/*

* Copyright (C) 2020-2026 MEmilio

*

* Authors: Lena Ploetzke

*

* Contact: Martin J. Kuehn <[email protected]>

*

* Licensed under the Apache License, Version 2.0 (the "License");

* you may not use this file except in compliance with the License.

* You may obtain a copy of the License at

*

* http://www.apache.org/licenses/LICENSE-2.0

*

* Unless required by applicable law or agreed to in writing, software

* distributed under the License is distributed on an "AS IS" BASIS,

* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

* See the License for the specific language governing permissions and

* limitations under the License.

*/

#include "glct_secir/model.h"

#include "glct_secir/parameters.h"

#include "memilio/config.h"

#include "memilio/utils/time_series.h"

#include "memilio/utils/logging.h"

#include "memilio/epidemiology/uncertain_matrix.h"

#include "memilio/compartments/simulation.h"

#include "memilio/math/eigen.h"

#include "load_test_data.h"

#include <gtest/gtest.h>

#include "boost/numeric/odeint/stepper/runge_kutta_cash_karp54.hpp"

// Test if the function eval_right_hand_side() is working using a hand calculated result.

TEST(TestGLCTSecir, testEvalRightHandSide)

{

// Define initial values, parameters and numbers of subcompartments according to the choices of the

// testEvalRightHandSide of the LCT testing suite. For more details,

// we refer to the example glct_secir.cpp.

using Model = mio::glsecir::Model<ScalarType, 2, 6, 4, 4, 4>;

using LctState = Model::LctState;

using InfectionState = LctState::InfectionState;

Model model;

// Set parameters such that the stay times are Erlang-distributed as in the corresponding LCT model.

// Exposed.

// Default functions are used to set the parameters but the corresponding dimensions have to be set manually.

model.parameters.get<mio::glsecir::StartingProbabilitiesExposed<ScalarType>>() =

mio::glsecir::StartingProbabilitiesExposed<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::Exposed>());

model.parameters.get<mio::glsecir::TransitionMatrixExposedToInfectedNoSymptoms<ScalarType>>() =

mio::glsecir::TransitionMatrixExposedToInfectedNoSymptoms<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::Exposed>(), 3.2);

// InfectedNoSymptoms.

Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedNoSymptoms = Eigen::VectorX<ScalarType>::Zero(

(Eigen::Index)LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>());

StartingProbabilitiesInfectedNoSymptoms[0] = 1 - 0.09;

StartingProbabilitiesInfectedNoSymptoms[(

Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>() / 2.)] = 0.09;

model.parameters.get<mio::glsecir::StartingProbabilitiesInfectedNoSymptoms<ScalarType>>() =

StartingProbabilitiesInfectedNoSymptoms;

model.parameters.get<mio::glsecir::TransitionMatrixInfectedNoSymptomsToInfectedSymptoms<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedNoSymptomsToInfectedSymptoms<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>() / 2.), 2.);

model.parameters.get<mio::glsecir::TransitionMatrixInfectedNoSymptomsToRecovered<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedNoSymptomsToRecovered<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>() / 2.), 2.);

// InfectedSymptoms.

Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedSymptoms = Eigen::VectorX<ScalarType>::Zero(

(Eigen::Index)LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>());

StartingProbabilitiesInfectedSymptoms[0] = 0.2;

StartingProbabilitiesInfectedSymptoms[(

Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>() / 2.)] = 1 - 0.2;

model.parameters.get<mio::glsecir::StartingProbabilitiesInfectedSymptoms<ScalarType>>() =

StartingProbabilitiesInfectedSymptoms;

model.parameters.get<mio::glsecir::TransitionMatrixInfectedSymptomsToInfectedSevere<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedSymptomsToInfectedSevere<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>() / 2.), 5.8);

model.parameters.get<mio::glsecir::TransitionMatrixInfectedSymptomsToRecovered<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedSymptomsToRecovered<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>() / 2.), 5.8);

// InfectedSevere.

Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedSevere = Eigen::VectorX<ScalarType>::Zero(

(Eigen::Index)LctState::get_num_subcompartments<InfectionState::InfectedSevere>());

StartingProbabilitiesInfectedSevere[0] = 0.25;

StartingProbabilitiesInfectedSevere[(

Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedSevere>() / 2.)] = 1 - 0.25;

model.parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>() =

StartingProbabilitiesInfectedSevere;

model.parameters.get<mio::glsecir::TransitionMatrixInfectedSevereToInfectedCritical<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedSevereToInfectedCritical<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedSevere>() / 2.), 9.5);

model.parameters.get<mio::glsecir::TransitionMatrixInfectedSevereToRecovered<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedSevereToRecovered<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedSevere>() / 2.), 9.5);

// InfectedCritical.

Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedCritical = Eigen::VectorX<ScalarType>::Zero(

(Eigen::Index)LctState::get_num_subcompartments<InfectionState::InfectedCritical>());

StartingProbabilitiesInfectedCritical[0] = 0.3;

StartingProbabilitiesInfectedCritical[(

Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedCritical>() / 2.)] = 1 - 0.3;

model.parameters.get<mio::glsecir::StartingProbabilitiesInfectedCritical<ScalarType>>() =

StartingProbabilitiesInfectedCritical;

model.parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToDead<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedCriticalToDead<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedCritical>() / 2.), 7.1);

model.parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToRecovered<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedCriticalToRecovered<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedCritical>() / 2.), 7.1);

model.parameters.get<mio::glsecir::TransmissionProbabilityOnContact<ScalarType>>() = 0.05;

mio::ContactMatrixGroup<ScalarType>& contact_matrix =

model.parameters.get<mio::glsecir::ContactPatterns<ScalarType>>();

contact_matrix[0] = mio::ContactMatrix<ScalarType>(Eigen::MatrixX<ScalarType>::Constant(1, 1, 10));

model.parameters.get<mio::glsecir::RelativeTransmissionNoSymptoms<ScalarType>>() = 0.7;

model.parameters.get<mio::glsecir::RiskOfInfectionFromSymptomatic<ScalarType>>() = 0.25;

model.parameters.get<mio::glsecir::Seasonality<ScalarType>>() = 0.;

model.parameters.get<mio::glsecir::StartDay<ScalarType>>() = 0;

// Define initial population distribution in infection states, one entry per subcompartment.

std::vector<std::vector<ScalarType>> initial_populations = {

{750},

{30, 20},

{20 * StartingProbabilitiesInfectedNoSymptoms[0], 10 * StartingProbabilitiesInfectedNoSymptoms[0],

10 * StartingProbabilitiesInfectedNoSymptoms[0], 20 * (1 - StartingProbabilitiesInfectedNoSymptoms[0]),

10 * (1 - StartingProbabilitiesInfectedNoSymptoms[0]), 10 * (1 - StartingProbabilitiesInfectedNoSymptoms[0])},

{30 * StartingProbabilitiesInfectedSymptoms[0], 20 * StartingProbabilitiesInfectedSymptoms[0],

30 * (1 - StartingProbabilitiesInfectedSymptoms[0]), 20 * (1 - StartingProbabilitiesInfectedSymptoms[0])},

{40 * StartingProbabilitiesInfectedSevere[0], 10 * StartingProbabilitiesInfectedSevere[0],

40 * (1 - StartingProbabilitiesInfectedSevere[0]), 10 * (1 - StartingProbabilitiesInfectedSevere[0])},

{10 * StartingProbabilitiesInfectedCritical[0], 20 * StartingProbabilitiesInfectedCritical[0],

10 * (1 - StartingProbabilitiesInfectedCritical[0]), 20 * (1 - StartingProbabilitiesInfectedCritical[0])},

{20},

{10}};

std::vector<ScalarType> flat_initial_populations;

for (auto&& vec : initial_populations) {

flat_initial_populations.insert(flat_initial_populations.end(), vec.begin(), vec.end());

}

Eigen::VectorX<ScalarType> pop(LctState::Count);

for (size_t i = 0; i < LctState::Count; i++) {

pop[i] = flat_initial_populations[i];

}

// Compare the result of get_derivatives() with a hand calculated result.

Eigen::VectorX<ScalarType> dydt(LctState::Count);

model.get_derivatives(pop, pop, 0, dydt);

// This vector is the equivalent of the result defined in the test suite testEvalRightHandSide of the LCT model.

