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323 SECIRTS model with waning and temporary immunity (#963)
- Add new ODE model including waning immunity and temporary immunity states build upon the secirvvs model - New initialization method - Allow to read booster vaccinations as optional args from vaccination data in cpp Co-authored-by: reneSchm <49305466+reneSchm@users.noreply.github.com> Co-authored-by: Martin J. Kühn <62713180+mknaranja@users.noreply.github.com>
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| /* | ||
| * Copyright (C) 2020-2024 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_secirts/analyze_result.h" | ||
| #include "ode_secirts/model.h" | ||
| #include "ode_secirts/parameters.h" | ||
| #include "memilio/compartments/simulation.h" | ||
| #include "memilio/utils/logging.h" | ||
|
|
||
| int main() | ||
| { | ||
| // This example demonstrates how to simulate a SECIRTS model. | ||
| // The SECIRTS model is an extension of the SECIRVVS model that includes waning and temporary immunity. | ||
| // After the simulation, the aggregated size of the temporary immunity states are printed. | ||
| mio::set_log_level(mio::LogLevel::debug); | ||
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| double t0 = 0; | ||
| double tmax = 100; | ||
| double dt = 0.1; | ||
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| mio::log_info("Simulating SECIRTS; t={} ... {} with dt = {}.", t0, tmax, dt); | ||
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| mio::osecirts::Model<double> model(3); | ||
| auto nb_groups = model.parameters.get_num_groups(); | ||
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| for (mio::AgeGroup i = 0; i < nb_groups; i++) { | ||
| // population | ||
| model.populations[{i, mio::osecirts::InfectionState::ExposedNaive}] = 20; | ||
| model.populations[{i, mio::osecirts::InfectionState::ExposedImprovedImmunity}] = 20; | ||
| model.populations[{i, mio::osecirts::InfectionState::ExposedPartialImmunity}] = 20; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedNoSymptomsNaive}] = 30; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedNoSymptomsNaiveConfirmed}] = 0; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedNoSymptomsPartialImmunity}] = 30; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedNoSymptomsPartialImmunityConfirmed}] = 0; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedNoSymptomsImprovedImmunity}] = 30; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedNoSymptomsImprovedImmunityConfirmed}] = 0; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedSymptomsNaive}] = 40; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedSymptomsNaiveConfirmed}] = 0; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedSymptomsPartialImmunity}] = 40; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedSymptomsPartialImmunityConfirmed}] = 0; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedSymptomsImprovedImmunity}] = 40; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedSymptomsImprovedImmunityConfirmed}] = 0; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedSevereNaive}] = 30; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedSevereImprovedImmunity}] = 30; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedSeverePartialImmunity}] = 30; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedCriticalNaive}] = 20; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedCriticalPartialImmunity}] = 20; | ||
| model.populations[{i, mio::osecirts::InfectionState::InfectedCriticalImprovedImmunity}] = 20; | ||
| model.populations[{i, mio::osecirts::InfectionState::SusceptibleNaive}] = 1000; | ||
| model.populations[{i, mio::osecirts::InfectionState::SusceptiblePartialImmunity}] = 1200; | ||
| model.populations[{i, mio::osecirts::InfectionState::SusceptibleImprovedImmunity}] = 1000; | ||
| model.populations[{i, mio::osecirts::InfectionState::TemporaryImmunePartialImmunity}] = 60; | ||
| model.populations[{i, mio::osecirts::InfectionState::TemporaryImmuneImprovedImmunity}] = 70; | ||
| model.populations[{i, mio::osecirts::InfectionState::DeadNaive}] = 0; | ||
| model.populations[{i, mio::osecirts::InfectionState::DeadPartialImmunity}] = 0; | ||
| model.populations[{i, mio::osecirts::InfectionState::DeadImprovedImmunity}] = 0; | ||
|
|
||
| // parameters | ||
| //times | ||
| model.parameters.get<mio::osecirts::TimeExposed<double>>()[i] = 3.33; | ||
| model.parameters.get<mio::osecirts::TimeInfectedNoSymptoms<double>>()[i] = 1.87; | ||
| model.parameters.get<mio::osecirts::TimeInfectedSymptoms<double>>()[i] = 7; | ||
| model.parameters.get<mio::osecirts::TimeInfectedSevere<double>>()[i] = 6; | ||
| model.parameters.get<mio::osecirts::TimeInfectedCritical<double>>()[i] = 7; | ||
| model.parameters.get<mio::osecirts::TimeTemporaryImmunityPI<double>>()[i] = 60; | ||
| model.parameters.get<mio::osecirts::TimeTemporaryImmunityII<double>>()[i] = 60; | ||
