Skip to content

964 Times for Exposed and INS instead of SerialInterval and IncubationTime #967

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
HenrZu merged 10 commits into from
Mar 18, 2024
Merged

964 Times for Exposed and INS instead of SerialInterval and IncubationTime #967

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
2c7f0f2
rm SI and INC for secir
HenrZu Mar 8, 2024
5a59614
same for the secirvvs
HenrZu Mar 8, 2024
0ced8ba
adjust pycode
HenrZu Mar 8, 2024
25bf9ca
Apply suggestions from code review
HenrZu Mar 11, 2024
24259c3
rm explicit rates from model eqs+adjusting values
HenrZu Mar 11, 2024
2d0d372
indx correction
HenrZu Mar 11, 2024
0aefbf1
old duplicates and move params to not age dep
HenrZu Mar 11, 2024
234eb0e
adjust delta osecir pycode
HenrZu Mar 11, 2024
2547e3a
fix odesecir model (better rounding)
HenrZu Mar 11, 2024
093d615
updated readme in simulations
HenrZu Mar 12, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
91 changes: 48 additions & 43 deletions cpp/benchmarks/flow_simulation_ode_secirvvs.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -64,10 +64,9 @@ class FlowlessModel : public CompartmentalModel<osecirvvs::InfectionState,
auto icu_occupancy = 0.0;
auto test_and_trace_required = 0.0;
for (auto i = AgeGroup(0); i < n_agegroups; ++i) {
auto rateINS =
0.5 / (params.get<osecirvvs::IncubationTime>()[i] - params.get<osecirvvs::SerialInterval>()[i]);
test_and_trace_required +=
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) * rateINS *
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) /
params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] *
(this->populations.get_from(pop, {i, InfectionState::InfectedNoSymptomsNaive}) +
this->populations.get_from(pop, {i, InfectionState::InfectedNoSymptomsPartialImmunity}) +
this->populations.get_from(pop, {i, InfectionState::InfectedNoSymptomsImprovedImmunity}) +
Expand Down Expand Up @@ -128,11 +127,6 @@ class FlowlessModel : public CompartmentalModel<osecirvvs::InfectionState,
dydt[SIIi] = 0;
dydt[EIIi] = 0;

double rateE =
1.0 / (2 * params.get<osecirvvs::SerialInterval>()[i] - params.get<osecirvvs::IncubationTime>()[i]);
double rateINS =
0.5 / (params.get<osecirvvs::IncubationTime>()[i] - params.get<osecirvvs::SerialInterval>()[i]);

double reducExposedPartialImmunity = params.get<osecirvvs::ReducExposedPartialImmunity>()[i];
double reducExposedImprovedImmunity = params.get<osecirvvs::ReducExposedImprovedImmunity>()[i];
double reducInfectedSymptomsPartialImmunity =
Expand Down Expand Up @@ -244,13 +238,17 @@ class FlowlessModel : public CompartmentalModel<osecirvvs::InfectionState,

/**** path of immune-naive ***/

dydt[ENi] -= rateE * y[ENi]; // only exchange of E and InfectedNoSymptoms done here
dydt[INSNi] = rateE * y[ENi] - rateINS * y[INSNi];
dydt[INSNCi] = -rateINS * y[INSNCi];
dydt[ENi] -=
y[ENi] / params.get<osecirvvs::TimeExposed>()[i]; // only exchange of E and InfectedNoSymptoms done here
dydt[INSNi] = y[ENi] / params.get<osecirvvs::TimeExposed>()[i] -
y[INSNi] / params.get<osecirvvs::TimeInfectedNoSymptoms>()[i];
dydt[INSNCi] = -y[INSNCi] / params.get<osecirvvs::TimeInfectedNoSymptoms>()[i];

dydt[ISyNi] = (1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) * rateINS * y[INSNi] -
dydt[ISyNi] = (1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) /
params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * y[INSNi] -
(y[ISyNi] / params.get<osecirvvs::TimeInfectedSymptoms>()[i]);
dydt[ISyNCi] = (1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) * rateINS * y[INSNCi] -
dydt[ISyNCi] = (1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) /
params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * y[INSNCi] -
(y[ISyNCi] / params.get<osecirvvs::TimeInfectedSymptoms>()[i]);

dydt[ISevNi] = params.get<osecirvvs::SeverePerInfectedSymptoms>()[i] /
Expand All @@ -262,16 +260,20 @@ class FlowlessModel : public CompartmentalModel<osecirvvs::InfectionState,

