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genParamStruct.m
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genParamStruct.m
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% Save all potentially calibrated parameters into structure
function [paramsAll] = genParamStruct()
numParams = 39;
paramsAll = cell(numParams,1);
% partnersM, [age x risk], (hr range by age(15-19,20-24,25-29,30-44,45-79), mr % of hr, lr % of mr)
paramsAll{1}.name = 'partnersM'; paramsAll{1}.length = 7; ... %1 %24;
paramsAll{1}.lb = [0.20; 5.00; 6.25; 6.25; 5.00; 0.11; 0.15]; %ones(paramsAll{1}.length,1).*0.2;
%[ones(paramsAll{1}.length*(1/3),1).*0.01; ones(paramsAll{1}.length*(1/3),1).*0.01; ...
% ones(paramsAll{1}.length*(1/3),1).*0.5]; ... %0.1;
paramsAll{1}.ub = [9.15; 18.30; 37.50; 37.50; 18.00; 0.87; 0.75]; %ones(paramsAll{1}.length,1).*5.0;
%[ones(paramsAll{1}.length*(1/3),1).*0.99; ones(paramsAll{1}.length*(1/3),1).*0.99; ...
% ones(paramsAll{1}.length*(1/3),1).*60.0]; %15;
% partnersF, [age x risk], (hr range by age (15-19,20-24,25-29,30-44,45-79), mr % of hr, lr % of mr)
paramsAll{2}.name = 'partnersF'; paramsAll{2}.length = 7; ... %1 %24;
paramsAll{2}.lb = [2.25; 6.50; 5.00; 5.00; 5.00; 0.11; 0.15]; %ones(paramsAll{2}.length,1).*0.2;
%[ones(paramsAll{2}.length*(1/3),1).*0.01; ones(paramsAll{2}.length*(1/3),1).*0.01; ...
% ones(paramsAll{2}.length*(1/3),1).*0.5]; ... %0.1;
paramsAll{2}.ub = [13.50; 39.00; 28.50; 21.00; 15.00; 0.87; 0.75]; %ones(paramsAll{2}.length,1).*5.0;
%[ones(paramsAll{2}.length*(1/3),1).*0.99; ones(paramsAll{2}.length*(1/3),1).*0.99; ...
% ones(paramsAll{2}.length*(1/3),1).*60.0]; %15;
% % % riskDistM, [age x risk], (0 to 1) ***Note: functionality not implemented***
% % paramsAll{3}.name = 'riskDistM'; paramsAll{3}.length = 42; ...
% % paramsAll{3}.lb = [ones(paramsAll{3}.length*(1/3),1).*0.5; ones(paramsAll{3}.length*(2/3),1).*0.001]; ...
% % paramsAll{3}.ub = ones(paramsAll{3}.length,1);
%
% % % riskDistF, [3:age x risk], (0 to 1)
% % paramsAll{4}.name = 'riskDistF'; paramsAll{4}.length = 42; ...
% % paramsAll{4}.lb = [ones(paramsAll{4}.length*(1/3),1).*0.5; ones(paramsAll{4}.length*(2/3),1).*0.001]; ...
% % paramsAll{4}.ub = ones(paramsAll{4}.length,1);
% condUse, [1 x 1], (0.11 to 0.45)
paramsAll{5}.name = 'condUse'; paramsAll{5}.length = 1; ...
paramsAll{5}.lb = 0.11; ...
paramsAll{5}.ub = 0.45;
% epsA, [1 x 1], (0.1 to 0.6)
paramsAll{6}.name = 'epsA'; paramsAll{6}.length = 1; ... %3
paramsAll{6}.lb = ones(paramsAll{6}.length,1).*0.1; ...
paramsAll{6}.ub = ones(paramsAll{6}.length,1).*0.6;
% epsR, [1 x 1], (0.1 to 1)
paramsAll{7}.name = 'epsR'; paramsAll{7}.length = 1; ... %3
paramsAll{7}.lb = ones(paramsAll{7}.length,1).*0.1; ...
paramsAll{7}.ub = ones(paramsAll{7}.length,1);
% maleActs, [age x risk], (10-24 multiplier on females, 25-49 multiplier on females)
paramsAll{8}.name = 'maleActs'; paramsAll{8}.length = 2; ... %1 %42;
paramsAll{8}.lb = [0.75; 0.75]; %ones(paramsAll{8}.length,1).*0.2;
%[ones(paramsAll{8}.length*(1/3),1).*1.0; ones(paramsAll{8}.length*(1/3),1).*0.01; ...
