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1386 Implement influenza model (#1387)
- Implement influenza model from doi.org/10.1186/s12879-017-2344-6 into our framework - Add flowchart and rtd documentation Co-authored-by: annawendler <[email protected]>
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‎cpp/CMakeLists.txt‎

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@@ -183,8 +183,9 @@ if(MEMILIO_BUILD_MODELS)
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add_subdirectory(models/glct_secir)
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add_subdirectory(models/ide_secir)
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add_subdirectory(models/ide_seir)
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add_subdirectory(models/ode_seir)
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add_subdirectory(models/ode_seirdb)
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add_subdirectory(models/ode_seir)
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add_subdirectory(models/ode_seirv)
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add_subdirectory(models/ode_seirdb)
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add_subdirectory(models/ode_seair)
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add_subdirectory(models/ode_sir)
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add_subdirectory(models/sde_sir)

‎cpp/examples/CMakeLists.txt‎

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@@ -72,6 +72,10 @@ add_executable(seir_flows_example ode_seir_flows.cpp)
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target_link_libraries(seir_flows_example PRIVATE memilio ode_seir)
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target_compile_options(seir_flows_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
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add_executable(ode_seirv_example ode_seirv_example.cpp)
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target_link_libraries(ode_seirv_example PRIVATE memilio ode_seirv)
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target_compile_options(ode_seirv_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
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add_executable(ode_secir_example ode_secir.cpp)
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target_link_libraries(ode_secir_example PRIVATE memilio ode_secir)
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target_compile_options(ode_secir_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})

‎cpp/examples/ode_seirv_example.cpp‎

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/*
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* Copyright (C) 2020-2025 MEmilio
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*
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* Authors: Henrik Zunker
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*
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* Contact: Martin J. Kuehn <[email protected]>
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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#include "ode_seirv/model.h"
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#include "memilio/compartments/simulation.h"
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#include "memilio/utils/logging.h"
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/**
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* @brief set_initial_population sets the initial population of the model
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*
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* We assume that no one is initially infected or exposed at the beginning of the season.
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* Infections are seeded later via the OutsideFoI parameter.
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* The distinction into the 2 layers of susceptibility is done via the parameters.
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* @tparam FP floating point type
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* @param[in, out] model SEIRV model
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* @param[in] total_pop total population size
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*/
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template <class FP>
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void set_initial_population(mio::oseirv::Model<FP>& model, const FP total_pop)
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{
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auto& params = model.parameters;
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auto& pop = model.populations;
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const size_t num_groups = (size_t)params.get_num_groups();
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for (size_t i = 0; i < num_groups; ++i) {
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pop.template set_difference_from_group_total<mio::AgeGroup>(
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{mio::AgeGroup(i), mio::oseirv::InfectionState::Susceptible}, total_pop / num_groups);
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// Total population N_i as currently stored in group totals
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FP Ni = pop.get_group_total(mio::AgeGroup(i));
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FP s_age = params.template get<mio::oseirv::SusceptibilityByAge<FP>>()[mio::AgeGroup(i)];
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FP s_frac = params.template get<mio::oseirv::SusceptibleFraction<FP>>();
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FP vc = params.template get<mio::oseirv::VaccineCoverage<FP>>()[mio::AgeGroup(i)];
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FP ve = params.template get<mio::oseirv::VaccineEffectiveness<FP>>()[mio::AgeGroup(i)];
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pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::Exposed}] = 0;
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pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::ExposedVaccinated}] = 0;
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pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::Infected}] = 0;
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pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::InfectedVaccinated}] = 0;
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pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::Susceptible}] = s_frac * s_age * (FP(1) - vc) * Ni;
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pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::SusceptibleVaccinated}] =
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s_frac * s_age * (FP(1) - ve) * vc * Ni;
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pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::Recovered}] = (FP(1) - s_frac * s_age) * (FP(1) - vc) * Ni;
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pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::RecoveredVaccinated}] =
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(FP(1) - s_frac * s_age * (FP(1) - ve)) * vc * Ni;
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}
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}
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// Example usage of the SEIRV ODE model presented in https://doi.org/10.1186/s12879-017-2344-6
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int main()
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{
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using FP = double;
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mio::set_log_level(mio::LogLevel::debug);
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const FP t0 = 0., tmax = 42.;
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const FP dt = 0.1;
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const size_t num_groups = 1;
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const auto total_pop = 1e5;
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mio::oseirv::Model<FP> model((int)num_groups);
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auto& parameters = model.parameters;
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FP cont_freq = 10.0;
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FP cont_freq_group = FP(1) / FP(num_groups);
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// Healthy contacts
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mio::ContactMatrixGroup<ScalarType>& contacts_healthy = parameters.get<mio::oseirv::ContactPatternsHealthy<FP>>();
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contacts_healthy[0] = mio::ContactMatrix<FP>(
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Eigen::MatrixXd::Constant((Eigen::Index)num_groups, (Eigen::Index)num_groups, cont_freq_group * cont_freq));
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// Sick contacts (here 20% reduced)
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mio::ContactMatrixGroup<ScalarType>& contacts_sick = parameters.get<mio::oseirv::ContactPatternsSick<FP>>();
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contacts_sick[0] = mio::ContactMatrix<FP>(Eigen::MatrixXd::Constant(
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(Eigen::Index)num_groups, (Eigen::Index)num_groups, cont_freq_group * cont_freq * 0.8));
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// Parameters
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parameters.get<mio::oseirv::BaselineTransmissibility<FP>>() = 1.2;
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parameters.get<mio::oseirv::TimeExposed<FP>>() = 2.0;
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parameters.get<mio::oseirv::TimeInfected<FP>>() = 2.0; // same duration for E->I and I->R
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parameters.get<mio::oseirv::SeasonalityAmplitude<FP>>() = 1.0;
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parameters.get<mio::oseirv::SeasonalityShiftPerSubtype<FP>>() = 0.0;
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parameters.get<mio::oseirv::SeasonalityShiftPerSeason<FP>>() = 0.0;
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parameters.get<mio::oseirv::OutsideFoI<FP>>() = 1e-6;
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parameters.get<mio::oseirv::ClusteringExponent<FP>>() = 0.9;
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parameters.get<mio::oseirv::SickMixing<FP>>() = 2.0;
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for (size_t i = 0; i < num_groups; ++i) {
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parameters.get<mio::oseirv::SusceptibilityByAge<FP>>()[mio::AgeGroup(i)] = 1.0;
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parameters.get<mio::oseirv::VaccineCoverage<FP>>()[mio::AgeGroup(i)] = 0.3;
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parameters.get<mio::oseirv::VaccineEffectiveness<FP>>()[mio::AgeGroup(i)] = 0.5;
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model.populations.set_difference_from_group_total<mio::AgeGroup>(
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{mio::AgeGroup(i), mio::oseirv::InfectionState::Susceptible}, 1e5 / num_groups);
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}
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set_initial_population(model, total_pop);
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auto seirv = mio::simulate<FP>(t0, tmax, dt, model);
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std::vector<std::string> vars = {"S", "SV", "E", "EV", "I", "IV", "R", "RV"};
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seirv.print_table(vars);
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}

