1277 Quarantine Effectiveness

cpp/models/abm/model.cpp

@@ -289,7 +289,7 @@ void Model::compute_exposure_caches(TimePoint t, TimeSpan dt)
                 assert(m_persons[i].get_location_model_id() == m_id && "Person is not in this model but still active.");
                 mio::abm::add_exposure_contribution(m_air_exposure_rates_cache[location],
                                                     m_contact_exposure_rates_cache[location], person,
-                                                    get_location(person.get_location()), t, dt);
+                                                    get_location(person.get_location()), parameters, t, dt);
             }
         } // implicit taskloop barrier
     } // implicit single barrier

cpp/models/abm/model_functions.cpp

@@ -98,7 +98,8 @@ void interact(PersonalRandomNumberGenerator& personal_rng, Person& person, const
 }
 
 void add_exposure_contribution(AirExposureRates& local_air_exposure, ContactExposureRates& local_contact_exposure,
-                               const Person& person, const Location& location, const TimePoint t, const TimeSpan dt)
+                               const Person& person, const Location& location, const Parameters& params,
+                               const TimePoint t, const TimeSpan dt)
 {
     if (person.get_location() != location.get_id()) {
         mio::log_debug("In add_exposure_contribution: Person {} is not at Location {}", person.get_id().get(),
@@ -110,16 +111,20 @@ void add_exposure_contribution(AirExposureRates& local_air_exposure, ContactExpo
         auto virus      = infection.get_virus_variant();
         auto age        = person.get_age();
         // average infectivity over the time step to second order accuracy using midpoint rule
+        const auto infectivity = infection.get_infectivity(t + dt / 2);
+        const auto quarantine_factor =
+            person.is_in_quarantine(t, params) ? (1.0 - params.get<QuarantineEffectiveness>()) : 1.0;
+
         for (CellIndex cell : person.get_cells()) {
+            auto air_contribution     = infectivity * quarantine_factor;
+            auto contact_contribution = infectivity * quarantine_factor;
+
             if (location.get_infection_parameters().get<UseLocationCapacityForTransmissions>()) {
-                local_air_exposure[{cell, virus}] +=
-                    infection.get_infectivity(t + dt / 2) *
-                    location.get_cells()[cell.get()].compute_space_per_person_relative();
+                air_contribution *= location.get_cells()[cell.get()].compute_space_per_person_relative();
             }
-            else {
-                local_air_exposure[{cell, virus}] += infection.get_infectivity(t + dt / 2);
-            }
-            local_contact_exposure[{cell, virus, age}] += infection.get_infectivity(t + dt / 2);
+
+            local_air_exposure[{cell, virus}] += air_contribution;
+            local_contact_exposure[{cell, virus, age}] += contact_contribution;
         }
     }
 }

cpp/models/abm/model_functions.h

@@ -61,11 +61,13 @@ ScalarType daily_transmissions_by_air(const AirExposureRates& rates, const CellI
  * @param[in, out] local_contact_exposure Exposure by rates contacts for the local population.
  * @param[in] person A person from the local population.
  * @param[in] location The person's current location.
+ * @param[in] params The parameter set of the Model.
  * @param[in] t Current Simulation time.
  * @param[in] dt Length of the current Simulation time step.
  */
 void add_exposure_contribution(AirExposureRates& local_air_exposure, ContactExposureRates& local_contact_exposure,
-                               const Person& person, const Location& location, const TimePoint t, const TimeSpan dt);
+                               const Person& person, const Location& location, const Parameters& params,
+                               const TimePoint t, const TimeSpan dt);
 
 /**
  * @brief Let a Person interact with the population at its current Location, possibly getting infected.

cpp/models/abm/parameters.h

@@ -530,6 +530,21 @@ struct QuarantineDuration {
     }
 };
 
+/**
+ * @brief Effectiveness of quarantine. 0.0 meaning no effect (percentage reduction of viral shed emission), 1.0 meaning full effect.
+ */
+struct QuarantineEffectiveness {
+    using Type = ScalarType;
+    static auto get_default(AgeGroup /*size*/)
+    {
+        return 0.0;
+    }
+    static std::string name()
+    {
+        return "QuarantineEffectivness";
+    }
+};
+
 /**
  * @brief Parameter for the exponential distribution to decide if a Person goes shopping.
  */
@@ -687,10 +702,10 @@ using ParametersBase =
                  TimeInfectedCriticalToRecovered, SymptomsPerInfectedNoSymptoms, SeverePerInfectedSymptoms,
                  CriticalPerInfectedSevere, DeathsPerInfectedSevere, DeathsPerInfectedCritical, ViralLoadDistributions,
                  InfectivityDistributions, VirusShedFactor, DetectInfection, MaskProtection, AerosolTransmissionRates,
-                 LockdownDate, QuarantineDuration, SocialEventRate, BasicShoppingRate, WorkRatio, SchoolRatio,
-                 GotoWorkTimeMinimum, GotoWorkTimeMaximum, GotoSchoolTimeMinimum, GotoSchoolTimeMaximum,
-                 AgeGroupGotoSchool, AgeGroupGotoWork, InfectionProtectionFactor, SeverityProtectionFactor,
-                 HighViralLoadProtectionFactor, TestData>;
+                 LockdownDate, QuarantineDuration, QuarantineEffectiveness, SocialEventRate, BasicShoppingRate,
+                 WorkRatio, SchoolRatio, GotoWorkTimeMinimum, GotoWorkTimeMaximum, GotoSchoolTimeMinimum,
+                 GotoSchoolTimeMaximum, AgeGroupGotoSchool, AgeGroupGotoWork, InfectionProtectionFactor,
+                 SeverityProtectionFactor, HighViralLoadProtectionFactor, TestData>;
 