Eigen::VectorX<ScalarType> compare(LctState::Count);

compare << -15.3409, -3.4091, 6.25, -17.5 * 0.91, 15 * 0.91, 0 * 0.91, -17.5 * 0.09, 15 * 0.09, 0 * 0.09,

3.3052 * 0.2, 3.4483 * 0.2, 3.3052 * 0.8, 3.4483 * 0.8, -7.0417 * 0.25, 6.3158 * 0.25, -7.0417 * 0.75,

6.3158 * 0.75, -2.2906 * 0.3, -2.8169 * 0.3, -2.2906 * 0.7, -2.8169 * 0.7, 12.3899, 1.6901;

for (size_t i = 0; i < LctState::Count; i++) {

EXPECT_NEAR(compare[i], dydt[i], 1e-3) << "Condition failed at index: " << i;

}

}

// Model setup to compare result with a previous output of an LCT model.

class ModelTestGLCTSecir : public testing::Test

{

public:

using Model = mio::glsecir::Model<ScalarType, 2, 6, 2, 2, 10>;

using LctState = Model::LctState;

using InfectionState = LctState::InfectionState;

protected:

virtual void SetUp()

{

model = new Model();

// --- Set parameters. ---

// Exposed.

model->parameters.get<mio::glsecir::StartingProbabilitiesExposed<ScalarType>>() =

mio::glsecir::StartingProbabilitiesExposed<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::Exposed>());

model->parameters.get<mio::glsecir::TransitionMatrixExposedToInfectedNoSymptoms<ScalarType>>() =

mio::glsecir::TransitionMatrixExposedToInfectedNoSymptoms<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::Exposed>(), 3.2);

// InfectedNoSymptoms.

Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedNoSymptoms = Eigen::VectorX<ScalarType>::Zero(

(Eigen::Index)LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>());

StartingProbabilitiesInfectedNoSymptoms[0] = 1 - 0.09;

StartingProbabilitiesInfectedNoSymptoms[(

Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>() / 2.)] = 0.09;

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedNoSymptoms<ScalarType>>() =

StartingProbabilitiesInfectedNoSymptoms;

model->parameters.get<mio::glsecir::TransitionMatrixInfectedNoSymptomsToInfectedSymptoms<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedNoSymptomsToInfectedSymptoms<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>() / 2.), 2.);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedNoSymptomsToRecovered<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedNoSymptomsToRecovered<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>() / 2.), 2.);

// InfectedSymptoms.

Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedSymptoms = Eigen::VectorX<ScalarType>::Zero(

(Eigen::Index)LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>());

StartingProbabilitiesInfectedSymptoms[0] = 0.2;

StartingProbabilitiesInfectedSymptoms[(

Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>() / 2.)] = 1 - 0.2;

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSymptoms<ScalarType>>() =

StartingProbabilitiesInfectedSymptoms;

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSymptomsToInfectedSevere<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedSymptomsToInfectedSevere<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>() / 2.), 5.8);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSymptomsToRecovered<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedSymptomsToRecovered<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>() / 2.), 5.8);

// InfectedSevere.

Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedSevere = Eigen::VectorX<ScalarType>::Zero(

(Eigen::Index)LctState::get_num_subcompartments<InfectionState::InfectedSevere>());

StartingProbabilitiesInfectedSevere[0] = 0.25;

StartingProbabilitiesInfectedSevere[(

Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedSevere>() / 2.)] = 1 - 0.25;

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>() =

StartingProbabilitiesInfectedSevere;

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSevereToInfectedCritical<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedSevereToInfectedCritical<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedSevere>() / 2.), 9.5);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSevereToRecovered<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedSevereToRecovered<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedSevere>() / 2.), 9.5);

// InfectedCritical.

Eigen::VectorX<ScalarType> StartingProbabilitiesInfectedCritical = Eigen::VectorX<ScalarType>::Zero(

(Eigen::Index)LctState::get_num_subcompartments<InfectionState::InfectedCritical>());

StartingProbabilitiesInfectedCritical[0] = 0.3;

StartingProbabilitiesInfectedCritical[(

Eigen::Index)(LctState::get_num_subcompartments<InfectionState::InfectedCritical>() / 2.)] = 1 - 0.3;

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedCritical<ScalarType>>() =

StartingProbabilitiesInfectedCritical;

model->parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToDead<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedCriticalToDead<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedCritical>() / 2.), 7.1);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToRecovered<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedCriticalToRecovered<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedCritical>() / 2.), 7.1);

model->parameters.get<mio::glsecir::TransmissionProbabilityOnContact<ScalarType>>() = 0.05;

mio::ContactMatrixGroup<ScalarType>& contact_matrix =

model->parameters.get<mio::glsecir::ContactPatterns<ScalarType>>();

contact_matrix[0] = mio::ContactMatrix<ScalarType>(Eigen::MatrixX<ScalarType>::Constant(1, 1, 10));

contact_matrix[0].add_damping(0.7, mio::SimulationTime<ScalarType>(2.));

model->parameters.get<mio::glsecir::RelativeTransmissionNoSymptoms<ScalarType>>() = 0.7;

model->parameters.get<mio::glsecir::RiskOfInfectionFromSymptomatic<ScalarType>>() = 0.25;

model->parameters.get<mio::glsecir::Seasonality<ScalarType>>() = 0.;

model->parameters.get<mio::glsecir::StartDay<ScalarType>>() = 0;

