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yearly branch update 28nov2023
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@janne-estill
janne-estill committed Nov 28, 2023
1 parent b2d8b24 commit 3080f07
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Showing 2 changed files with 27 additions and 23 deletions.
12 changes: 6 additions & 6 deletions src/hiv-ops.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -119,24 +119,24 @@ void GetOlderOperation::ProcessAgent(Agent* agent) {
// year_population_category =
// sim->GetParam()->Get<SimParam>()->ComputeYearPopulationCategory(year,
// person->age_, person->sex_);
if (year < (2003 - 1975) * 12) { // 2003) { // Prior to 2003
if (year < 2003) { // Prior to 2003
year_population_category =
0; // All (No difference in ART between people. ART not available.)
} else if (year < (2011 - 2003) * 12) { // 2011) { // Between 2003 and
} else if (year < 2011) { // Between 2003 and
// 2010
if (person->sex_ == Sex::kFemale && person->age_ >= 15 * 12 and
if (person->sex_ == Sex::kFemale && person->age_ >= 15 and
person->age_ <= 40) {
year_population_category = 1; // Female between 15 and 40
} else if (person->age_ < 15 * 12) {
} else if (person->age_ < 15) {
year_population_category = 2; // Child
} else {
year_population_category = 3; // Others (Male over 15 and Female over 40)
}
} else { // After 2011
if (person->sex_ == Sex::kFemale && person->age_ >= 15 * 12 and
if (person->sex_ == Sex::kFemale && person->age_ >= 15 and
person->age_ <= 40) {
year_population_category = 4; // Female between 15 and 40
} else if (person->age_ < 15 * 12) {
} else if (person->age_ < 15 ) {
year_population_category = 5; // Child
} else {
year_population_category =
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38 changes: 21 additions & 17 deletions src/sim-param.h
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Original file line number Diff line number Diff line change
Expand Up @@ -63,18 +63,18 @@ class SimParam : public ParamGroup {
// Mortality rate by age. Size(mortality_rate_by_age) must be equal to
// 1+size(mortality_rate_age_transition).
std::vector<int> mortality_rate_age_transition{15, 50, 90};
std::vector<float> mortality_rate_by_age{0.01, 0.005, 0.05, 1.0};
std::vector<float> mortality_rate_by_age{0.0, 0.0, 0.0, 0.0}; //0.01, 0.005, 0.05, 1.0};
// Test - No death
// std::vector<float> mortality_rate_by_age{0.0, 0.0, 0.0, 0.0};

// HIV-related mortality. For Healthy, Acute, Chronic, Treated, Failing states
std::vector<float> hiv_mortality_rate{0.0, 0.0, 0.05, 0.01, 0.1};
//std::vector<float> hiv_mortality_rate{0.0, 0.0, 0.05, 0.01, 0.1};
// Test - No death
// std::vector<float> hiv_mortality_rate{0.0, 0.0, 0.0, 0.0, 0.0};
std::vector<float> hiv_mortality_rate{0.0, 0.0, 0.0, 0.0, 0.0};

// AM: Probability to migrate
// TO DO AM: Make this probability dependent on the origin location?
float migration_probability = 0.01; // 0.0; // No Mogration //0.01;
float migration_probability = 0.0; //0.01; // 0.0; // No Mogration //0.01;
// AM: Migration year index
const std::vector<int> migration_year_transition{1960};
// AM: Migration Matrix. Year index x Location x Location
Expand Down Expand Up @@ -135,13 +135,14 @@ class SimParam : public ParamGroup {

// Mean number of sexual acts with regular partner per year.
// const float no_regular_acts_mean = 50.0; // 150;
const std::vector<float> no_regular_acts_mean{50, 47, 44, 41, 38, 34, 31,
28, 25, 22, 19, 16, 12};
const std::vector<float> no_regular_acts_mean{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
//50, 47, 44, 41, 38, 34, 31,
// 28, 25, 22, 19, 16, 12};
//{90, 84, 79, 73, 68, 62, 56, 51, 45, 39, 34, 28, 22};