‎cpp/models/ode_seirv/CMakeLists.txt‎

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add_library(ode_seirv
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infection_state.h
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model.h
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model.cpp
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parameters.h
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)
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target_link_libraries(ode_seirv PUBLIC memilio)
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target_include_directories(ode_seirv PUBLIC
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$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/..>
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$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
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)
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target_compile_options(ode_seirv PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})

‎cpp/models/ode_seirv/README.md‎

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# ODE SEIRV (seasonal influenza)
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A age‑structured **SEIRV** model implemented into the MEmilio ODE framework.
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It extends the classic SEIR by a vaccinated layer (Sᵛ, Eᵛ, Iᵛ, Rᵛ) and follows the seasonal influenza
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model structure from:
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> **Weidemann, F., Remschmidt, C., Buda, S. et al.**
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> *Is the impact of childhood influenza vaccination less than expected: a transmission modelling study.*
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> **BMC Infectious Diseases** 17, 258 (2017).
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> https://doi.org/10.1186/s12879-017-2344-6
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## Get started
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To get started, check out the
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[official documentation](https://memilio.readthedocs.io/en/latest/cpp/models/oseirv.html)
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or the [code example](../../examples/ode_seirv_example.cpp).
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## Reference
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Please cite the original study if you use this model:
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> Weidemann, F., Remschmidt, C., Buda, S. et al. *Is the impact of childhood influenza vaccination less than expected: a transmission modelling study.* **BMC Infect Dis** 17, 258 (2017).
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> https://doi.org/10.1186/s12879-017-2344-6

‎cpp/models/ode_seirv/infection_state.h‎

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/*
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* Copyright (C) 2020-2025 MEmilio
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*
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* Authors: Henrik Zunker
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*
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* Contact: Martin J. Kuehn <[email protected]>
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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#ifndef SEIRV_INFECTIONSTATE_H
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#define SEIRV_INFECTIONSTATE_H
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namespace mio
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{
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namespace oseirv
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{
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enum class InfectionState
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{
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Susceptible,
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SusceptibleVaccinated,
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Exposed,
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ExposedVaccinated,
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Infected,
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InfectedVaccinated,
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Recovered,
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RecoveredVaccinated,
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Count
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};
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} // namespace oseirv
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} // namespace mio
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#endif

‎cpp/models/ode_seirv/model.cpp‎

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/*
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* Copyright (C) 2020-2025 MEmilio
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*
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* Authors: Henrik Zunker
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*
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* Contact: Martin J. Kuehn <[email protected]>
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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#include "ode_seirv/model.h"

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