// --- Define initial distribution of the population in the subcompartments. ---

std::vector<std::vector<ScalarType>> initial_populations = {

{750},

{30, 20},

{20 * StartingProbabilitiesInfectedNoSymptoms[0], 10 * StartingProbabilitiesInfectedNoSymptoms[0],

10 * StartingProbabilitiesInfectedNoSymptoms[0], 20 * (1 - StartingProbabilitiesInfectedNoSymptoms[0]),

10 * (1 - StartingProbabilitiesInfectedNoSymptoms[0]),

10 * (1 - StartingProbabilitiesInfectedNoSymptoms[0])},

{50 * StartingProbabilitiesInfectedSymptoms[0], 50 * (1 - StartingProbabilitiesInfectedSymptoms[0])},

{50 * StartingProbabilitiesInfectedSevere[0], 50 * (1 - StartingProbabilitiesInfectedSevere[0])},

{10 * StartingProbabilitiesInfectedCritical[0], 10 * StartingProbabilitiesInfectedCritical[0],

5 * StartingProbabilitiesInfectedCritical[0], 3 * StartingProbabilitiesInfectedCritical[0],

2 * StartingProbabilitiesInfectedCritical[0], 10 * (1 - StartingProbabilitiesInfectedCritical[0]),

10 * (1 - StartingProbabilitiesInfectedCritical[0]), 5 * (1 - StartingProbabilitiesInfectedCritical[0]),

3 * (1 - StartingProbabilitiesInfectedCritical[0]), 2 * (1 - StartingProbabilitiesInfectedCritical[0])},

{20},

{10}};

// Transfer the initial values in initial_populations to the model->

std::vector<ScalarType> flat_initial_populations;

for (auto&& vec : initial_populations) {

flat_initial_populations.insert(flat_initial_populations.end(), vec.begin(), vec.end());

}

for (size_t i = 0; i < LctState::Count; i++) {

model->populations[mio::Index<LctState>(i)] = flat_initial_populations[i];

}

}

virtual void TearDown()

{

delete model;

}

public:

Model* model = nullptr;

};

// Test compares a simulation with a previous output of an LCT model stored in a .csv file.

// This tests that the GLCT model reduces to an LCT model with the default parameters as well as nothing has changed

// in the implementation such that we still obtain an previous result.

TEST_F(ModelTestGLCTSecir, compareWithPreviousRun)

{

ScalarType tmax = 3;

mio::TimeSeries<ScalarType> result = mio::simulate<ScalarType, ModelTestGLCTSecir::Model>(

0, tmax, 0.5, *model,

std::make_unique<mio::ControlledStepperWrapper<ScalarType, boost::numeric::odeint::runge_kutta_cash_karp54>>());

// Compare InfectionState compartments.

mio::TimeSeries<ScalarType> population = model->calculate_compartments(result);

auto compare_population = load_test_data_csv<ScalarType>("lct-secir-compartments-compare.csv");

ASSERT_EQ(compare_population.size(), static_cast<size_t>(population.get_num_time_points()));

for (size_t i = 0; i < compare_population.size(); i++) {

ASSERT_EQ(compare_population[i].size(), static_cast<size_t>(population.get_num_elements()) + 1)

<< "at row " << i;

EXPECT_NEAR(population.get_time(i), compare_population[i][0], 1e-3) << "at row " << i;

for (size_t j = 1; j < compare_population[i].size(); j++) {

EXPECT_NEAR(population.get_value(i)[j - 1], compare_population[i][j], 1e-3) << " at row " << i;

}

}

}

// Check constraints of Parameters class.

TEST_F(ModelTestGLCTSecir, testConstraintsModel)

{

// Deactivate temporarily log output for next tests.

mio::set_log_level(mio::LogLevel::off);

// --- Check correct setup. ---

bool constraint_check = model->check_constraints();

EXPECT_FALSE(constraint_check);

// Check if the number of subcompartments does not match the dimension of the vector with StartingProbabilities.

