932 Get_default of Parameter HighViralLoadProtectionFactor doesn't work as expected

cpp/models/abm/infection.cpp

@@ -38,8 +38,8 @@ Infection::Infection(PersonalRandomNumberGenerator& rng, VirusVariant virus, Age
     auto vl_params                    = params.get<ViralLoadDistributions>()[{virus, age}];
     ScalarType high_viral_load_factor = 1;
     if (latest_exposure.first != ExposureType::NoProtection) {
-        high_viral_load_factor -=
-            params.get<HighViralLoadProtectionFactor>()(init_date.days() - latest_exposure.second.days());
+        high_viral_load_factor -= params.get<HighViralLoadProtectionFactor>()[{latest_exposure.first, age, virus}](
+            init_date.days() - latest_exposure.second.days());
     }
     m_viral_load.peak = vl_params.viral_load_peak.get_distribution_instance()(rng, vl_params.viral_load_peak.params) *
                         high_viral_load_factor;

cpp/models/abm/parameters.h

@@ -296,13 +296,14 @@ struct SeverityProtectionFactor {
 };
 
 /**
- * @brief Personal protective factor against high viral load. Its value is between 0 and 1.
+ * @brief Personal protective factor against high viral load, which depends on #ExposureType,
+ * #AgeGroup and #VirusVariant. Its value is between 0 and 1.
  */
 struct HighViralLoadProtectionFactor {
-    using Type = InputFunctionForProtectionLevel;
-    static auto get_default()
+    using Type = CustomIndexArray<InputFunctionForProtectionLevel, ExposureType, AgeGroup, VirusVariant>;
+    static auto get_default(AgeGroup size)
     {
-        return Type([](ScalarType /*days*/) -> ScalarType {
+        return Type({ExposureType::Count, size, VirusVariant::Count}, [](ScalarType /*days*/) -> ScalarType {
             return 0;
         });
     }

cpp/simulations/abm.cpp

@@ -468,12 +468,6 @@ void set_parameters(mio::abm::Parameters params)
 
     params.set<mio::abm::IncubationPeriod>({{mio::abm::VirusVariant::Count, mio::AgeGroup(num_age_groups)}, 4.});
 
-    // Set protection level from high viral load. Information based on: https://doi.org/10.1093/cid/ciaa886
-    params.get<mio::abm::HighViralLoadProtectionFactor>() = [](ScalarType days) -> ScalarType {
-        return mio::linear_interpolation_of_data_set<ScalarType, ScalarType>(
-            {{0, 0.863}, {1, 0.969}, {7, 0.029}, {10, 0.002}, {14, 0.0014}, {21, 0}}, days);
-    };
-
     //0-4
     params.get<mio::abm::InfectedNoSymptomsToSymptoms>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}]  = 0.276;
     params.get<mio::abm::InfectedNoSymptomsToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.092;

cpp/simulations/abm_braunschweig.cpp

@@ -399,12 +399,6 @@ void set_parameters(mio::abm::Parameters params)
 
     params.set<mio::abm::IncubationPeriod>({{mio::abm::VirusVariant::Count, mio::AgeGroup(num_age_groups)}, 4.});
 
-    // Set protection level from high viral load. Information based on: https://doi.org/10.1093/cid/ciaa886
-    params.get<mio::abm::HighViralLoadProtectionFactor>() = [](ScalarType days) -> ScalarType {
-        return mio::linear_interpolation_of_data_set<ScalarType, ScalarType>(
-            {{0, 0.863}, {1, 0.969}, {7, 0.029}, {10, 0.002}, {14, 0.0014}, {21, 0}}, days);
-    };
-
     //0-4
     params.get<mio::abm::InfectedNoSymptomsToSymptoms>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}]  = 0.276;
     params.get<mio::abm::InfectedNoSymptomsToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.092;

cpp/tests/test_abm_infection.cpp

@@ -1,7 +1,7 @@
 /*
 * Copyright (C) 2020-2024 MEmilio
 *
-* Authors: David Kerkmann
+* Authors: David Kerkmann, Khoa Nguyen
 *
 * Contact: Martin J. Kuehn <[email protected]>
 *
@@ -82,7 +82,8 @@ TEST(TestInfection, init)
                                                       virus_variant_test}] = [](ScalarType days) -> ScalarType {
         return mio::linear_interpolation_of_data_set<ScalarType, ScalarType>({{0, 0.91}, {30, 0.81}}, days);
     };
-    params.get<mio::abm::HighViralLoadProtectionFactor>() = [](ScalarType days) -> ScalarType {
+    params.get<mio::abm::HighViralLoadProtectionFactor>()[{mio::abm::ExposureType::GenericVaccine, age_group_test,
+                                                           virus_variant_test}] = [](ScalarType days) -> ScalarType {
         return mio::linear_interpolation_of_data_set<ScalarType, ScalarType>({{0, 0.91}, {30, 0.81}}, days);
     };
     auto infection_w_previous_exp =
@@ -183,12 +184,15 @@ TEST(TestInfection, getPersonalProtectiveFactor)
 