% ones(paramsAll{8}.length*(1/3),1).*0.01]; ... %0.1;
paramsAll{8}.ub = [1.25; 1.25]; %ones(paramsAll{8}.length,1).*2.0;
%[ones(paramsAll{8}.length*(1/3),1).*90.0; ones(paramsAll{8}.length*(1/3),1).*0.99; ...
% ones(paramsAll{8}.length*(1/3),1).*0.99]; %15;
% femaleActs, [age x risk], (lr range by age (15-19,20-24,25-29,30-44,45-79))
paramsAll{9}.name = 'femaleActs'; paramsAll{9}.length = 5; ... %1 %42; ...
paramsAll{9}.lb = [53.13; 52.47; 42.15; 40.95; 39.53]; %ones(paramsAll{9}.length,1).*0.2;
%[ones(paramsAll{9}.length*(1/3),1).*1.0; ones(paramsAll{9}.length*(1/3),1).*0.01; ...
% ones(paramsAll{9}.length*(1/3),1).*0.01]; ... %0.1;
paramsAll{9}.ub = [88.56; 87.44; 70.25; 68.25; 65.88]; %ones(paramsAll{9}.length,1).*2.0;
%[ones(paramsAll{9}.length*(1/3),1).*90.0; ones(paramsAll{9}.length*(1/3),1).*0.99; ...
% ones(paramsAll{9}.length*(1/3),1).*0.99]; %15;
% perPartnerHpv_vax, [1 x 1], (0.01 to 0.85)
paramsAll{10}.name = 'perPartnerHpv_vax'; paramsAll{10}.length = 1; ...
paramsAll{10}.lb = 0.001; ...
paramsAll{10}.ub = 0.04;
% perPartnerHpv_nonV, [1 x 1], (0.001 to 1.0)
paramsAll{11}.name = 'perPartnerHpv_nonV'; paramsAll{11}.length = 1; ...
paramsAll{11}.lb = 0.001; ...
paramsAll{11}.ub = 1.0;
% % % hpv_hivMult, [dec CD4 x --hrHPV type--], (0.25x to 4x) ***Note: functionality not implemented***
% % paramsAll{12}.name = 'hpv_hivMult'; paramsAll{12}.length = 4; ...
% % paramsAll{12}.lb = ones(paramsAll{12}.length,1).*0.25; ...
% % paramsAll{12}.ub = ones(paramsAll{12}.length,1).*4.0;
% hpv_hivClear, [dec CD4], (0.25x to 4x)
paramsAll{14}.name = 'hpv_hivClear'; paramsAll{14}.length = 4; ...
paramsAll{14}.lb = [0.5 ; 0.01; 0.01; 0.01]; ... %ones(paramsAll{15}.length,1).*0.25;
paramsAll{14}.ub = [1.0; 0.99; 0.99; 0.99]; %ones(paramsAll{15}.length,1).*4.0;
% c3c2Mults, [dec CD4], (0.5x to 1x)
paramsAll{15}.name = 'c3c2Mults'; paramsAll{15}.length = 1; ...
paramsAll{15}.lb = 0.5; ...
paramsAll{15}.ub = 1.0;
% c2c1Mults, [dec CD4], (0.55x to 1x)
paramsAll{16}.name = 'c2c1Mults'; paramsAll{16}.length = 1; ...
paramsAll{16}.lb = 0.8; ...
paramsAll{16}.ub = 1.5;
% lambdaMultImm, [age x 1], (0.5 to 1.0)
paramsAll{18}.name = 'lambdaMultImm'; paramsAll{18}.length = 1; ...
paramsAll{18}.lb = ones(paramsAll{18}.length,1).*0.5; ...
paramsAll{18}.ub = ones(paramsAll{18}.length,1).*1.0;
% artHpvMult, [1 x 1], (1 to 2.32)
paramsAll{21}.name = 'artHpvMult'; paramsAll{21}.length = 1; ...
paramsAll{21}.lb = ones(paramsAll{21}.length,1).*1.0; ...
paramsAll{21}.ub = ones(paramsAll{21}.length,1).*2.32;
% % %kProgrsMult , [1 x 1] ***Note: functionality not implemented***
% % paramsAll{25}.name = 'kProgrsMult'; paramsAll{25}.length = 1; ...
