1386 implement influenza model

cpp/CMakeLists.txt

@@ -183,6 +183,7 @@ if(MEMILIO_BUILD_MODELS)
     add_subdirectory(models/ide_secir)
     add_subdirectory(models/ide_seir)
     add_subdirectory(models/ode_seir)
+    add_subdirectory(models/ode_seirv)
     add_subdirectory(models/ode_seair)
     add_subdirectory(models/ode_sir)
     add_subdirectory(models/sde_sir)

cpp/examples/CMakeLists.txt

@@ -68,6 +68,10 @@ add_executable(seir_flows_example ode_seir_flows.cpp)
 target_link_libraries(seir_flows_example PRIVATE memilio ode_seir)
 target_compile_options(seir_flows_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
 
+add_executable(ode_seirv_example ode_seirv_example.cpp)
+target_link_libraries(ode_seirv_example PRIVATE memilio ode_seirv)
+target_compile_options(ode_seirv_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
+
 add_executable(ode_secir_example ode_secir.cpp)
 target_link_libraries(ode_secir_example PRIVATE memilio ode_secir)
 target_compile_options(ode_secir_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})

cpp/examples/ode_seirv_example.cpp

@@ -0,0 +1,120 @@
+/*
+* Copyright (C) 2020-2025 MEmilio
+*
+* Authors: Henrik Zunker
+*
+* Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
+*
+* 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_seirv/model.h"
+#include "memilio/compartments/simulation.h"
+#include "memilio/utils/logging.h"
+
+/**
+ * @brief set_initial_population sets the initial population of the model 
+ * 
+ * We assume that no one is initially infected or exposed at the beginning of the season.
+ * Infections are seeded later via the OutsideFoI parameter.
+ * The destinction into the 2 layers of susceptibility is done via the parameters.
+ * @tparam FP floating point type
+ * @param[in, out] model SEIRV model
+ * @param[in] total_pop total population size
+ */
+template <class FP>
+void set_initial_population(mio::oseirv::Model<FP>& model, const FP total_pop)
+{
+    auto& params            = model.parameters;
+    auto& pop               = model.populations;
+    const size_t num_groups = (size_t)params.get_num_groups();
+
+    for (size_t i = 0; i < num_groups; ++i) {
+        pop.template set_difference_from_group_total<mio::AgeGroup>(
+            {mio::AgeGroup(i), mio::oseirv::InfectionState::Susceptible}, total_pop / num_groups);
+
+        // Total population N_i as currently stored in group totals
+        FP Ni = pop.get_group_total(mio::AgeGroup(i));
+
+        FP s_age  = params.template get<mio::oseirv::SusceptibilityByAge<FP>>()[mio::AgeGroup(i)];
+        FP s_frac = params.template get<mio::oseirv::SusceptibleFraction<FP>>();
+        FP vc     = params.template get<mio::oseirv::VaccineCoverage<FP>>()[mio::AgeGroup(i)];
+        FP ve     = params.template get<mio::oseirv::VaccineEffectiveness<FP>>()[mio::AgeGroup(i)];
+
+        pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::Exposed}]            = 0;
+        pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::ExposedVaccinated}]  = 0;
+        pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::Infected}]           = 0;
+        pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::InfectedVaccinated}] = 0;
+
+        pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::Susceptible}] = s_frac * s_age * (FP(1) - vc) * Ni;
+        pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::SusceptibleVaccinated}] =
+            s_frac * s_age * (FP(1) - ve) * vc * Ni;
+
+        pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::Recovered}] = (FP(1) - s_frac * s_age) * (FP(1) - vc) * Ni;
+        pop[{mio::AgeGroup(i), mio::oseirv::InfectionState::RecoveredVaccinated}] =
+            (FP(1) - s_frac * s_age * (FP(1) - ve)) * vc * Ni;
+    }
+}
+
+// Example usage of the SEIRV ODE model presented in https://doi.org/10.1186/s12879-017-2344-6
+int main()
+{
+    using FP = double;
+    mio::set_log_level(mio::LogLevel::debug);
+
+    const FP t0 = 0., tmax = 42.;
+    const FP dt = 0.1;
+
+    const size_t num_groups = 1;
+    const auto total_pop    = 1e5;
+    mio::oseirv::Model<FP> model((int)num_groups);
+    auto& parameters = model.parameters;
+
+    FP cont_freq       = 10.0;
+    FP cont_freq_group = FP(1) / FP(num_groups);
+
+    // Healthy contacts
+    mio::ContactMatrixGroup<ScalarType>& contacts_healthy = parameters.get<mio::oseirv::ContactPatternsHealthy<FP>>();
+    contacts_healthy[0]                                   = mio::ContactMatrix<FP>(
+        Eigen::MatrixXd::Constant((Eigen::Index)num_groups, (Eigen::Index)num_groups, cont_freq_group * cont_freq));
+
+    // Sick contacts (here 20% reduced)
+    mio::ContactMatrixGroup<ScalarType>& contacts_sick = parameters.get<mio::oseirv::ContactPatternsSick<FP>>();
+    contacts_sick[0]                                   = mio::ContactMatrix<FP>(Eigen::MatrixXd::Constant(
+        (Eigen::Index)num_groups, (Eigen::Index)num_groups, cont_freq_group * cont_freq * 0.8));
+
+    // Parameters
+    parameters.get<mio::oseirv::BaselineTransmissibility<FP>>()   = 1.2;
+    parameters.get<mio::oseirv::RecoveryRate<FP>>()               = 1.0 / 2.0;
+    parameters.get<mio::oseirv::SeasonalityAmplitude<FP>>()       = 1.0;
+    parameters.get<mio::oseirv::SeasonalityShiftPerSubtype<FP>>() = 0.0;
+    parameters.get<mio::oseirv::SeasonalityShiftPerSeason<FP>>()  = 0.0;
+    parameters.get<mio::oseirv::OutsideFoI<FP>>()                 = 1e-6;
+    parameters.get<mio::oseirv::ClusteringExponent<FP>>()         = 0.9;
+    parameters.get<mio::oseirv::SickMixing<FP>>()                 = 2.0;
+
+    for (size_t i = 0; i < num_groups; ++i) {
+        parameters.get<mio::oseirv::SusceptibilityByAge<FP>>()[mio::AgeGroup(i)]  = 1.0;
+        parameters.get<mio::oseirv::VaccineCoverage<FP>>()[mio::AgeGroup(i)]      = 0.3;
+        parameters.get<mio::oseirv::VaccineEffectiveness<FP>>()[mio::AgeGroup(i)] = 0.5;
+        model.populations.set_difference_from_group_total<mio::AgeGroup>(
+            {mio::AgeGroup(i), mio::oseirv::InfectionState::Susceptible}, 1e5 / num_groups);
+    }
+
+    set_initial_population(model, total_pop);
+
+    auto seirv = mio::simulate<FP>(t0, tmax, dt, model);
+
+    std::vector<std::string> vars = {"S", "SV", "E", "EV", "I", "IV", "R", "RV"};
+    seirv.print_table(vars);
+}

