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Merged
annawendler merged 39 commits into from
May 13, 2024
Merged

899 new add gamma distribution and other parameters to state age function 1 #1004

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5075322
added first ideas
lenaploetzke Apr 3, 2024
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just b2
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lenaploetzke Apr 9, 2024
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Merge branch '983-bundle-the-boost-git-repo-instead-of-using-the-targ…
lenaploetzke Apr 11, 2024
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readd changes in state age function
lenaploetzke Apr 11, 2024
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added tests for the constructors of derived classes
lenaploetzke Apr 12, 2024
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Merge branch 'main' into 899-new-add-gamma-distribution-and-other-par…
lenaploetzke Apr 19, 2024
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resolve error
lenaploetzke Apr 19, 2024
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Merge branch 'main' into 899-new-add-gamma-distribution-and-other-par…
lenaploetzke Apr 29, 2024
86b8766
add test for mean to other StateAgeFunctions
lenaploetzke Apr 30, 2024
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lenaploetzke May 13, 2024
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changed smoothercosine to lognorm in test
lenaploetzke May 13, 2024
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9 changes: 5 additions & 4 deletions cpp/examples/ide_secir.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -74,8 +74,9 @@ int main()
mio::StateAgeFunctionWrapper delaydistribution(smoothcos);
std::vector<mio::StateAgeFunctionWrapper> vec_delaydistrib(num_transitions, delaydistribution);
// TransitionDistribution is not used for SusceptibleToExposed. Therefore, the parameter can be set to any value.
vec_delaydistrib[(int)mio::isecir::InfectionTransition::SusceptibleToExposed].set_parameter(-1.);
vec_delaydistrib[(int)mio::isecir::InfectionTransition::InfectedNoSymptomsToInfectedSymptoms].set_parameter(4.0);
vec_delaydistrib[(int)mio::isecir::InfectionTransition::SusceptibleToExposed].set_distribution_parameter(-1.);
vec_delaydistrib[(int)mio::isecir::InfectionTransition::InfectedNoSymptomsToInfectedSymptoms]
.set_distribution_parameter(4.0);
model.parameters.set<mio::isecir::TransitionDistributions>(vec_delaydistrib);

std::vector<ScalarType> vec_prob(num_transitions, 0.5);
Expand All @@ -88,8 +89,8 @@ int main()
contact_matrix[0] = mio::ContactMatrix(Eigen::MatrixXd::Constant(1, 1, 10.));
model.parameters.get<mio::isecir::ContactPatterns>() = mio::UncertainContactMatrix(contact_matrix);

mio::ExponentialDecay expdecay(0.5);
mio::StateAgeFunctionWrapper prob(expdecay);
mio::ExponentialSurvivalFunction exponential(0.5);
mio::StateAgeFunctionWrapper prob(exponential);
model.parameters.set<mio::isecir::TransmissionProbabilityOnContact>(prob);
model.parameters.set<mio::isecir::RelativeTransmissionNoSymptoms>(prob);
model.parameters.set<mio::isecir::RiskOfInfectionFromSymptomatic>(prob);
Expand Down
520 changes: 448 additions & 72 deletions cpp/memilio/epidemiology/state_age_function.h
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2 changes: 1 addition & 1 deletion cpp/models/ode_secir/parameters_io.cpp
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Expand Up @@ -423,4 +423,4 @@ IOResult<void> set_divi_data(std::vector<Model>& model, const std::string& path,

#endif // MEMILIO_HAS_JSONCPP

GCC_CLANG_DIAGNOSTIC(pop)
GCC_CLANG_DIAGNOSTIC(pop)
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3 changes: 2 additions & 1 deletion cpp/tests/test_ide_parameters_io.cpp
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Expand Up @@ -50,7 +50,8 @@ TEST(TestIDEParametersIo, RKIcompareWithPreviousRun)
mio::StateAgeFunctionWrapper delaydistribution(smoothcos);
std::vector<mio::StateAgeFunctionWrapper> vec_delaydistrib((int)mio::isecir::InfectionTransition::Count,
delaydistribution);
vec_delaydistrib[(int)mio::isecir::InfectionTransition::InfectedSymptomsToInfectedSevere].set_parameter(1.7);
vec_delaydistrib[(int)mio::isecir::InfectionTransition::InfectedSymptomsToInfectedSevere]
.set_distribution_parameter(1.7);
model.parameters.set<mio::isecir::TransitionDistributions>(vec_delaydistrib);

std::vector<ScalarType> vec_prob((int)mio::isecir::InfectionTransition::Count, 0.5);
Expand Down
32 changes: 17 additions & 15 deletions cpp/tests/test_ide_secir.cpp
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Expand Up @@ -78,8 +78,8 @@ class ModelTestIdeSecir : public testing::Test
contact_matrix[0] = mio::ContactMatrix(Eigen::MatrixXd::Constant(1, 1, 10.));
model->parameters.get<mio::isecir::ContactPatterns>() = mio::UncertainContactMatrix(contact_matrix);

mio::ExponentialDecay expdecay(0.5);
mio::StateAgeFunctionWrapper prob(expdecay);
mio::ExponentialSurvivalFunction exponential(0.5);
mio::StateAgeFunctionWrapper prob(exponential);
model->parameters.set<mio::isecir::TransmissionProbabilityOnContact>(prob);
model->parameters.set<mio::isecir::RelativeTransmissionNoSymptoms>(prob);
model->parameters.set<mio::isecir::RiskOfInfectionFromSymptomatic>(prob);
Expand Down Expand Up @@ -467,8 +467,8 @@ TEST(IdeSecir, testModelConstraints)
// Initialize a model.
mio::isecir::Model model(std::move(init_few_timepoints), N, deaths);

