/*

* Copyright (C) 2020-2026 MEmilio

*

* Authors: Daniel Abele, Martin J. Kuehn

*

* 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 "ode_seir/model.h"

#include "ode_seir/infection_state.h"

#include "ode_seir/parameters.h"

#include "memilio/compartments/simulation.h"

#include "memilio/utils/logging.h"

#include "memilio/utils/time_series.h"

#include "memilio/utils/time_series.h"

int main()

{

mio::set_log_level(mio::LogLevel::debug);

ScalarType t0 = 0;

ScalarType tmax = 50.;

ScalarType dt = 1.0;

mio::log_info("Simulating ODE SEIR; t={} ... {} with dt = {}.", t0, tmax, dt);

mio::oseir::Model<ScalarType> model(1);

ScalarType total_population = 10000;

model.populations[{mio::AgeGroup(0), mio::oseir::InfectionState::Exposed}] = 100;

model.populations[{mio::AgeGroup(0), mio::oseir::InfectionState::Infected}] = 100;

model.populations[{mio::AgeGroup(0), mio::oseir::InfectionState::Recovered}] = 100;

model.populations[{mio::AgeGroup(0), mio::oseir::InfectionState::Susceptible}] =

total_population - model.populations[{mio::AgeGroup(0), mio::oseir::InfectionState::Exposed}] -

model.populations[{mio::AgeGroup(0), mio::oseir::InfectionState::Infected}] -

model.populations[{mio::AgeGroup(0), mio::oseir::InfectionState::Recovered}];

model.parameters.set<mio::oseir::TimeExposed<ScalarType>>(5.2);

model.parameters.set<mio::oseir::TimeInfected<ScalarType>>(6);

model.parameters.set<mio::oseir::TransmissionProbabilityOnContact<ScalarType>>(0.1);

mio::ContactMatrixGroup<ScalarType>& contact_matrix =

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

contact_matrix[0].get_baseline().setConstant(2.7);

contact_matrix[0].add_damping(0.7, mio::SimulationTime<ScalarType>(30.));

model.check_constraints();

auto seir = mio::simulate<ScalarType>(t0, tmax, dt, model);

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

std::cout << "\nnumber total: " << seir.get_last_value().sum() << "\n";

}