/**** path of partially immune (e.g., one dose of vaccination) ***/

dydt[EPIi] -= rateE * y[EPIi]; // only exchange of E and InfectedNoSymptoms done here
dydt[INSPIi] = rateE * y[EPIi] - (rateINS / reducTimeInfectedMild) * y[INSPIi];
dydt[INSPICi] = -(rateINS / reducTimeInfectedMild) * y[INSPICi];
dydt[EPIi] -=
y[EPIi] /
params.get<osecirvvs::TimeExposed>()[i]; // only exchange of E and InfectedNoSymptoms done here
dydt[INSPIi] = y[EPIi] / params.get<osecirvvs::TimeExposed>()[i] -
y[INSPIi] / (params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * reducTimeInfectedMild);
dydt[INSPICi] = -y[INSPICi] / (params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * reducTimeInfectedMild);
dydt[ISyPIi] = (reducInfectedSymptomsPartialImmunity / reducExposedPartialImmunity) *
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) *
(rateINS / reducTimeInfectedMild) * y[INSPIi] -
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) * y[INSPIi] /
(params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * reducTimeInfectedMild) -
(y[ISyPIi] / (params.get<osecirvvs::TimeInfectedSymptoms>()[i] * reducTimeInfectedMild));
dydt[ISyPICi] = (reducInfectedSymptomsPartialImmunity / reducExposedPartialImmunity) *
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) *
(rateINS / reducTimeInfectedMild) * y[INSPICi] -
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) /
(params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * reducTimeInfectedMild) *
y[INSPICi] -
(y[ISyPICi] / (params.get<osecirvvs::TimeInfectedSymptoms>()[i] * reducTimeInfectedMild));
dydt[ISevPIi] = reducInfectedSevereCriticalDeadPartialImmunity / reducInfectedSymptomsPartialImmunity *
params.get<osecirvvs::SeverePerInfectedSymptoms>()[i] /
Expand All @@ -286,19 +288,20 @@ class FlowlessModel : public CompartmentalModel<osecirvvs::InfectionState,

/**** path of twice vaccinated, here called immune although reinfection is possible now ***/

dydt[EIIi] -= rateE * y[EIIi]; // only exchange of E and C done here
dydt[EIIi] -= y[EIIi] / params.get<osecirvvs::TimeExposed>()[i]; // only exchange of E and C done here

dydt[INSIIi] = rateE * y[EIIi] - (rateINS / reducTimeInfectedMild) * y[INSIIi];
dydt[INSIICi] = -(rateINS / reducTimeInfectedMild) * y[INSIICi];
dydt[INSIIi] = y[EIIi] / params.get<osecirvvs::TimeExposed>()[i] -
y[INSIIi] / (params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * reducTimeInfectedMild);
dydt[INSIICi] = -y[INSIICi] / (params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * reducTimeInfectedMild);

dydt[ISyIIi] = (reducInfectedSymptomsImprovedImmunity / reducExposedImprovedImmunity) *
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) *
(rateINS / reducTimeInfectedMild) * y[INSIIi] -
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) * y[INSIIi] /
(params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * reducTimeInfectedMild) -
(1 / (params.get<osecirvvs::TimeInfectedSymptoms>()[i] * reducTimeInfectedMild)) * y[ISyIIi];
dydt[ISyIICi] =
(reducInfectedSymptomsImprovedImmunity / reducExposedImprovedImmunity) *
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) *
(rateINS / reducTimeInfectedMild) * y[INSIICi] -
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i]) * y[INSIICi] /
(params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * reducTimeInfectedMild) -
(1 / (params.get<osecirvvs::TimeInfectedSymptoms>()[i] * reducTimeInfectedMild)) * y[ISyIICi];
dydt[ISevIIi] = reducInfectedSevereCriticalDeadImprovedImmunity / reducInfectedSymptomsImprovedImmunity *
params.get<osecirvvs::SeverePerInfectedSymptoms>()[i] /
Expand All @@ -312,19 +315,20 @@ class FlowlessModel : public CompartmentalModel<osecirvvs::InfectionState,
params.get<osecirvvs::TimeInfectedSevere>()[i] * y[ISevIIi];

