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1185 wrong index in ode seir model #1186

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Merged
HenrZu merged 4 commits into from
Jan 16, 2025
Merged

1185 wrong index in ode seir model #1186

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aa5ed9e
FIX: Changed index from i to j
kilianvolmer Jan 13, 2025
3e042b5
Add test with two age groups to find bug
kilianvolmer Jan 13, 2025
f3e8888
CHG: Improve code quality by utilising age group structure
kilianvolmer Jan 14, 2025
79db64d
Change Contact Matrix initialisation
kilianvolmer Jan 16, 2025
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2 changes: 1 addition & 1 deletion cpp/models/ode_seir/model.h
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ class Model
const size_t Ii = this->populations.get_flat_index({i, InfectionState::Infected});

for (auto j : make_index_range(age_groups)) {
const size_t Sj = this->populations.get_flat_index({i, InfectionState::Susceptible});
const size_t Sj = this->populations.get_flat_index({j, InfectionState::Susceptible});
const size_t Ej = this->populations.get_flat_index({j, InfectionState::Exposed});
const size_t Ij = this->populations.get_flat_index({j, InfectionState::Infected});
const size_t Rj = this->populations.get_flat_index({j, InfectionState::Recovered});
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44 changes: 44 additions & 0 deletions cpp/tests/test_odeseir.cpp
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Expand Up @@ -362,6 +362,50 @@ TEST(TestSeir, get_flows)
EXPECT_NEAR(dydt_default[2], 25, 1e-12);
}

TEST(TestSeir, get_flows_two_agegroups)
{
mio::oseir::Model<double> model(2);
auto nb_groups = model.parameters.get_num_groups();

constexpr double total_first_population = 400;
constexpr double total_second_population = 200;

auto& params = model.parameters;

model.populations[{mio::AgeGroup(0), mio::oseir::InfectionState::Exposed}] = 100;
model.populations[{mio::AgeGroup(0), mio::oseir::InfectionState::Infected}] = 100;
model.populations[{mio::AgeGroup(0), mio::oseir::InfectionState::Recovered}] = 100;
model.populations.set_difference_from_group_total<mio::AgeGroup>({mio::AgeGroup(0), mio::oseir::InfectionState::Susceptible},
total_first_population);
model.populations[{mio::AgeGroup(1), mio::oseir::InfectionState::Exposed}] = 10;
model.populations[{mio::AgeGroup(1), mio::oseir::InfectionState::Infected}] = 10;
model.populations[{mio::AgeGroup(1), mio::oseir::InfectionState::Recovered}] = 10;
model.populations.set_difference_from_group_total<mio::AgeGroup>({mio::AgeGroup(1), mio::oseir::InfectionState::Susceptible},
total_second_population);

for (auto i = mio::AgeGroup(0); i <= mio::AgeGroup(1); i++) {
model.parameters.get<mio::oseir::TimeExposed<double>>()[i] = 2;
model.parameters.get<mio::oseir::TimeInfected<double>>()[i] = 4;
model.parameters.get<mio::oseir::TransmissionProbabilityOnContact<double>>()[i] = 1;
}

mio::ContactMatrixGroup& contact_matrix = params.get<mio::oseir::ContactPatterns<double>>();
contact_matrix[0] = mio::ContactMatrix(Eigen::MatrixXd::Constant((size_t)nb_groups, (size_t)nb_groups, 1.0));
model.check_constraints();

auto dydt_default = Eigen::VectorXd(6);
dydt_default.setZero();
auto y0 = model.get_initial_values();
model.get_flows(y0, y0, 0, dydt_default);

EXPECT_NEAR(dydt_default[0], 30, 1e-12);
EXPECT_NEAR(dydt_default[1], 50, 1e-12);
EXPECT_NEAR(dydt_default[2], 25, 1e-12);
EXPECT_NEAR(dydt_default[3], 51, 1e-12);
EXPECT_NEAR(dydt_default[4], 5, 1e-12);
EXPECT_NEAR(dydt_default[5], 2.5, 1e-12);
}

TEST(TestSeir, Simulation)
{
double t0 = 0;
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