/*

* Copyright (C) 2020-2026 MEmilio

*

* Authors: Daniel Abele, 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 "memilio/config.h"

#include "ode_secir/model.h"

#include "ode_secir/infection_state.h"

#include "ode_secir/parameters.h"

#include "memilio/mobility/metapopulation_mobility_instant.h"

#include "memilio/compartments/simulation.h"

#include <iostream>

int main()

{

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

const auto t0 = 0.;

const auto tmax = 30.;

const auto dt = 0.5; //time step of Mobility, daily Mobility every second step

const size_t num_groups = 1;

mio::osecir::Model<ScalarType> model(num_groups);

model.populations[{mio::AgeGroup(0), mio::osecir::InfectionState::Susceptible}] = 10000;

model.parameters.set<mio::osecir::StartDay<ScalarType>>(0);

model.parameters.set<mio::osecir::Seasonality<ScalarType>>(0.2);

model.parameters.get<mio::osecir::TimeExposed<ScalarType>>() = 3.2;

model.parameters.get<mio::osecir::TimeInfectedNoSymptoms<ScalarType>>() = 2.0;

model.parameters.get<mio::osecir::TimeInfectedSymptoms<ScalarType>>() = 5.8;

model.parameters.get<mio::osecir::TimeInfectedSevere<ScalarType>>() = 9.5;

model.parameters.get<mio::osecir::TimeInfectedCritical<ScalarType>>() = 7.1;

model.parameters.get<mio::osecir::TransmissionProbabilityOnContact<ScalarType>>() = 0.1;

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

model.parameters.get<mio::osecir::RecoveredPerInfectedNoSymptoms<ScalarType>>() = 0.09;

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

model.parameters.get<mio::osecir::MaxRiskOfInfectionFromSymptomatic<ScalarType>>() = 0.45;

model.parameters.get<mio::osecir::TestAndTraceCapacity<ScalarType>>() = 35;

model.parameters.get<mio::osecir::SeverePerInfectedSymptoms<ScalarType>>() = 0.2;

model.parameters.get<mio::osecir::CriticalPerSevere<ScalarType>>() = 0.25;

model.parameters.get<mio::osecir::DeathsPerCritical<ScalarType>>() = 0.3;

mio::ContactMatrixGroup<ScalarType>& contact_matrix =

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

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

//two mostly identical groups

auto model_group1 = model;

auto model_group2 = model;

//some contact restrictions in model_group1

mio::ContactMatrixGroup<ScalarType>& contact_matrix_m1 =

model_group1.parameters.get<mio::osecir::ContactPatterns<ScalarType>>();

contact_matrix_m1[0].add_damping(0.7, mio::SimulationTime<ScalarType>(15.0));

//infection starts in group 1

model_group1.populations[{mio::AgeGroup(0), mio::osecir::InfectionState::Susceptible}] = 9990;

model_group1.populations[{mio::AgeGroup(0), mio::osecir::InfectionState::Exposed}] = 100;

// get indices of INS and ISy compartments.

std::vector<std::vector<size_t>> indices_save_edges(2);

// Reserve Space. The multiplication by 2 is necessary because we have the

// base and the confirmed compartments for each age group.

for (auto& vec : indices_save_edges) {

vec.reserve(2 * num_groups);

}

// get indices and write them to the vector

for (auto i = mio::AgeGroup(0); i < mio::AgeGroup(num_groups); ++i) {

indices_save_edges[0].emplace_back(

model.populations.get_flat_index({i, mio::osecir::InfectionState::InfectedNoSymptoms}));

indices_save_edges[0].emplace_back(

model.populations.get_flat_index({i, mio::osecir::InfectionState::InfectedNoSymptomsConfirmed}));

indices_save_edges[1].emplace_back(

model.populations.get_flat_index({i, mio::osecir::InfectionState::InfectedSymptoms}));

indices_save_edges[1].emplace_back(

model.populations.get_flat_index({i, mio::osecir::InfectionState::InfectedSymptomsConfirmed}));

}

mio::Graph<mio::SimulationNode<ScalarType, mio::osecir::Simulation<ScalarType>>, mio::MobilityEdge<ScalarType>> g;

g.add_node(1001, model_group1, t0);

g.add_node(1002, model_group2, t0);

g.add_edge(0, 1, Eigen::VectorX<ScalarType>::Constant((size_t)mio::osecir::InfectionState::Count, 0.1),

indices_save_edges);

g.add_edge(1, 0, Eigen::VectorX<ScalarType>::Constant((size_t)mio::osecir::InfectionState::Count, 0.1),

indices_save_edges);

auto sim = mio::make_mobility_sim<ScalarType>(t0, dt, std::move(g));

sim.advance(tmax);

auto& edge_1_0 = sim.get_graph().edges()[1];

auto& results = edge_1_0.property.get_mobility_results();

results.print_table({"Commuter INS", "Commuter ISy", "Commuter Total"});

return 0;

}