     mio::abm::Parameters params = mio::abm::Parameters(num_age_groups);
     // Test default parameter functions
-    auto defaut_infection_protection = params.get<mio::abm::InfectionProtectionFactor>()[{
+    auto defaut_infection_protection       = params.get<mio::abm::InfectionProtectionFactor>()[{
         mio::abm::ExposureType::GenericVaccine, mio::AgeGroup(0), mio::abm::VirusVariant::Wildtype}](0);
-    auto defaut_severity_protection  = params.get<mio::abm::SeverityProtectionFactor>()[{
+    auto defaut_severity_protection        = params.get<mio::abm::SeverityProtectionFactor>()[{
         mio::abm::ExposureType::GenericVaccine, mio::AgeGroup(0), mio::abm::VirusVariant::Wildtype}](0);
-    ASSERT_NEAR(defaut_infection_protection, 0, 0.0001);
-    ASSERT_NEAR(defaut_severity_protection, 0, 0.0001);
+    auto defaut_high_viral_load_protection = params.get<mio::abm::HighViralLoadProtectionFactor>()[{
+        mio::abm::ExposureType::GenericVaccine, mio::AgeGroup(0), mio::abm::VirusVariant::Wildtype}](0);
+    EXPECT_NEAR(defaut_infection_protection, 0, 0.0001);
+    EXPECT_NEAR(defaut_severity_protection, 0, 0.0001);
+    EXPECT_NEAR(defaut_high_viral_load_protection, 0, 0.0001);
 
     // Test linear interpolation with one node
     mio::set_log_level(mio::LogLevel::critical); //this throws an error either way
@@ -198,7 +202,7 @@ TEST(TestInfection, getPersonalProtectiveFactor)
         return mio::linear_interpolation_of_data_set<ScalarType, ScalarType>({{2, 0.91}}, days);
     };
     auto t = mio::abm::TimePoint(6 * 24 * 60 * 60);
-    ASSERT_NEAR(person.get_protection_factor(t, mio::abm::VirusVariant::Wildtype, params), 0, 0.001);
+    EXPECT_NEAR(person.get_protection_factor(t, mio::abm::VirusVariant::Wildtype, params), 0, 0.001);
     mio::set_log_level(mio::LogLevel::warn); //this throws an error either way
     params.get<mio::abm::InfectionProtectionFactor>()[{mio::abm::ExposureType::GenericVaccine, person.get_age(),
                                                        mio::abm::VirusVariant::Wildtype}] =
@@ -210,7 +214,9 @@ TEST(TestInfection, getPersonalProtectiveFactor)
         [](ScalarType days) -> ScalarType {
         return mio::linear_interpolation_of_data_set<ScalarType, ScalarType>({{2, 0.91}, {30, 0.81}}, days);
     };
-    params.get<mio::abm::HighViralLoadProtectionFactor>() = [](ScalarType days) -> ScalarType {
+    params.get<mio::abm::HighViralLoadProtectionFactor>()[{mio::abm::ExposureType::GenericVaccine, person.get_age(),
+                                                           mio::abm::VirusVariant::Wildtype}] =
+        [](ScalarType days) -> ScalarType {
         return mio::linear_interpolation_of_data_set<ScalarType, ScalarType>({{2, 0.91}, {30, 0.81}}, days);
     };
 
@@ -219,47 +225,53 @@ TEST(TestInfection, getPersonalProtectiveFactor)
     auto infection_protection_factor = params.get<mio::abm::InfectionProtectionFactor>()[{
         latest_protection.first, age_group_15_to_34, mio::abm::VirusVariant::Wildtype}](
         t.days() - latest_protection.second.days());
-    ASSERT_NEAR(infection_protection_factor, 0.91, 0.0001);
-    ASSERT_NEAR(person.get_protection_factor(t, mio::abm::VirusVariant::Wildtype, params), 0.91, 0.0001);
+    EXPECT_NEAR(infection_protection_factor, 0.91, 0.0001);
+    EXPECT_NEAR(person.get_protection_factor(t, mio::abm::VirusVariant::Wildtype, params), 0.91, 0.0001);
 