// recovered and deaths from all paths
dydt[SIIi] +=
params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i] * rateINS * (y[INSNi] + y[INSNCi]) +
(1 - params.get<osecirvvs::SeverePerInfectedSymptoms>()[i]) /
params.get<osecirvvs::TimeInfectedSymptoms>()[i] * (y[ISyNi] + y[ISyNCi]) +
(1 - params.get<osecirvvs::CriticalPerSevere>()[i]) / params.get<osecirvvs::TimeInfectedSevere>()[i] *
y[ISevNi] +
(1 - params.get<osecirvvs::DeathsPerCritical>()[i]) / params.get<osecirvvs::TimeInfectedCritical>()[i] *
y[ICrNi];
dydt[SIIi] += params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i] /
params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * (y[INSNi] + y[INSNCi]) +
(1 - params.get<osecirvvs::SeverePerInfectedSymptoms>()[i]) /
params.get<osecirvvs::TimeInfectedSymptoms>()[i] * (y[ISyNi] + y[ISyNCi]) +
(1 - params.get<osecirvvs::CriticalPerSevere>()[i]) /
params.get<osecirvvs::TimeInfectedSevere>()[i] * y[ISevNi] +
(1 - params.get<osecirvvs::DeathsPerCritical>()[i]) /
params.get<osecirvvs::TimeInfectedCritical>()[i] * y[ICrNi];

dydt[SIIi] +=
(1 - (reducInfectedSymptomsPartialImmunity / reducExposedPartialImmunity) *
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i])) *
rateINS / reducTimeInfectedMild * (y[INSPIi] + y[INSPICi]) +
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i])) /
(params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * reducTimeInfectedMild) *
(y[INSPIi] + y[INSPICi]) +
(1 - (reducInfectedSevereCriticalDeadPartialImmunity / reducInfectedSymptomsPartialImmunity) *
params.get<osecirvvs::SeverePerInfectedSymptoms>()[i]) /
(params.get<osecirvvs::TimeInfectedSymptoms>()[i] * reducTimeInfectedMild) *
Expand All @@ -339,7 +343,8 @@ class FlowlessModel : public CompartmentalModel<osecirvvs::InfectionState,
dydt[SIIi] +=
(1 - (reducInfectedSymptomsImprovedImmunity / reducExposedImprovedImmunity) *
(1 - params.get<osecirvvs::RecoveredPerInfectedNoSymptoms>()[i])) *
rateINS / reducTimeInfectedMild * (y[INSIIi] + y[INSIICi]) +
(params.get<osecirvvs::TimeInfectedNoSymptoms>()[i] * reducTimeInfectedMild) *
(y[INSIIi] + y[INSIICi]) +
(1 - (reducInfectedSevereCriticalDeadImprovedImmunity / reducInfectedSymptomsImprovedImmunity) *
params.get<osecirvvs::SeverePerInfectedSymptoms>()[i]) /
(params.get<osecirvvs::TimeInfectedSymptoms>()[i] * reducTimeInfectedMild) *
Expand Down Expand Up @@ -650,11 +655,11 @@ void setup_model(Model& model)
contact_matrix[0].add_damping(0.3, SimulationTime(5.0));

//times
model.parameters.template get<osecirvvs::IncubationTime>()[AgeGroup(0)] = 5.2;
model.parameters.template get<osecirvvs::SerialInterval>()[AgeGroup(0)] = 0.5 * 3.33 + 0.5 * 5.2;
model.parameters.template get<osecirvvs::TimeInfectedSymptoms>()[AgeGroup(0)] = 7;
model.parameters.template get<osecirvvs::TimeInfectedSevere>()[AgeGroup(0)] = 6;
model.parameters.template get<osecirvvs::TimeInfectedCritical>()[AgeGroup(0)] = 7;
model.parameters.template get<osecirvvs::TimeExposed>()[AgeGroup(0)] = 3.33;
model.parameters.template get<osecirvvs::TimeInfectedNoSymptoms>()[AgeGroup(0)] = 1.87;
model.parameters.template get<osecirvvs::TimeInfectedSymptoms>()[AgeGroup(0)] = 7;
model.parameters.template get<osecirvvs::TimeInfectedSevere>()[AgeGroup(0)] = 6;
model.parameters.template get<osecirvvs::TimeInfectedCritical>()[AgeGroup(0)] = 7;