| model.parameters.get<mio::osecirts::TimeWaningPartialImmunity<double>>()[i] = 180; | ||
| model.parameters.get<mio::osecirts::TimeWaningImprovedImmunity<double>>()[i] = 180; | ||
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| //probabilities | ||
| model.parameters.get<mio::osecirts::TransmissionProbabilityOnContact<double>>()[i] = 0.15; | ||
| model.parameters.get<mio::osecirts::RelativeTransmissionNoSymptoms<double>>()[i] = 0.5; | ||
| model.parameters.get<mio::osecirts::RiskOfInfectionFromSymptomatic<double>>()[i] = 0.0; | ||
| model.parameters.get<mio::osecirts::MaxRiskOfInfectionFromSymptomatic<double>>()[i] = 0.4; | ||
| model.parameters.get<mio::osecirts::RecoveredPerInfectedNoSymptoms<double>>()[i] = 0.2; | ||
| model.parameters.get<mio::osecirts::SeverePerInfectedSymptoms<double>>()[i] = 0.1; | ||
| model.parameters.get<mio::osecirts::CriticalPerSevere<double>>()[i] = 0.1; | ||
| model.parameters.get<mio::osecirts::DeathsPerCritical<double>>()[i] = 0.1; | ||
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| model.parameters.get<mio::osecirts::ReducExposedPartialImmunity<double>>()[i] = 0.8; | ||
| model.parameters.get<mio::osecirts::ReducExposedImprovedImmunity<double>>()[i] = 0.331; | ||
| model.parameters.get<mio::osecirts::ReducInfectedSymptomsPartialImmunity<double>>()[i] = 0.65; | ||
| model.parameters.get<mio::osecirts::ReducInfectedSymptomsImprovedImmunity<double>>()[i] = 0.243; | ||
| model.parameters.get<mio::osecirts::ReducInfectedSevereCriticalDeadPartialImmunity<double>>()[i] = 0.1; | ||
| model.parameters.get<mio::osecirts::ReducInfectedSevereCriticalDeadImprovedImmunity<double>>()[i] = 0.091; | ||
| model.parameters.get<mio::osecirts::ReducTimeInfectedMild<double>>()[i] = 0.9; | ||
| } | ||
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| model.parameters.get<mio::osecirts::ICUCapacity<double>>() = 100; | ||
| model.parameters.get<mio::osecirts::TestAndTraceCapacity<double>>() = 0.0143; | ||
| const size_t daily_vaccinations = 10; | ||
| const size_t num_days = 300; | ||
| model.parameters.get<mio::osecirts::DailyPartialVaccinations<double>>().resize(mio::SimulationDay(num_days)); | ||
| model.parameters.get<mio::osecirts::DailyFullVaccinations<double>>().resize(mio::SimulationDay(num_days)); | ||
| model.parameters.get<mio::osecirts::DailyBoosterVaccinations<double>>().resize(mio::SimulationDay(num_days)); | ||
| for (size_t i = 0; i < num_days; ++i) { | ||
| for (mio::AgeGroup j = 0; j < nb_groups; ++j) { | ||
| auto num_vaccinations = static_cast<double>(i * daily_vaccinations); | ||
| model.parameters.get<mio::osecirts::DailyPartialVaccinations<double>>()[{j, mio::SimulationDay(i)}] = | ||
| num_vaccinations; | ||
| model.parameters.get<mio::osecirts::DailyFullVaccinations<double>>()[{j, mio::SimulationDay(i)}] = | ||
| num_vaccinations; | ||
| model.parameters.get<mio::osecirts::DailyBoosterVaccinations<double>>()[{j, mio::SimulationDay(i)}] = | ||
| num_vaccinations; | ||
| } | ||
| } | ||
|
|
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| mio::ContactMatrixGroup& contact_matrix = model.parameters.get<mio::osecirts::ContactPatterns<double>>(); | ||
| const double cont_freq = 10; | ||
| const double fact = 1.0 / (double)(size_t)nb_groups; | ||
| contact_matrix[0] = | ||
| mio::ContactMatrix(Eigen::MatrixXd::Constant((size_t)nb_groups, (size_t)nb_groups, fact * cont_freq)); | ||
| contact_matrix.add_damping(Eigen::MatrixXd::Constant((size_t)nb_groups, (size_t)nb_groups, 0.7), | ||
| mio::SimulationTime(30.)); | ||
|
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| model.parameters.get<mio::osecirts::Seasonality<double>>() = 0.2; | ||
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| model.apply_constraints(); | ||
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| mio::TimeSeries<double> result = simulate(t0, tmax, dt, model); | ||
|
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| bool print_to_terminal = true; | ||
|
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| if (print_to_terminal) { | ||
| auto result_interpolated = mio::interpolate_simulation_result(result); | ||
| for (auto t_indx = 0; t_indx < result_interpolated.get_num_time_points(); t_indx++) { | ||
| double timm_pi = 0.0; | ||
| double timm_ii = 0.0; | ||
| for (mio::AgeGroup i = 0; i < nb_groups; i++) { | ||
| timm_pi += result_interpolated.get_value(t_indx)[model.populations.get_flat_index( | ||
| {i, mio::osecirts::InfectionState::TemporaryImmunePartialImmunity})]; | ||
| timm_ii += result_interpolated.get_value(t_indx)[model.populations.get_flat_index( | ||
| {i, mio::osecirts::InfectionState::TemporaryImmuneImprovedImmunity})]; | ||
| } | ||
| printf("t=%i, timm_pi=%f, timm_ii=%f\n", int(result_interpolated.get_time(t_indx)), timm_pi, timm_ii); | ||
| } | ||
| } | ||
| } |
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