% % paramsAll{25}.lb = ones(paramsAll{25}.length,1).*0.2; ...
% % paramsAll{25}.ub = ones(paramsAll{25}.length,1).*1.0;
% % %kRegrsMult , [1 x 1]
% % paramsAll{26}.name = 'kRegrsMult'; paramsAll{26}.length = 1; ...
% % paramsAll{26}.lb = ones(paramsAll{26}.length,1).*1.0; ...
% % paramsAll{26}.ub = ones(paramsAll{26}.length,1).*5.0;
% kCin1_InfMult , [1 x hpvTypeGroups]
paramsAll{27}.name = 'kCin1_InfMult'; paramsAll{27}.length = 2; ...
paramsAll{27}.lb = [0.4 ; 0.5]; ...
paramsAll{27}.ub = [1.5 ; 4.0];
% kCin2_Cin1Mult , [1 x hpvTypeGroups]
paramsAll{28}.name = 'kCin2_Cin1Mult'; paramsAll{28}.length = 2; ...
paramsAll{28}.lb = [1.0 ; 1.0]; ...
paramsAll{28}.ub = [10.0 ; 20.0];
% kCin3_Cin2Mult , [1 x hpvTypeGroups]
paramsAll{29}.name = 'kCin3_Cin2Mult'; paramsAll{29}.length = 2; ...
paramsAll{29}.lb = [0.5 ; 1.0]; ...
paramsAll{29}.ub = [3.0 ; 10.0];
% kCC_Cin3Mult , [1 x hpvTypeGroups]
paramsAll{30}.name = 'kCC_Cin3Mult'; paramsAll{30}.length = 2; ...
paramsAll{30}.lb = [0.8 ; 4.0]; ...
paramsAll{30}.ub = [8.0 ; 20.0];
% rNormal_InfMult , [1 x hpvTypeGroups]
paramsAll{31}.name = 'rNormal_InfMult'; paramsAll{31}.length = 2; ...
paramsAll{31}.lb = [0.8 ; 0.75]; ...
paramsAll{31}.ub = [2.8 ; 1.8];
% kInf_Cin1Mult , [1 x hpvTypeGroups]
paramsAll{32}.name = 'kInf_Cin1Mult'; paramsAll{32}.length = 2; ...
paramsAll{32}.lb = [1.0 ; 0.1]; ...
paramsAll{32}.ub = [3.5 ; 1.0];
% kCin1_Cin2Mult , [1 x hpvTypeGroups]
paramsAll{33}.name = 'kCin1_Cin2Mult'; paramsAll{33}.length = 2; ...
paramsAll{33}.lb = [0.05 ; 0.05]; ...
paramsAll{33}.ub = [2.0 ; 1.0];
% kCin2_Cin3Mult , [1 x hpvTypeGroups]
paramsAll{34}.name = 'kCin2_Cin3Mult'; paramsAll{34}.length = 2; ...
paramsAll{34}.lb = [0.05 ; 0.05]; ...
paramsAll{34}.ub = [1.5 ; 0.8];
% baseVagTrans , [1 x 2]
paramsAll{35}.name = 'baseVagTrans'; paramsAll{35}.length = 1; ...
paramsAll{35}.lb = [0.0004]; ...
paramsAll{35}.ub = [0.0020];
% fertDeclineProp , [1 x 2]
paramsAll{36}.name = 'fertDeclineProp'; paramsAll{36}.length = 2; ...
paramsAll{36}.lb = [0.35 ; 0.50]; ...
paramsAll{36}.ub = [0.75 ; 0.90];
% maleHpvClearMult , [1 x 1]
paramsAll{37}.name = 'maleHpvClearMult'; paramsAll{37}.length = 1; ...
paramsAll{37}.lb = [1.0]; ...
paramsAll{37}.ub = [3.5];
% c2c3Mults, [dec CD4], (1x to 1.66x)
paramsAll{38}.name = 'c2c3Mults'; paramsAll{38}.length = 1; ...
paramsAll{38}.lb = 1.2; ...
paramsAll{38}.ub = 1.66;
% c1c2Mults, [dec CD4], (1x to 1.66x)
paramsAll{39}.name = 'c1c2Mults'; paramsAll{39}.length = 1; ...
paramsAll{39}.lb = 0.75; ...
paramsAll{39}.ub = 1.4;