//probabilities
model.parameters.template get<osecirvvs::TransmissionProbabilityOnContact>()[AgeGroup(0)] = 0.15;
Expand Down
10 changes: 5 additions & 5 deletions cpp/benchmarks/graph_simulation.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -81,11 +81,11 @@ mio::osecirvvs::Model create_model(size_t num_agegroups, const ScalarType tmax)

for (mio::AgeGroup i = 0; i < (mio::AgeGroup)num_agegroups; i++) {
//times
model.parameters.get<mio::osecirvvs::IncubationTime>()[i] = 5.2;
model.parameters.get<mio::osecirvvs::SerialInterval>()[i] = 0.5 * 3.33 + 0.5 * 5.2;
model.parameters.get<mio::osecirvvs::TimeInfectedSymptoms>()[i] = 7;
model.parameters.get<mio::osecirvvs::TimeInfectedSevere>()[i] = 6;
model.parameters.get<mio::osecirvvs::TimeInfectedCritical>()[i] = 7;
model.parameters.get<mio::osecirvvs::TimeExposed>()[i] = 3.33;
model.parameters.get<mio::osecirvvs::TimeInfectedNoSymptoms>()[i] = 1.87;
model.parameters.get<mio::osecirvvs::TimeInfectedSymptoms>()[i] = 7;
model.parameters.get<mio::osecirvvs::TimeInfectedSevere>()[i] = 6;
model.parameters.get<mio::osecirvvs::TimeInfectedCritical>()[i] = 7;

//probabilities
model.parameters.get<mio::osecirvvs::TransmissionProbabilityOnContact>()[i] = 0.15;
Expand Down
10 changes: 5 additions & 5 deletions cpp/benchmarks/secir_ageres_setups.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,11 +54,11 @@ mio::osecir::Model make_model(int num)
params.set<mio::osecir::Seasonality>(0);

for (auto i = mio::AgeGroup(0); i < nb_groups; i++) {
params.get<mio::osecir::IncubationTime>()[i] = 5.2;
params.get<mio::osecir::TimeInfectedSymptoms>()[i] = 6.;
params.get<mio::osecir::SerialInterval>()[i] = 4.2;
params.get<mio::osecir::TimeInfectedSevere>()[i] = 12;
params.get<mio::osecir::TimeInfectedCritical>()[i] = 8;
params.get<mio::osecir::TimeExposed>()[i] = 3.2;
params.get<mio::osecir::TimeInfectedNoSymptoms>()[i] = 2.;
params.get<mio::osecir::TimeInfectedSymptoms>()[i] = 6.;
params.get<mio::osecir::TimeInfectedSevere>()[i] = 12;
params.get<mio::osecir::TimeInfectedCritical>()[i] = 8;

model.populations[{i, mio::osecir::InfectionState::Exposed}] = fact * nb_exp_t0;
model.populations[{i, mio::osecir::InfectionState::InfectedNoSymptoms}] = fact * nb_car_t0;
Expand Down
10 changes: 5 additions & 5 deletions cpp/examples/graph_stochastic_mobility.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,11 +47,11 @@ int main(int /*argc*/, char** /*argv*/)

//set initialization and model parameters
for (auto i = mio::AgeGroup(0); i < num_age_groups; i++) {
params.get<mio::osecir::IncubationTime>()[i] = 5.2;
params.get<mio::osecir::TimeInfectedSymptoms>()[i] = 6.;
params.get<mio::osecir::SerialInterval>()[i] = 4.2;
params.get<mio::osecir::TimeInfectedSevere>()[i] = 12;
params.get<mio::osecir::TimeInfectedCritical>()[i] = 8;
params.get<mio::osecir::TimeExposed>()[i] = 3.2;
params.get<mio::osecir::TimeInfectedNoSymptoms>()[i] = 2.;
params.get<mio::osecir::TimeInfectedSymptoms>()[i] = 6.;
params.get<mio::osecir::TimeInfectedSevere>()[i] = 12.;
params.get<mio::osecir::TimeInfectedCritical>()[i] = 8.;

//initial populations is equally distributed among age groups
model.populations[{i, mio::osecir::InfectionState::Exposed}] = fact * num_exp;
Expand Down
2 changes: 1 addition & 1 deletion cpp/examples/lct_secir.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@ int main()

// Set Parameters.
model.parameters.get<mio::lsecir::TimeExposed>() = 3.2;
model.parameters.get<mio::lsecir::TimeInfectedNoSymptoms>() = 2;
model.parameters.get<mio::lsecir::TimeInfectedNoSymptoms>() = 2.;
model.parameters.get<mio::lsecir::TimeInfectedSymptoms>() = 5.8;
model.parameters.get<mio::lsecir::TimeInfectedSevere>() = 9.5;
// It is also possible to change values with the set function.
Expand Down
10 changes: 5 additions & 5 deletions cpp/examples/ode_secir.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,11 +41,11 @@ int main()
model.parameters.set<mio::osecir::StartDay>(60);
model.parameters.set<mio::osecir::Seasonality>(0.2);