     t                           = mio::abm::TimePoint(0) + mio::abm::days(15);
     infection_protection_factor = params.get<mio::abm::InfectionProtectionFactor>()[{
         latest_protection.first, age_group_15_to_34, mio::abm::VirusVariant::Wildtype}](
         t.days() - latest_protection.second.days());
-    ASSERT_NEAR(infection_protection_factor, 0.8635, 0.0001);
-    ASSERT_NEAR(person.get_protection_factor(t, mio::abm::VirusVariant::Wildtype, params), 0.8635, 0.0001);
+    EXPECT_NEAR(infection_protection_factor, 0.8635, 0.0001);
+    EXPECT_NEAR(person.get_protection_factor(t, mio::abm::VirusVariant::Wildtype, params), 0.8635, 0.0001);
 
     t                           = mio::abm::TimePoint(0) + mio::abm::days(40);
     infection_protection_factor = params.get<mio::abm::InfectionProtectionFactor>()[{
         latest_protection.first, age_group_15_to_34, mio::abm::VirusVariant::Wildtype}](
         t.days() - latest_protection.second.days());
-    ASSERT_NEAR(infection_protection_factor, 0, 0.0001);
-    ASSERT_NEAR(person.get_protection_factor(t, mio::abm::VirusVariant::Wildtype, params), 0, 0.0001);
+    EXPECT_NEAR(infection_protection_factor, 0, 0.0001);
+    EXPECT_NEAR(person.get_protection_factor(t, mio::abm::VirusVariant::Wildtype, params), 0, 0.0001);
 
     // Test Parameter SeverityProtectionFactor
     t                               = mio::abm::TimePoint(0) + mio::abm::days(2);
     auto severity_protection_factor = params.get<mio::abm::SeverityProtectionFactor>()[{
         latest_protection.first, age_group_15_to_34, mio::abm::VirusVariant::Wildtype}](
         t.days() - latest_protection.second.days());
-    ASSERT_NEAR(severity_protection_factor, 0.91, 0.0001);
+    EXPECT_NEAR(severity_protection_factor, 0.91, 0.0001);
 
     t                          = mio::abm::TimePoint(0) + mio::abm::days(15);
     severity_protection_factor = params.get<mio::abm::SeverityProtectionFactor>()[{
         latest_protection.first, age_group_15_to_34, mio::abm::VirusVariant::Wildtype}](
         t.days() - latest_protection.second.days());
-    ASSERT_NEAR(severity_protection_factor, 0.8635, 0.0001);
+    EXPECT_NEAR(severity_protection_factor, 0.8635, 0.0001);
 
     t                          = mio::abm::TimePoint(0) + mio::abm::days(40);
     severity_protection_factor = params.get<mio::abm::SeverityProtectionFactor>()[{
         latest_protection.first, age_group_15_to_34, mio::abm::VirusVariant::Wildtype}](
         t.days() - latest_protection.second.days());
-    ASSERT_NEAR(severity_protection_factor, 0, 0.0001);
+    EXPECT_NEAR(severity_protection_factor, 0, 0.0001);
 
     // Test Parameter HighViralLoadProtectionFactor
-    t = mio::abm::TimePoint(0) + mio::abm::days(2);
-    ASSERT_NEAR(params.get<mio::abm::HighViralLoadProtectionFactor>()(t.days()), 0.91, 0.0001);
-    t = mio::abm::TimePoint(0) + mio::abm::days(15);
-    ASSERT_NEAR(params.get<mio::abm::HighViralLoadProtectionFactor>()(t.days()), 0.8635, 0.0001);
-    t = mio::abm::TimePoint(0) + mio::abm::days(40);
-    ASSERT_NEAR(params.get<mio::abm::HighViralLoadProtectionFactor>()(t.days()), 0, 0.0001);
+    t                                 = mio::abm::TimePoint(0) + mio::abm::days(2);
+    auto high_viral_protection_factor = params.get<mio::abm::HighViralLoadProtectionFactor>()[{
+        latest_protection.first, age_group_15_to_34, mio::abm::VirusVariant::Wildtype}](t.days());
+    EXPECT_NEAR(high_viral_protection_factor, 0.91, 0.0001);
+    t                            = mio::abm::TimePoint(0) + mio::abm::days(15);
+    high_viral_protection_factor = params.get<mio::abm::HighViralLoadProtectionFactor>()[{
+        latest_protection.first, age_group_15_to_34, mio::abm::VirusVariant::Wildtype}](t.days());
+    EXPECT_NEAR(high_viral_protection_factor, 0.8635, 0.0001);
+    t                            = mio::abm::TimePoint(0) + mio::abm::days(40);
+    high_viral_protection_factor = params.get<mio::abm::HighViralLoadProtectionFactor>()[{
+        latest_protection.first, age_group_15_to_34, mio::abm::VirusVariant::Wildtype}](t.days());
+    EXPECT_NEAR(high_viral_protection_factor, 0, 0.0001);
 }

pycode/memilio-simulation/memilio/simulation/bindings/models/abm.cpp

@@ -27,9 +27,9 @@
 //Includes from MEmilio
 #include "abm/simulation.h"
 
