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@hatrit
hatrit committed Nov 14, 2024
1 parent 9d99ff2 commit dae92dd
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Showing 4 changed files with 34 additions and 27 deletions.
6 changes: 3 additions & 3 deletions cpp/examples/ide_secir.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -73,9 +73,9 @@ int main()

// Uncomment one of the two lines to use a different method to initialize the model using the TimeSeries init.
// Initialization method with Susceptibles.
model.m_populations.get_last_value()[(Eigen::Index)mio::isecir::InfectionState::Susceptible] = 1000;
// Initialization mehtod with Recovered.
model.m_populations.get_last_value()[(Eigen::Index)mio::isecir::InfectionState::Recovered] = 0;
// model.m_populations.get_last_value()[(Eigen::Index)mio::isecir::InfectionState::Susceptible] = 1000;
// Initialization method with Recovered.
// model.m_populations.get_last_value()[(Eigen::Index)mio::isecir::InfectionState::Recovered] = 0;

// Set working parameters.
mio::SmootherCosine smoothcos(2.0);
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43 changes: 25 additions & 18 deletions cpp/examples/ide_secir_ageres.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ int main()
size_t num_agegroups = 2;

ScalarType tmax = 5;
std::vector<ScalarType> N = std::vector<ScalarType>(num_agegroups, 5000.);
std::vector<ScalarType> N = std::vector<ScalarType>(num_agegroups, 10000.);
std::vector<ScalarType> deaths = std::vector<ScalarType>(num_agegroups, 6.);
ScalarType dt = 1.;

Expand All @@ -32,16 +32,19 @@ int main()
Vec vec_init(num_transitions * num_agegroups);
// Values for the Infectiontransitions are the same for all AgeGroups.
for (size_t group = 0; group < num_agegroups; ++group) {
vec_init[group + (int)mio::isecir::InfectionTransition::SusceptibleToExposed] = 25.0;
vec_init[group + (int)mio::isecir::InfectionTransition::ExposedToInfectedNoSymptoms] = 15.0;
vec_init[group + (int)mio::isecir::InfectionTransition::InfectedNoSymptomsToInfectedSymptoms] = 8.0;
vec_init[group + (int)mio::isecir::InfectionTransition::InfectedNoSymptomsToRecovered] = 4.0;
vec_init[group + (int)mio::isecir::InfectionTransition::InfectedSymptomsToInfectedSevere] = 1.0;
vec_init[group + (int)mio::isecir::InfectionTransition::InfectedSymptomsToRecovered] = 4.0;
vec_init[group + (int)mio::isecir::InfectionTransition::InfectedSevereToInfectedCritical] = 1.0;
vec_init[group + (int)mio::isecir::InfectionTransition::InfectedSevereToRecovered] = 1.0;
vec_init[group + (int)mio::isecir::InfectionTransition::InfectedCriticalToDead] = 1.0;
vec_init[group + (int)mio::isecir::InfectionTransition::InfectedCriticalToRecovered] = 1.0;
vec_init[group * num_transitions + (int)mio::isecir::InfectionTransition::SusceptibleToExposed] = 25.0;
vec_init[group * num_transitions + (int)mio::isecir::InfectionTransition::ExposedToInfectedNoSymptoms] = 15.0;
vec_init[group * num_transitions +
(int)mio::isecir::InfectionTransition::InfectedNoSymptomsToInfectedSymptoms] = 8.0;
vec_init[group * num_transitions + (int)mio::isecir::InfectionTransition::InfectedNoSymptomsToRecovered] = 4.0;
vec_init[group * num_transitions + (int)mio::isecir::InfectionTransition::InfectedSymptomsToInfectedSevere] =
1.0;
vec_init[group * num_transitions + (int)mio::isecir::InfectionTransition::InfectedSymptomsToRecovered] = 4.0;
vec_init[group * num_transitions + (int)mio::isecir::InfectionTransition::InfectedSevereToInfectedCritical] =
1.0;
vec_init[group * num_transitions + (int)mio::isecir::InfectionTransition::InfectedSevereToRecovered] = 1.0;
vec_init[group * num_transitions + (int)mio::isecir::InfectionTransition::InfectedCriticalToDead] = 1.0;
vec_init[group * num_transitions + (int)mio::isecir::InfectionTransition::InfectedCriticalToRecovered] = 1.0;
}

// Add initial time point to time series.
Expand All @@ -52,15 +55,15 @@ int main()
}

// Initialize model.
mio::isecir::Model model(std::move(init), N, deaths, num_agegroups, std::vector<ScalarType>(num_agegroups, 100.));
mio::isecir::Model model(std::move(init), N, deaths, num_agegroups);

// Uncomment these lines to use a different method to initialize the model using the TimeSeries init.
// Initialization method with Susceptibles.
//model.m_populations.get_last_value()[(Eigen::Index)mio::isecir::InfectionState::Susceptible] = 1000;
// model.m_populations.get_last_value()[(Eigen::Index)mio::isecir::InfectionState::Susceptible] = 1000;
// model.m_populations.get_last_value()[(Eigen::Index)mio::isecir::InfectionState::Count +
// (Eigen::Index)mio::isecir::InfectionState::Susceptible] = 1000;
// Initialization method with Recovered.
//model.m_populations.get_last_value()[(Eigen::Index)mio::isecir::InfectionState::Recovered] = 0;
// model.m_populations.get_last_value()[(Eigen::Index)mio::isecir::InfectionState::Recovered] = 0;
// model.m_populations.get_last_value()[(Eigen::Index)mio::isecir::InfectionState::Count +
// (Eigen::Index)mio::isecir::InfectionState::Recovered] = 0;