// AM: Probability of getting infected depends on
// 1) disease state, 2) sex of partners Male-to-female
float coef_infection_probability = 2;
float coef_infection_probability = 0;
float infection_probability_acute_mf = 9.3e-3 * coef_infection_probability;
float infection_probability_chronic_mf = 1.9e-3 * coef_infection_probability;
float infection_probability_treated_mf = 1.3e-4 * coef_infection_probability;
Expand Down Expand Up @@ -177,7 +178,7 @@ class SimParam : public ParamGroup {
}};

// Number of locations
int nb_locations = Location::kLocLast; // 1; //Location::kLocLast;
int nb_locations = 1; //Location::kLocLast; // 1; //Location::kLocLast;

// AM: Location Mixing Matrix used for casual partner selection.
// Location->Location
Expand Down Expand Up @@ -223,9 +224,10 @@ class SimParam : public ParamGroup {

// Districts where HIV infected agents are initially located
const std::vector<bool> seed_districts{
false, true, false, false, false, false, false, false, false, false,
true, false, true, false, true, true, true, true, true, true,
true, true, true, true, true, true, true, true, false};
true};
// false, true, false, false, false, false, false, false, false, false,
// true, false, true, false, true, true, true, true, true, true,
// true, true, true, true, true, true, true, true, false};

// One Location
/*const std::vector<bool> seed_districts{
Expand All @@ -237,7 +239,7 @@ class SimParam : public ParamGroup {
// typical birth rate in the region. We substracted 0.06 to account for child
// motability and reach a realistic demographic development from 1960-2020.
// Parameter 0.21 is used in Janne's R implementation.
float give_birth_probability = 0.188; // 0.18
float give_birth_probability = 0.0; //0.188; // 0.18

// AM : Probability for agent to be infected at birth, if its mother is
// infected and treated
Expand All @@ -260,9 +262,10 @@ class SimParam : public ParamGroup {
// depending on year (see sociobehavioural_risk_year_transition) and health
// state (Healthy, Acute, Chronic, Treated, Failing)
const std::vector<std::vector<float>> sociobehavioural_risk_probability{
{0.05, 0.5, 0.5, 0.5, 0.5}, {0.05, 0.05, 0.05, 0.05, 0.05}};
{0.0, 0.0, 0.0, 0.0, 0.0}, {0.0, 0.0, 0.0, 0.0, 0.0}};
//{0.05, 0.5, 0.5, 0.5, 0.5}, {0.05, 0.05, 0.05, 0.05, 0.05}};

float biomedical_risk_probability = 0.05;
float biomedical_risk_probability = 0.0; //0.05;

// Age distribution for population initialization. Given in a summed up form.
// Each vector component corresponds to a age bin of 5 years, e.g. x1 (0-5),
Expand All @@ -278,9 +281,10 @@ class SimParam : public ParamGroup {
// Location distribution for population initialization, same logic as for age
// distribution.
const std::vector<float> location_distribution{
0.012, 0.03, 0.031, 0.088, 0.104, 0.116, 0.175, 0.228, 0.273, 0.4,
0.431, 0.453, 0.498, 0.517, 0.54, 0.569, 0.645, 0.679, 0.701, 0.736,
0.794, 0.834, 0.842, 0.86, 0.903, 0.925, 0.995, 1, 1};
1};
// 0.012, 0.03, 0.031, 0.088, 0.104, 0.116, 0.175, 0.228, 0.273, 0.4,
// 0.431, 0.453, 0.498, 0.517, 0.54, 0.569, 0.645, 0.679, 0.701, 0.736,
// 0.794, 0.834, 0.842, 0.86, 0.903, 0.925, 0.995, 1, 1};
// One Location
/*const std::vector<float> location_distribution{
1.0, 1.0};*/
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