mio::ExponentialDecay expdecay(4.0);
mio::StateAgeFunctionWrapper delaydistribution(expdecay);
mio::ExponentialSurvivalFunction exponential(4.0);
mio::StateAgeFunctionWrapper delaydistribution(exponential);
std::vector<mio::StateAgeFunctionWrapper> vec_delaydistrib(num_transitions, delaydistribution);
model.parameters.set<mio::isecir::TransitionDistributions>(vec_delaydistrib);

Expand Down Expand Up @@ -659,8 +659,8 @@ TEST(IdeSecir, testParametersConstraints)
EXPECT_TRUE(constraint_check);

// Check wrong value for Seasonality.
mio::ExponentialDecay expdecay(4.0);
mio::StateAgeFunctionWrapper delaydistribution2(expdecay);
mio::ExponentialSurvivalFunction exponential(4.0);
mio::StateAgeFunctionWrapper delaydistribution2(exponential);
std::vector<mio::StateAgeFunctionWrapper> vec_delaydistrib2((int)mio::isecir::InfectionTransition::Count,
delaydistribution2);
parameters.set<mio::isecir::TransitionDistributions>(vec_delaydistrib2);
Expand Down Expand Up @@ -707,13 +707,14 @@ TEST(IdeSecir, checkProportionRecoveredDeath)
mio::isecir::Model model(std::move(init), N, deaths);

// Set working parameters.
// All TransitionDistribution%s are ExponentialDecay functions.
// All TransitionDistribution%s are ExponentialSurvivalFunction functions.
// For all TransitionDistribution%s init_parameter=2 is used except for InfectedCriticalToRecovered
// where init_parameter=3 is used.
mio::ExponentialDecay expdecay(4.0);
mio::StateAgeFunctionWrapper delaydistribution(expdecay);
mio::ExponentialSurvivalFunction exponential(4.0);
mio::StateAgeFunctionWrapper delaydistribution(exponential);
std::vector<mio::StateAgeFunctionWrapper> vec_delaydistrib(num_transitions, delaydistribution);
vec_delaydistrib[(int)mio::isecir::InfectionTransition::InfectedCriticalToRecovered].set_parameter(3.0);
vec_delaydistrib[(int)mio::isecir::InfectionTransition::InfectedCriticalToRecovered].set_distribution_parameter(
3.0);
model.parameters.set<mio::isecir::TransitionDistributions>(vec_delaydistrib);

// Set probabilities so that all individuals go from Susceptible to InfectedCritical with probability 1,
Expand All @@ -730,8 +731,8 @@ TEST(IdeSecir, checkProportionRecoveredDeath)
contact_matrix[0] = mio::ContactMatrix(Eigen::MatrixXd::Constant(1, 1, 1.));
model.parameters.get<mio::isecir::ContactPatterns>() = mio::UncertainContactMatrix(contact_matrix);

mio::ExponentialDecay expdecay2(0.5);
mio::StateAgeFunctionWrapper prob(expdecay2);
mio::ExponentialSurvivalFunction exponential2(0.5);
mio::StateAgeFunctionWrapper prob(exponential2);
model.parameters.set<mio::isecir::TransmissionProbabilityOnContact>(prob);
model.parameters.set<mio::isecir::RelativeTransmissionNoSymptoms>(prob);
model.parameters.set<mio::isecir::RiskOfInfectionFromSymptomatic>(prob);
Expand Down Expand Up @@ -806,7 +807,8 @@ TEST(IdeSecir, compareEquilibria)
mio::SmootherCosine smoothcos2(2.0);
mio::StateAgeFunctionWrapper delaydistribution2(smoothcos);
std::vector<mio::StateAgeFunctionWrapper> vec_delaydistrib2(num_transitions, delaydistribution2);
vec_delaydistrib2[(int)mio::isecir::InfectionTransition::InfectedCriticalToRecovered].set_parameter(7.0);
vec_delaydistrib2[(int)mio::isecir::InfectionTransition::InfectedCriticalToRecovered].set_distribution_parameter(
7.0);
model2.parameters.set<mio::isecir::TransitionDistributions>(vec_delaydistrib2);

// All remaining parameters are equal for both models.
Expand All @@ -826,8 +828,8 @@ TEST(IdeSecir, compareEquilibria)
model.parameters.get<mio::isecir::ContactPatterns>() = mio::UncertainContactMatrix(contact_matrix);
model2.parameters.get<mio::isecir::ContactPatterns>() = mio::UncertainContactMatrix(contact_matrix);

mio::ExponentialDecay expdecay(0.5);
mio::StateAgeFunctionWrapper prob(expdecay);
mio::ExponentialSurvivalFunction exponential(0.5);
mio::StateAgeFunctionWrapper prob(exponential);
model.parameters.set<mio::isecir::TransmissionProbabilityOnContact>(prob);
model.parameters.set<mio::isecir::RelativeTransmissionNoSymptoms>(prob);
model.parameters.set<mio::isecir::RiskOfInfectionFromSymptomatic>(prob);
Expand Down
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