 /**
  * @brief Maximum number of Person%s an infectious Person can infect at the respective Location.
@@ -984,6 +999,11 @@ class Parameters : public ParametersBase
             return true;
         }
 
+        if (this->get<QuarantineEffectiveness>() < 0.0 || this->get<QuarantineEffectiveness>() > 1.0) {
+            log_error("Constraint check: Parameter QuarantineEffectiveness not between {:d,:d}", 0.0, 1.0);
+            return true;
+        }
+
         return false;
     }
 

cpp/tests/abm_helpers.cpp

@@ -61,9 +61,9 @@ void interact_testing(mio::abm::PersonalRandomNumberGenerator& personal_rng, mio
     std::for_each(local_contact_exposure.begin(), local_contact_exposure.end(), [](auto& r) {
         r = 0.0;
     });
-    // caclculate current exposures
+    // calculate current exposures
     for (const mio::abm::Person& p : local_population) {
-        add_exposure_contribution(local_air_exposure, local_contact_exposure, p, location, t, dt);
+        add_exposure_contribution(local_air_exposure, local_contact_exposure, p, location, global_parameters, t, dt);
     }
     // run interaction
     mio::abm::interact(personal_rng, person, location, local_air_exposure, local_contact_exposure, t, dt,

cpp/tests/test_abm_location.cpp

@@ -103,6 +103,7 @@ TEST_F(TestLocation, interact)
 
     // Setup location with some chance of exposure
     mio::abm::Location location(mio::abm::LocationType::Work, 0, num_age_groups);
+    location.get_infection_parameters().get<mio::abm::UseLocationCapacityForTransmissions>() = true;
     auto infected1 = make_test_person(this->get_rng(), location, age_group_15_to_34,
                                       mio::abm::InfectionState::InfectedNoSymptoms, t, params);
     auto infected2 = make_test_person(this->get_rng(), location, age_group_80_plus,
@@ -185,4 +186,4 @@ TEST_F(TestLocation, adjustContactRates)
     auto adjusted_contacts_rate =
         loc.get_infection_parameters().get<mio::abm::ContactRates>()[{mio::AgeGroup(0), mio::AgeGroup(0)}];
     EXPECT_EQ(adjusted_contacts_rate, 2);
-}
+}

cpp/tests/test_abm_model.cpp

@@ -691,6 +691,8 @@ TEST_F(TestModel, checkParameterConstraints)
     params.get<mio::abm::MaskProtection>()[mio::abm::MaskType::Community] = 0.5;
     params.get<mio::abm::MaskProtection>()[mio::abm::MaskType::FFP2]      = 0.6;
     params.get<mio::abm::MaskProtection>()[mio::abm::MaskType::Surgical]  = 0.7;
+    params.get<mio::abm::QuarantineEffectiveness>()                       = 0.5;
+    params.get<mio::abm::QuarantineDuration>()                            = mio::abm::days(14);
     params.get<mio::abm::LockdownDate>()                                  = mio::abm::TimePoint(0);
     ASSERT_EQ(params.check_constraints(), false);
 
@@ -789,6 +791,12 @@ TEST_F(TestModel, checkParameterConstraints)
     EXPECT_TRUE(params.check_constraints());
     params.get<mio::abm::MaskProtection>()[mio::abm::MaskType::Surgical] = 0.7;
 
+    params.get<mio::abm::QuarantineEffectiveness>() = -0.1;
+    EXPECT_TRUE(params.check_constraints());
+    params.get<mio::abm::QuarantineEffectiveness>() = 1.5;
+    EXPECT_TRUE(params.check_constraints());
+    params.get<mio::abm::QuarantineEffectiveness>() = 0.8;
+
     params.get<mio::abm::LockdownDate>() = mio::abm::TimePoint(-2);
     EXPECT_TRUE(params.check_constraints());
     mio::set_log_level(mio::LogLevel::warn);

pycode/memilio-surrogatemodel/memilio/surrogatemodel_test/test_surrogatemodel_ode_secir_groups.py

@@ -502,6 +502,7 @@ def test_network_fit(self, mock_population, mock_baseline, mock_minimum):
             model.network_fit(
                 path=self.path, model=md,
                 modeltype='classic', training_parameter=training_parameter, filename="data_secir_groups.pickle")
+
         # check error message
         error_message_part1 = "[Errno 2] No such file or directory"
         error_message_part2 = self.path