/*

* 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 "ide_seir/model.h"

#include "memilio/utils/time_series.h"

#include "memilio/epidemiology/uncertain_matrix.h"

int main()

{

/**

* Note: the initial values as well as all other parameters are randomly chosen for this example and are not

* intended to characterize the real world.

* This example has the purpose to show how the IDE SEIR model can be applied.

*/

using Vector = Eigen::Matrix<ScalarType, Eigen::Dynamic, 1>;

int tmax = 15;

int N = 810000;

ScalarType dt = 0.1;

mio::TimeSeries<ScalarType> init(1);

/**

* Construction of the initial TimeSeries with point of times and the corresponding number of susceptibles.

* The smallest time should be small enough. See the documentation of the IdeSeirModel constructor for

* detailed information. Initial data are chosen randomly.

*/

init.add_time_point<Eigen::VectorXd>(-15.0, Vector::Constant(1, N * 0.95));

while (init.get_last_time() < 0) {

init.add_time_point(init.get_last_time() + dt,

Vector::Constant(1, (ScalarType)init.get_last_value()[0] + init.get_last_time()));

}

// Initialize model.

mio::iseir::Model model(std::move(init), dt, N);

// Set working parameters.

model.parameters.set<mio::iseir::LatencyTime>(3.3);

model.parameters.set<mio::iseir::InfectiousTime>(8.2);

model.parameters.set<mio::iseir::TransmissionRisk>(0.015);

mio::ContactMatrixGroup<ScalarType> contact_matrix = mio::ContactMatrixGroup<ScalarType>(1, 1);

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

// Add damping.

contact_matrix[0].add_damping(0.7, mio::SimulationTime<ScalarType>(10.));

model.parameters.get<mio::iseir::ContactFrequency>() = mio::UncertainContactMatrix<ScalarType>(contact_matrix);

// Carry out simulation.

model.simulate(tmax);

// Calculate values for compartments EIR.

auto result = model.calculate_EIR();

//Print results.

result.print_table({"S", "E", "I", "R"});

}