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664 Define and use parameters that handle the state transitions in the Infection #710

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664 Define and use parameters that handle the state transitions in the Infection #710

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3fcb877
firstcommit
xsaschako Jul 31, 2023
3113609
add first draft for tree
xsaschako Aug 25, 2023
cb2a563
Merge main to update to newest version
DavidKerkmann Oct 17, 2023
59d10be
Merge branch 'main' into 664-define-and-use-parameters-that-handle-th…
DavidKerkmann Nov 20, 2023
25e7905
Update parameters
DavidKerkmann Nov 20, 2023
7d92aa8
Use new enum iterator
DavidKerkmann Nov 20, 2023
a4f16e8
Fix parameters
DavidKerkmann Nov 20, 2023
64f2edf
Fix infection setup
DavidKerkmann Nov 20, 2023
8b995e2
Fix analyze_result
DavidKerkmann Nov 20, 2023
e74c26c
Fix error in transmission
DavidKerkmann Nov 20, 2023
e5afe7c
Merge branch 'main' into 664-define-and-use-parameters-that-handle-th…
DavidKerkmann Dec 14, 2023
c7d6f12
Some fixes
DavidKerkmann Dec 20, 2023
5100fb8
Add author
DavidKerkmann Jan 25, 2024
85ab275
Fix recovered people not beeing able to reinfect.
DavidKerkmann Jan 29, 2024
10bd31e
Change back to infection course related time parameters and fix build.
DavidKerkmann Jan 31, 2024
4a47c69
Merge branch main into 664-define-and-use-parameters-that-handle-the-…
DavidKerkmann Jan 31, 2024
6f489f6
Fix from merge
DavidKerkmann Jan 31, 2024
054b746
Fix infection tests
DavidKerkmann Feb 1, 2024
e9069a4
Adjust contact rates correctly and fix dividing by 0 in exposure rate.
DavidKerkmann Feb 2, 2024
223e281
Merge branch 'main' into 664-define-and-use-parameters-that-handle-th…
DavidKerkmann Feb 13, 2024
0703b8d
bug in draw_infection_course_backward
jubicker Aug 20, 2024
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123 changes: 111 additions & 12 deletions cpp/models/abm/analyze_result.h
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Original file line number Diff line number Diff line change
Expand Up @@ -62,39 +62,128 @@ std::vector<Model> ensemble_params_percentile(const std::vector<std::vector<Mode

for (size_t node = 0; node < num_nodes; node++) {
for (auto age_group = AgeGroup(0); age_group < AgeGroup(num_groups); age_group++) {
for (auto virus_variant = VirusVariant(0); virus_variant < VirusVariant::Count;
virus_variant = static_cast<VirusVariant>((uint32_t)virus_variant + 1)) {
for (auto virus_variant : enum_members<VirusVariant>()) {
// Global infection parameters
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<IncubationPeriod>()[{virus_variant, age_group}];
static auto result =
model.parameters.template get<IncubationPeriod>()[{virus_variant, age_group}].params.a();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
static auto result =
model.parameters.template get<IncubationPeriod>()[{virus_variant, age_group}].params.b();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
static auto result =
model.parameters.template get<TimeInfectedNoSymptomsToSymptoms>()[{virus_variant, age_group}]
.params.a();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
static auto result =
model.parameters.template get<TimeInfectedNoSymptomsToSymptoms>()[{virus_variant, age_group}]
.params.b();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
static auto result =
model.parameters.template get<TimeInfectedNoSymptomsToRecovered>()[{virus_variant, age_group}]
.params.a();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
static auto result =
model.parameters.template get<TimeInfectedNoSymptomsToRecovered>()[{virus_variant, age_group}]
.params.b();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
static auto result =
model.parameters.template get<TimeInfectedSymptomsToSevere>()[{virus_variant, age_group}]
.params.a();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
static auto result =
model.parameters.template get<TimeInfectedSymptomsToSevere>()[{virus_variant, age_group}]
.params.b();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
static auto result =
model.parameters.template get<TimeInfectedSymptomsToRecovered>()[{virus_variant, age_group}]
.params.a();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
static auto result =
model.parameters.template get<TimeInfectedSymptomsToRecovered>()[{virus_variant, age_group}]
.params.b();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<InfectedNoSymptomsToSymptoms>()[{virus_variant, age_group}];
static auto result =
model.parameters.template get<TimeInfectedSevereToCritical>()[{virus_variant, age_group}]
.params.a();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<InfectedNoSymptomsToRecovered>()[{virus_variant, age_group}];
static auto result =
model.parameters.template get<TimeInfectedSevereToCritical>()[{virus_variant, age_group}]
.params.b();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<InfectedSymptomsToRecovered>()[{virus_variant, age_group}];
static auto result =
model.parameters.template get<TimeInfectedSevereToRecovered>()[{virus_variant, age_group}]
.params.a();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<InfectedSymptomsToSevere>()[{virus_variant, age_group}];
static auto result =
model.parameters.template get<TimeInfectedSevereToRecovered>()[{virus_variant, age_group}]
.params.b();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<SevereToCritical>()[{virus_variant, age_group}];
static auto result =
model.parameters.template get<TimeInfectedCriticalToDead>()[{virus_variant, age_group}]
.params.a();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<SevereToRecovered>()[{virus_variant, age_group}];
static auto result =
model.parameters.template get<TimeInfectedCriticalToDead>()[{virus_variant, age_group}]
.params.b();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<CriticalToDead>()[{virus_variant, age_group}];
static auto result =
model.parameters.template get<TimeInfectedCriticalToRecovered>()[{virus_variant, age_group}]
.params.a();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<CriticalToRecovered>()[{virus_variant, age_group}];
static auto result =
model.parameters.template get<TimeInfectedCriticalToRecovered>()[{virus_variant, age_group}]
.params.b();
return result;
});

param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<RecoveredToSusceptible>()[{virus_variant, age_group}];
return model.parameters.template get<SymptomsPerInfectedNoSymptoms>()[{virus_variant, age_group}];
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<SeverePerInfectedSymptoms>()[{virus_variant, age_group}];
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<CriticalPerInfectedSevere>()[{virus_variant, age_group}];
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<DeathsPerInfectedCritical>()[{virus_variant, age_group}];
});

param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
return model.parameters.template get<DetectInfection>()[{virus_variant, age_group}];
});
Expand Down Expand Up @@ -158,6 +247,16 @@ std::vector<Model> ensemble_params_percentile(const std::vector<std::vector<Mode
.infectivity_beta.params.b();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
static auto result =
model.parameters.template get<VirusShedFactor>()[{virus_variant, age_group}].params.a();
return result;
});
param_percentil(node, [age_group, virus_variant](auto&& model) -> auto& {
static auto result =
model.parameters.template get<VirusShedFactor>()[{virus_variant, age_group}].params.b();
return result;
});
param_percentil(node, [virus_variant](auto&& model) -> auto& {
return model.parameters.template get<AerosolTransmissionRates>()[{virus_variant}];
});
Expand Down
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