Eigen::VectorX<ScalarType> wrong_size = Eigen::VectorX<ScalarType>::Zero(3);

wrong_size[0] = 1;

// Exposed.

model->parameters.get<mio::glsecir::StartingProbabilitiesExposed<ScalarType>>() = wrong_size;

constraint_check = model->check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesExposed<ScalarType>>() =

mio::glsecir::StartingProbabilitiesExposed<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::Exposed>());

// InfectedNoSymptoms.

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedNoSymptoms<ScalarType>>() = wrong_size;

constraint_check = model->check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedNoSymptoms<ScalarType>>() =

mio::glsecir::StartingProbabilitiesInfectedNoSymptoms<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>());

// InfectedSymptoms.

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSymptoms<ScalarType>>() = wrong_size;

constraint_check = model->check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSymptoms<ScalarType>>() =

mio::glsecir::StartingProbabilitiesInfectedSymptoms<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>());

// InfectedSevere.

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>() = wrong_size;

constraint_check = model->check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>() =

mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::InfectedSevere>());

// InfectedCritical.

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedCritical<ScalarType>>() = wrong_size;

constraint_check = model->check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedCritical<ScalarType>>() =

mio::glsecir::StartingProbabilitiesInfectedCritical<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::InfectedCritical>());

}

// Check constraints of Parameters class.

TEST_F(ModelTestGLCTSecir, testConstraintsParameters)

{

// Deactivate temporarily log output for next tests.

mio::set_log_level(mio::LogLevel::off);

// --- Check correct setup. ---

bool constraint_check = model->parameters.check_constraints();

EXPECT_FALSE(constraint_check);

// --- Parameters affecting the transmission of the virus. ---

// Check TransmissionProbabilityOnContact.

model->parameters.get<mio::glsecir::TransmissionProbabilityOnContact<ScalarType>>() = 5.1;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::TransmissionProbabilityOnContact<ScalarType>>() = 0.05;

// Check RelativeTransmissionNoSymptoms.

model->parameters.get<mio::glsecir::RelativeTransmissionNoSymptoms<ScalarType>>() = -0.05;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::RelativeTransmissionNoSymptoms<ScalarType>>() = 0.7;

// Check RiskOfInfectionFromSymptomatic.

model->parameters.get<mio::glsecir::RiskOfInfectionFromSymptomatic<ScalarType>>() = 1.1;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::RiskOfInfectionFromSymptomatic<ScalarType>>() = 0.25;

// Check Seasonality.

model->parameters.get<mio::glsecir::Seasonality<ScalarType>>() = 0.6;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::Seasonality<ScalarType>>() = 0.;

// --- Check with incorrect dimensions. ---

// Check non-quadratic TransitionMatrixInfectedCriticalToRecovered.

model->parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToRecovered<ScalarType>>() =

Eigen::MatrixX<ScalarType>::Zero(2, 3);

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToRecovered<ScalarType>>() =

mio::glsecir::TransitionMatrixInfectedCriticalToRecovered<ScalarType>().get_default(

(size_t)(LctState::get_num_subcompartments<InfectionState::InfectedCritical>() / 2.), 7.1);

// Check non matching dimensions of TransitionMatrix and vector with StartingProbabilities.

Eigen::VectorX<ScalarType> wrong_size = Eigen::VectorX<ScalarType>::Zero(3);

wrong_size[0] = 1;

// Exposed.

model->parameters.get<mio::glsecir::StartingProbabilitiesExposed<ScalarType>>() = wrong_size;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesExposed<ScalarType>>() =

mio::glsecir::StartingProbabilitiesExposed<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::Exposed>());

// InfectedNoSymptoms.

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedNoSymptoms<ScalarType>>() = wrong_size;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedNoSymptoms<ScalarType>>() =

mio::glsecir::StartingProbabilitiesInfectedNoSymptoms<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::InfectedNoSymptoms>());

// InfectedSymptoms.

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSymptoms<ScalarType>>() = wrong_size;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSymptoms<ScalarType>>() =

mio::glsecir::StartingProbabilitiesInfectedSymptoms<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::InfectedSymptoms>());

// InfectedSevere.

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>() = wrong_size;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>() =

mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::InfectedSevere>());

// InfectedCritical.