-#include "pybind11/pybind11.h"
 #include "pybind11/attr.h"
 #include "pybind11/cast.h"
+#include "pybind11/pybind11.h"
 #include "pybind11/operators.h"
 #include <cstdint>
 #include <type_traits>
@@ -72,23 +72,6 @@ PYBIND11_MODULE(_simulation_abm, m)
         .value("Antigen", mio::abm::TestType::Antigen)
         .value("PCR", mio::abm::TestType::PCR);
 
-    pymio::bind_class<mio::abm::TestParameters, pymio::EnablePickling::Never>(m, "TestParameters")
-        .def(py::init<double, double>())
-        .def_readwrite("sensitivity", &mio::abm::TestParameters::sensitivity)
-        .def_readwrite("specificity", &mio::abm::TestParameters::specificity);
-
-    pymio::bind_CustomIndexArray<mio::UncertainValue<double>, mio::abm::VirusVariant, mio::AgeGroup>(
-        m, "_AgeParameterArray");
-    pymio::bind_CustomIndexArray<mio::abm::TestParameters, mio::abm::TestType>(m, "_TestData");
-    pymio::bind_Index<mio::abm::ExposureType>(m, "ExposureTypeIndex");
-    pymio::bind_ParameterSet<mio::abm::ParametersBase, pymio::EnablePickling::Never>(m, "ParametersBase");
-    pymio::bind_class<mio::abm::Parameters, pymio::EnablePickling::Never, mio::abm::ParametersBase>(m, "Parameters")
-        .def(py::init<int>())
-        .def("check_constraints", &mio::abm::Parameters::check_constraints);
-
-    pymio::bind_ParameterSet<mio::abm::LocalInfectionParameters, pymio::EnablePickling::Never>(
-        m, "LocalInfectionParameters")
-        .def(py::init<size_t>());
 
     pymio::bind_class<mio::abm::TimeSpan, pymio::EnablePickling::Never>(m, "TimeSpan")
         .def(py::init<int>(), py::arg("seconds") = 0)
@@ -134,6 +117,26 @@ PYBIND11_MODULE(_simulation_abm, m)
         .def(py::self += mio::abm::TimeSpan{})
         .def(py::self - mio::abm::TimeSpan{})
         .def(py::self -= mio::abm::TimeSpan{});
+
+    pymio::bind_class<mio::abm::TestParameters, pymio::EnablePickling::Never>(m, "TestParameters")
+        .def(py::init<double, double, mio::abm::TimeSpan, mio::abm::TestType>())
+        .def_readwrite("sensitivity", &mio::abm::TestParameters::sensitivity)
+        .def_readwrite("specificity", &mio::abm::TestParameters::specificity)
+        .def_readwrite("required_time", &mio::abm::TestParameters::required_time)
+        .def_readwrite("type", &mio::abm::TestParameters::type);
+
+    pymio::bind_CustomIndexArray<mio::UncertainValue<double>, mio::abm::VirusVariant, mio::AgeGroup>(
+        m, "_AgeParameterArray");
+    pymio::bind_CustomIndexArray<mio::abm::TestParameters, mio::abm::TestType>(m, "_TestData");
+    pymio::bind_Index<mio::abm::ExposureType>(m, "ExposureTypeIndex");
+    pymio::bind_ParameterSet<mio::abm::ParametersBase, pymio::EnablePickling::Never>(m, "ParametersBase");
+    pymio::bind_class<mio::abm::Parameters, pymio::EnablePickling::Never, mio::abm::ParametersBase>(m, "Parameters")
+        .def(py::init<int>())
+        .def("check_constraints", &mio::abm::Parameters::check_constraints);
+
+    pymio::bind_ParameterSet<mio::abm::LocalInfectionParameters, pymio::EnablePickling::Never>(
+        m, "LocalInfectionParameters")
+        .def(py::init<size_t>());
 
     pymio::bind_class<mio::abm::LocationId, pymio::EnablePickling::Never>(m, "LocationId")
         .def(py::init<uint32_t>(), py::arg("id"))