end , toV) , 2) / (sum(pop(end , fromNonV) , 2) + sum(pop(end , toV) , 2));
if fracVaxd < vaxRate
vaxCover = max(0 , (vaxRate - fracVaxd) ./ (1 - fracVaxd));
pop(end , toV) = pop(end , toV) + pop(end , fromNonV) .* vaxCover;
pop(end , fromNonV) = pop(end , fromNonV) .* (1 - vaxCover);
vaxd(i , :) = sumall(pop(end , fromNonV).* vaxCover);
end
% add results to population vector
popVec(i , :) = pop(end , :);
end
popLast = popVec(end , :);
popVec = sparse(popVec); % compress population vectors
filename = ['CEA_VaxCover_' , num2str(vaxRate) , '_Eff_' , ...
num2str(vaxEff) , '.mat']; %sprintf('test_output%d.mat' , n);
parsave(filename , tVec , popVec , newHiv ,...
newImmHpv , newVaxHpv , newHpv , deaths , hivDeaths , ccDeath , ...
newCC , artTreatTracker , vaxd , ccTreated , ...
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')