1003 implement ODE SEIR metapopulation model

cpp/CMakeLists.txt

@@ -188,6 +188,7 @@ if(MEMILIO_BUILD_MODELS)
     add_subdirectory(models/ode_seirdb)
     add_subdirectory(models/ode_seair)
     add_subdirectory(models/ode_sir)
+    add_subdirectory(models/ode_seir_metapop)
     add_subdirectory(models/sde_sir)
     add_subdirectory(models/sde_sirs)
     add_subdirectory(models/sde_seirvv)

cpp/examples/CMakeLists.txt

@@ -112,6 +112,10 @@ add_executable(graph_stochastic_mobility_example graph_stochastic_mobility.cpp)
 target_link_libraries(graph_stochastic_mobility_example PRIVATE memilio ode_secir)
 target_compile_options(graph_stochastic_mobility_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
 
+add_executable(ode_metapop_seir_example ode_seir_metapop.cpp)
+target_link_libraries(ode_metapop_seir_example PRIVATE memilio ode_seir_metapop)
+target_compile_options(ode_metapop_seir_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
+
 add_executable(abm_minimal_example abm_minimal.cpp)
 target_link_libraries(abm_minimal_example PRIVATE memilio abm)
 target_compile_options(abm_minimal_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})

cpp/examples/ode_seir_metapop.cpp

@@ -0,0 +1,44 @@
+#include "memilio/compartments/simulation.h"
+#include "memilio/utils/custom_index_array.h"
+#include "models/ode_seir_metapop/model.h"
+#include "models/ode_seir_metapop/parameters.h"
+#include "memilio/geography/regions.h"
+
+int main()
+{
+    const ScalarType t0   = 0.;
+    const ScalarType tmax = 10;
+    ScalarType dt         = 0.1;
+
+    using namespace mio::oseirmetapop;
+
+    Model<ScalarType> model(3, 1);
+
+    for (size_t i = 0; i < (size_t)model.parameters.get_num_regions(); i++) {
+        model.populations[{mio::regions::Region(i), mio::AgeGroup(0), InfectionState::Susceptible}] =
+            10000;
+    }
+
+    model.populations[{mio::regions::Region(0), mio::AgeGroup(0), InfectionState::Exposed}] += 100;
+    model.populations[{mio::regions::Region(0), mio::AgeGroup(0), InfectionState::Susceptible}] -=
+        100;
+
+    Eigen::MatrixXd mobility_data_commuter(3, 3);
+    mobility_data_commuter << 0.4, 0.3, 0.3, 0.2, 0.7, 0.1, 0.4, 0.1, 0.5;
+
+    model.set_commuting_strengths(mobility_data_commuter);
+
+    model.parameters.template get<ContactPatterns<>>()
+        .get_cont_freq_mat()[0]
+        .get_baseline()
+        .setConstant(2.7);
+
+    model.parameters.set<TimeExposed<>>(3.335);
+    model.parameters.set<TimeInfected<>>(8.097612257);
+    model.parameters.set<TransmissionProbabilityOnContact<>>(0.07333);
+
+    auto result = simulate(t0, tmax, dt, model);
+
+    result.print_table();
+    return 0;
+}

cpp/memilio/epidemiology/contact_matrix.h

@@ -34,7 +34,7 @@ namespace mio
 {
 
 /**
- * represents the coefficient wise matrix (or vector) expression B - D * M
+ * Represents the coefficient wise matrix (or vector) expression B - D * (B - M)
  * where B is a baseline, M is a minimum and D is some time dependent complex damping factor.
  * Base class for e.g. time dependent contact matrices.
  * Coefficient wise expression, so B, D, M matrices must have the same shape.

cpp/models/ode_seir_metapop/CMakeLists.txt

@@ -0,0 +1,11 @@
+add_library(ode_seir_metapop
+    model.h
+    model.cpp
+    parameters.h
+)
+target_link_libraries(ode_seir_metapop PUBLIC memilio)
+target_include_directories(ode_seir_metapop PUBLIC
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/..>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
+target_compile_options(ode_seir_metapop PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})

cpp/models/ode_seir_metapop/infection_state.h

@@ -0,0 +1,36 @@
+/* 
+* Copyright (C) 2020-2025 MEmilio
+*
+* Authors: Carlotta Gerstein
+*
+* 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 SEIRMETAPOP_INFECTIONSTATE_H
+#define SEIRMETAPOP_INFECTIONSTATE_H
+
+#include "models/ode_seir/infection_state.h"
+
+namespace mio
+{
+namespace oseirmetapop
+{
+
+using mio::oseir::InfectionState;
+
+} // namespace oseirmetapop
+} // namespace mio
+
+#endif // SEIRMETAPOP_INFECTIONSTATE_H

cpp/models/ode_seir_metapop/model.cpp

@@ -0,0 +1,28 @@
+/* 
+* Copyright (C) 2020-2025 MEmilio
+*
+* Authors: Carlotta Gerstein
+*
+* 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_seir_metapop/model.h"
+
+namespace mio
+{
+namespace oseirmetapop
+{
+
+} // namespace oseirmetapop
+} // namespace mio