/*

* Copyright (C) 2020-2026 MEmilio

*

* Authors: Daniel Abele, Martin J. Kuehn, Rene Schmieding, Henrik Zunker

*

* 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/flow_simulation.h"

#include "memilio/utils/logging.h"

#include <vector>

int main()

{

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

ScalarType t0 = 0;

ScalarType tmax = 1;

ScalarType dt = 0.001;

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

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

constexpr 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.set_difference_from_group_total<mio::AgeGroup>(

{mio::AgeGroup(0), mio::oseir::InfectionState::Susceptible}, total_population);

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

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

model.parameters.set<mio::oseir::TransmissionProbabilityOnContact<ScalarType>>(0.04);

mio::ContactMatrixGroup<ScalarType>& contact_matrix =

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

contact_matrix[0].get_baseline().setConstant(10);

model.check_constraints();

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

printf("Compartments: \n");

seir[0].print_table({"S", "E", "I", "R"});

printf("Flows: \n");

seir[1].print_table({"S->E", "E->I", "I->R"});

printf("\n number total: %f\n", seir[0].get_last_value()[0] + seir[0].get_last_value()[1] +

seir[0].get_last_value()[2] + seir[0].get_last_value()[3]);

}