846 adjust naming and assignment of abm age groups (#871)

Author: khoanguyen-dev

cpp/examples/abm_history_object.cpp

@@ -61,14 +61,14 @@ int main()
 {
     // This is a minimal example with children and adults < 60y.
     // We divided them into 4 different age groups, which are defined as follows:
-    const size_t NUM_AGE_GROUPS   = 4;
-    const auto AGE_GROUP_0_TO_4   = mio::AgeGroup(NUM_AGE_GROUPS - 4);
-    const auto AGE_GROUP_5_TO_14  = mio::AgeGroup(NUM_AGE_GROUPS - 3);
-    const auto AGE_GROUP_15_TO_34 = mio::AgeGroup(NUM_AGE_GROUPS - 2);
-    const auto AGE_GROUP_35_TO_59 = mio::AgeGroup(NUM_AGE_GROUPS - 1);
+    size_t num_age_groups         = 4;
+    const auto age_group_0_to_4   = mio::AgeGroup(0);
+    const auto age_group_5_to_14  = mio::AgeGroup(1);
+    const auto age_group_15_to_34 = mio::AgeGroup(2);
+    const auto age_group_35_to_59 = mio::AgeGroup(3);
 
     // Create the world with 4 age groups.
-    auto world = mio::abm::World(NUM_AGE_GROUPS);
+    auto world = mio::abm::World(num_age_groups);
 
     // Set same infection parameter for all age groups. For example, the incubation period is 4 days.
     world.parameters.get<mio::abm::IncubationPeriod>() = 4.;
@@ -77,13 +77,13 @@ int main()
     int n_households = 3;
 
     // For more than 1 family households we need families. These are parents and children and randoms (which are distributed like the data we have for these households).
-    auto child = mio::abm::HouseholdMember(NUM_AGE_GROUPS); // A child is 50/50% 0-4 or 5-14.
-    child.set_age_weight(AGE_GROUP_0_TO_4, 1);
-    child.set_age_weight(AGE_GROUP_5_TO_14, 1);
+    auto child = mio::abm::HouseholdMember(num_age_groups); // A child is 50/50% 0-4 or 5-14.
+    child.set_age_weight(age_group_0_to_4, 1);
+    child.set_age_weight(age_group_5_to_14, 1);
 
-    auto parent = mio::abm::HouseholdMember(NUM_AGE_GROUPS); // A parent is 50/50% 15-34 or 35-59.
-    parent.set_age_weight(AGE_GROUP_15_TO_34, 1);
-    parent.set_age_weight(AGE_GROUP_35_TO_59, 1);
+    auto parent = mio::abm::HouseholdMember(num_age_groups); // A parent is 50/50% 15-34 or 35-59.
+    parent.set_age_weight(age_group_15_to_34, 1);
+    parent.set_age_weight(age_group_35_to_59, 1);
 
     // Two-person household with one parent and one child.
     auto twoPersonHousehold_group = mio::abm::HouseholdGroup();
@@ -152,10 +152,10 @@ int main()
         person.set_assigned_location(hospital);
         person.set_assigned_location(icu);
         //assign work/school to people depending on their age
-        if (person.get_age() == AGE_GROUP_5_TO_14) {
+        if (person.get_age() == age_group_5_to_14) {
             person.set_assigned_location(school);
         }
-        if (person.get_age() == AGE_GROUP_15_TO_34 || person.get_age() == AGE_GROUP_35_TO_59) {
+        if (person.get_age() == age_group_15_to_34 || person.get_age() == age_group_35_to_59) {
             person.set_assigned_location(work);
         }
     }

cpp/models/abm/README.md

@@ -82,8 +82,8 @@ child.set_age_weight(age_group_0_to_4, 1);
 child.set_age_weight(age_group_0_to_4, 1);
 
 auto parent = mio::abm::HouseholdMember(num_age_groups);
-parent.set_age_weight(AGE_GROUP_15_TO_34, 1);
-parent.set_age_weight(AGE_GROUP_35_TO_59, 1);
+parent.set_age_weight(age_groups_15_to_34, 1);
+parent.set_age_weight(age_groups_35_to_59, 1);
 
 // Two-person household with one parent and one child.
 auto twoPersonHousehold_group = mio::abm::HouseholdGroup();

cpp/models/abm/household.h

@@ -68,6 +68,7 @@ class HouseholdMember
      */
     void set_age_weight(mio::AgeGroup age_group, int weight)
     {
+        assert((size_t)age_group.size < m_age_weights.numel());
         m_age_weights[age_group] = weight;
     }
 

cpp/models/abm/infection.cpp

@@ -32,6 +32,7 @@ Infection::Infection(Person::RandomNumberGenerator& rng, VirusVariant virus, Age
     : m_virus_variant(virus)
     , m_detected(detected)
 {
+    assert((size_t)age.size < (size_t)params.get_num_groups());
     m_viral_load.start_date = draw_infection_course(rng, age, params, init_date, init_state, latest_exposure);
 
     auto vl_params                    = params.get<ViralLoadDistributions>()[{virus, age}];
@@ -115,6 +116,7 @@ TimePoint Infection::draw_infection_course(Person::RandomNumberGenerator& rng, A
                                            TimePoint init_date, InfectionState init_state,
                                            std::pair<ExposureType, TimePoint> latest_protection)
 {
+    assert((size_t)age.size < (size_t)params.get_num_groups());
     TimePoint start_date = draw_infection_course_backward(rng, age, params, init_date, init_state);
     draw_infection_course_forward(rng, age, params, init_date, init_state, latest_protection);
     return start_date;
@@ -124,6 +126,7 @@ void Infection::draw_infection_course_forward(Person::RandomNumberGenerator& rng
                                               const Parameters& params, TimePoint init_date, InfectionState start_state,
                                               std::pair<ExposureType, TimePoint> latest_exposure)
 {
+    assert((size_t)age.size < (size_t)params.get_num_groups());
     auto t = init_date;
     TimeSpan time_period{}; // time period for current infection state
     InfectionState next_state{start_state}; // next state to enter
@@ -211,6 +214,7 @@ TimePoint Infection::draw_infection_course_backward(Person::RandomNumberGenerato
                                                     const Parameters& params, TimePoint init_date,
                                                     InfectionState init_state)
 {
+    assert((size_t)age.size < (size_t)params.get_num_groups());
     auto start_date = init_date;
     TimeSpan time_period{}; // time period for current infection state
     InfectionState previous_state{init_state}; // next state to enter

cpp/models/abm/location.cpp

@@ -58,6 +58,7 @@ Location Location::copy_location_without_persons(size_t num_agegroups)
 ScalarType Location::transmission_contacts_per_day(uint32_t cell_index, VirusVariant virus, AgeGroup age_receiver,
                                                    size_t num_agegroups) const
 {
+    assert((size_t)age_receiver.size < num_agegroups);
     ScalarType prob = 0;
     for (uint32_t age_transmitter = 0; age_transmitter != num_agegroups; ++age_transmitter) {
         prob += m_cells[cell_index].m_cached_exposure_rate_contacts[{virus, static_cast<AgeGroup>(age_transmitter)}] *

cpp/models/abm/testing_strategy.cpp

@@ -43,6 +43,7 @@ bool TestingCriteria::operator==(const TestingCriteria& other) const
 
 void TestingCriteria::add_age_group(const AgeGroup age_group)
 {
+    
     m_ages.insert(static_cast<size_t>(age_group));
 }