model.parameters.get<mio::osecir::IncubationTime>() = 5.2;
model.parameters.get<mio::osecir::TimeInfectedSymptoms>() = 5.8;
model.parameters.get<mio::osecir::SerialInterval>() = 4.2;
model.parameters.get<mio::osecir::TimeInfectedSevere>() = 9.5;
model.parameters.get<mio::osecir::TimeInfectedCritical>() = 7.1;
model.parameters.get<mio::osecir::TimeExposed>() = 3.2;
model.parameters.get<mio::osecir::TimeInfectedNoSymptoms>() = 2.0;
model.parameters.get<mio::osecir::TimeInfectedSymptoms>() = 5.8;
model.parameters.get<mio::osecir::TimeInfectedSevere>() = 9.5;
model.parameters.get<mio::osecir::TimeInfectedCritical>() = 7.1;

mio::ContactMatrixGroup& contact_matrix = model.parameters.get<mio::osecir::ContactPatterns>();
contact_matrix[0] = mio::ContactMatrix(Eigen::MatrixXd::Constant(1, 1, cont_freq));
Expand Down
12 changes: 6 additions & 6 deletions cpp/examples/ode_secir_ageres.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -55,11 +55,11 @@ int main()
params.get<mio::osecir::TestAndTraceCapacity>() = 35;

for (auto i = mio::AgeGroup(0); i < nb_groups; i++) {
params.get<mio::osecir::IncubationTime>()[i] = 5.2;
params.get<mio::osecir::TimeInfectedSymptoms>()[i] = 5.8;
params.get<mio::osecir::SerialInterval>()[i] = 4.2;
params.get<mio::osecir::TimeInfectedSevere>()[i] = 9.5;
params.get<mio::osecir::TimeInfectedCritical>()[i] = 7.1;
params.get<mio::osecir::TimeExposed>()[i] = 3.2;
params.get<mio::osecir::TimeInfectedNoSymptoms>()[i] = 2.;
params.get<mio::osecir::TimeInfectedSymptoms>()[i] = 5.8;
params.get<mio::osecir::TimeInfectedSevere>()[i] = 9.5;
params.get<mio::osecir::TimeInfectedCritical>()[i] = 7.1;

model.populations[{i, mio::osecir::InfectionState::Exposed}] = fact * nb_exp_t0;
model.populations[{i, mio::osecir::InfectionState::InfectedNoSymptoms}] = fact * nb_car_t0;
Expand Down Expand Up @@ -106,7 +106,7 @@ int main()

for (size_t i = 0; i < (size_t)params.get_num_groups(); i++) {
printf("\t %s[%d]: %.0f", vars[k].c_str(), (int)i,
secir.get_last_value()[k + (size_t)mio::osecir::InfectionState::Count * (int)i]);
secir.get_last_value()[k + (size_t)mio::osecir::InfectionState::Count * (int)i]);
dummy += secir.get_last_value()[k + (size_t)mio::osecir::InfectionState::Count * (int)i];
}

Expand Down
12 changes: 6 additions & 6 deletions cpp/examples/ode_secir_parameter_study.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -99,11 +99,11 @@ int main()
params.set<mio::osecir::Seasonality>(0);

for (auto i = mio::AgeGroup(0); i < num_groups; i++) {
params.get<mio::osecir::IncubationTime>()[i] = 5.2;
params.get<mio::osecir::TimeInfectedSymptoms>()[i] = 6.;
params.get<mio::osecir::SerialInterval>()[i] = 4.2;
params.get<mio::osecir::TimeInfectedSevere>()[i] = 12;
params.get<mio::osecir::TimeInfectedCritical>()[i] = 8;
params.get<mio::osecir::TimeExposed>()[i] = 3.2;
params.get<mio::osecir::TimeInfectedNoSymptoms>()[i] = 2.;
params.get<mio::osecir::TimeInfectedSymptoms>()[i] = 6.;
params.get<mio::osecir::TimeInfectedSevere>()[i] = 12;
params.get<mio::osecir::TimeInfectedCritical>()[i] = 8;

model.populations[{i, mio::osecir::InfectionState::Exposed}] = fact * num_exp_t0;
model.populations[{i, mio::osecir::InfectionState::InfectedNoSymptoms}] = fact * num_car_t0;
Expand Down Expand Up @@ -150,7 +150,7 @@ int main()
auto write_result_status = write_single_run_result(run, graph);
if (!write_result_status) {
std::cout << "Error writing result: " << write_result_status.error().formatted_message();
}
}
return 0; //Result handler must return something, but only meaningful when using MPI.
};
parameter_study.run(sample_graph, handle_result);
Expand Down
Loading