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedCritical<ScalarType>>() = wrong_size;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedCritical<ScalarType>>() =

mio::glsecir::StartingProbabilitiesInfectedCritical<ScalarType>().get_default(

LctState::get_num_subcompartments<InfectionState::InfectedCritical>());

// --- Check constraints of the starting probability vectors. ---

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>()[1] = 1.5;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>()[0] = 1.1;

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>()[1] = -0.1;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>()[0] = 1.;

model->parameters.get<mio::glsecir::StartingProbabilitiesInfectedSevere<ScalarType>>()[1] = 0.;

// --- Check with invalid transition matrices. ---

// ExposedToInfectedNoSymptoms.

model->parameters.get<mio::glsecir::TransitionMatrixExposedToInfectedNoSymptoms<ScalarType>>()(1, 0) = 10;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::TransitionMatrixExposedToInfectedNoSymptoms<ScalarType>>()(1, 0) = 0.1;

// InfectedNoSymptomsToInfectedSymptoms.

model->parameters.get<mio::glsecir::TransitionMatrixInfectedNoSymptomsToInfectedSymptoms<ScalarType>>()(2, 1) = 50;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedNoSymptomsToInfectedSymptoms<ScalarType>>()(2, 1) = 0.1;

// InfectedNoSymptomsToRecovered.

model->parameters.get<mio::glsecir::TransitionMatrixInfectedNoSymptomsToRecovered<ScalarType>>()(1, 1) = -1.45;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedNoSymptomsToRecovered<ScalarType>>()(1, 1) = -1.5;

// InfectedSymptomsToInfectedSevere.

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSymptomsToInfectedSevere<ScalarType>>()(0, 0) = 1.;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSymptomsToInfectedSevere<ScalarType>>()(0, 0) = -1.;

// InfectedSymptomsToRecovered.

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSymptomsToRecovered<ScalarType>>()(0, 0) = 0.1;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSymptomsToRecovered<ScalarType>>()(0, 0) = -0.1;

// InfectedSevereToInfectedCritical.

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSevereToInfectedCritical<ScalarType>>()(0, 0) = 0.01;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSevereToInfectedCritical<ScalarType>>()(0, 0) = -0.01;

// InfectedSevereToRecovered.

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSevereToRecovered<ScalarType>>()(0, 0) = 50;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedSevereToRecovered<ScalarType>>()(0, 0) = -0.1;

// InfectedCriticalToDead.

model->parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToDead<ScalarType>>()(3, 1) = 6;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToDead<ScalarType>>()(3, 1) = 0.;

// InfectedCriticalToRecovered.

model->parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToRecovered<ScalarType>>()(0, 4) = 3;

constraint_check = model->parameters.check_constraints();

EXPECT_TRUE(constraint_check);

model->parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToRecovered<ScalarType>>()(0, 0) = -3.;

model->parameters.get<mio::glsecir::TransitionMatrixInfectedCriticalToRecovered<ScalarType>>()(0, 4) = 1.2;

// --- Check with correct parameters. ---

constraint_check = model->parameters.check_constraints();

EXPECT_FALSE(constraint_check);

// Reactive log output.

mio::set_log_level(mio::LogLevel::warn);

}

// Test calculate_compartments with a TimeSeries that has an incorrect number of elements.

TEST_F(ModelTestGLCTSecir, testCalculatePopWrongSize)

{

// Deactivate temporarily log output because an error is expected.

mio::set_log_level(mio::LogLevel::off);

// TimeSeries has to have LctState::Count elements.

size_t wrong_size = LctState::Count - 2;

// Define TimeSeries with wrong_size elements.

mio::TimeSeries<ScalarType> wrong_num_elements(wrong_size);

Eigen::VectorX<ScalarType> vec_wrong_size = Eigen::VectorX<ScalarType>::Ones(wrong_size);

wrong_num_elements.add_time_point(-10, vec_wrong_size);

wrong_num_elements.add_time_point(-9, vec_wrong_size);

// Call the calculate_compartments function with the TimeSeries with a wrong number of elements.

mio::TimeSeries<ScalarType> population = model->calculate_compartments(wrong_num_elements);

// A TimeSeries of the right size with values -1 is expected.

ASSERT_EQ(1, population.get_num_time_points());

for (int i = 0; i < population.get_num_elements(); i++) {

EXPECT_EQ(-1, population.get_last_value()[i]);

}

// Reactive log output.

mio::set_log_level(mio::LogLevel::warn);

}