cpp/models/ode_seirv/CMakeLists.txt

@@ -0,0 +1,12 @@
+add_library(ode_seirv
+    infection_state.h
+    model.h
+    model.cpp
+    parameters.h
+)
+target_link_libraries(ode_seirv PUBLIC memilio)
+target_include_directories(ode_seirv PUBLIC
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/..>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
+target_compile_options(ode_seirv PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})

cpp/models/ode_seirv/README.md

@@ -0,0 +1,23 @@
+# ODE SEIRV (seasonal influenza)
+
+A age‑structured **SEIRV** model implemented into the MEmilio ODE framework.  
+It extends the classic SEIR by a vaccinated layer (Sᵛ, Eᵛ, Iᵛ, Rᵛ) and follows the seasonal influenza
+model structure from:
+
+> **Weidemann, F., Remschmidt, C., Buda, S. et al.**  
+> *Is the impact of childhood influenza vaccination less than expected: a transmission modelling study.*  
+> **BMC Infectious Diseases** 17, 258 (2017).  
+> https://doi.org/10.1186/s12879-017-2344-6
+
+## Get started
+
+To get started, check out the
+[official documentation](https://memilio.readthedocs.io/en/latest/cpp/models/oseirv.html)
+or the [code example](../../examples/ode_seirv_example.cpp).
+
+## Reference
+
+Please cite the original study if you use this model:
+
+> 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).  
+> https://doi.org/10.1186/s12879-017-2344-6

cpp/models/ode_seirv/infection_state.h

@@ -0,0 +1,42 @@
+/*
+* Copyright (C) 2020-2025 MEmilio
+*
+* Authors: Henrik Zunker
+*
+* Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
+*
+* 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.
+*/
+#ifndef SEIRV_INFECTIONSTATE_H
+#define SEIRV_INFECTIONSTATE_H
+namespace mio
+{
+namespace oseirv
+{
+
+enum class InfectionState
+{
+    Susceptible,
+    SusceptibleVaccinated,
+    Exposed,
+    ExposedVaccinated,
+    Infected,
+    InfectedVaccinated,
+    Recovered,
+    RecoveredVaccinated,
+    Count
+};
+
+} // namespace oseirv
+} // namespace mio
+#endif

cpp/models/ode_seirv/model.cpp

@@ -0,0 +1,20 @@
+/*
+* Copyright (C) 2020-2025 MEmilio
+*
+* Authors: Henrik Zunker
+*
+* Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
+*
+* 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_seirv/model.h"