Expand All @@ -69,13 +72,17 @@ int main()
mio::SmootherCosine smoothcos1(2.0);
mio::StateAgeFunctionWrapper delaydistribution1(smoothcos1);
std::vector<mio::StateAgeFunctionWrapper> vec_delaydistrib1(num_transitions, delaydistribution1);
// TransitionDistribution is not used for SusceptibleToExposed. Therefore, the parameter can be set to any value.
vec_delaydistrib1[(int)mio::isecir::InfectionTransition::SusceptibleToExposed].set_distribution_parameter(-1.);

model.parameters.get<mio::isecir::TransitionDistributions>()[mio::AgeGroup(0)] = vec_delaydistrib1;

//Second AgeGroup for Transition Distributions.
mio::SmootherCosine smoothcos2(3.0);
mio::StateAgeFunctionWrapper delaydistribution2(smoothcos2);
std::vector<mio::StateAgeFunctionWrapper> vec_delaydistrib2(num_transitions, delaydistribution2);
// TransitionDistribution is not used for SusceptibleToExposed. Therefore, the parameter can be set to any value.
vec_delaydistrib2[(int)mio::isecir::InfectionTransition::SusceptibleToExposed].set_distribution_parameter(-1.);

model.parameters.get<mio::isecir::TransitionDistributions>()[mio::AgeGroup(1)] = vec_delaydistrib2;

Expand Down Expand Up @@ -113,8 +120,8 @@ int main()
interpolated_results.print_table(
{"S1", "E1", "C1", "I1", "H1", "U1", "R1", "D1 ", "S2", "E2", "C2", "I2", "H2", "U2", "R2", "D2 "}, 16, 8);
// Uncomment this line to print the transitions.
// sim.get_transitions().print_table({"S->E 1", "E->C 1", "C->I 1", "C->R 1", "I->H 1", "I->R 1", "H->U 1",
// "H->R 1", "U->D 1", "U->R 1", "S->E 2", "E->C 2", "C->I 2", "C->R 2",
// "I->H 2", "I->R 2", "H->U 2", "H->R 2", "U->D 2", "U->R 2"},
// 16, 8);
sim.get_transitions().print_table({"S->E 1", "E->C 1", "C->I 1", "C->R 1", "I->H 1", "I->R 1", "H->U 1",
"H->R 1", "U->D 1", "U->R 1", "S->E 2", "E->C 2", "C->I 2", "C->R 2",
"I->H 2", "I->R 2", "H->U 2", "H->R 2", "U->D 2", "U->R 2"},
16, 8);
}
10 changes: 5 additions & 5 deletions cpp/models/ide_secir/model.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -390,7 +390,7 @@ void Model::flows_current_timestep(ScalarType dt)
void Model::update_compartments()
{
// Update compartments for every AgeGroup.
for (AgeGroup group = AgeGroup(0); group < AgeGroup(m_num_agegroups); ++group) {
for (size_t group = 0; group < m_num_agegroups; ++group) {
// Exposed
update_compartment_from_flow(InfectionState::Exposed, {InfectionTransition::SusceptibleToExposed},
{InfectionTransition::ExposedToInfectedNoSymptoms}, group);
Expand Down Expand Up @@ -437,18 +437,18 @@ void Model::update_compartments()

void Model::update_compartment_from_flow(InfectionState infectionState,
std::vector<InfectionTransition> const& IncomingFlows,
std::vector<InfectionTransition> const& OutgoingFlows, AgeGroup group)
std::vector<InfectionTransition> const& OutgoingFlows, size_t group)
{
int state_idx = get_state_flat_index(Eigen::Index(infectionState), size_t(group));
int state_idx = get_state_flat_index(Eigen::Index(infectionState), group);

Eigen::Index num_time_points = m_populations.get_num_time_points();
ScalarType updated_compartment = m_populations[num_time_points - 2][state_idx];
for (const InfectionTransition& inflow : IncomingFlows) {
int inflow_idx = get_transition_flat_index(Eigen::Index(inflow), size_t(group));
int inflow_idx = get_transition_flat_index(Eigen::Index(inflow), group);
updated_compartment += m_transitions.get_last_value()[inflow_idx];
}
for (const InfectionTransition& outflow : OutgoingFlows) {
int outflow_idx = get_transition_flat_index(Eigen::Index(outflow), size_t(group));
int outflow_idx = get_transition_flat_index(Eigen::Index(outflow), group);
updated_compartment -= m_transitions.get_last_value()[outflow_idx];
}
m_populations.get_last_value()[state_idx] = updated_compartment;
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2 changes: 1 addition & 1 deletion cpp/models/ide_secir/model.h
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Original file line number Diff line number Diff line change
Expand Up @@ -384,7 +384,7 @@ class Model
*/
void update_compartment_from_flow(InfectionState infectionState,
std::vector<InfectionTransition> const& IncomingFlows,
std::vector<InfectionTransition> const& OutgoingFlows, AgeGroup group);
std::vector<InfectionTransition> const& OutgoingFlows, size_t group);

// ---- Private parameters. ----
std::vector<ScalarType> m_forceofinfection{0}; ///< Force of infection term needed for numerical scheme.
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