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1075 Let persons die from hospital (non ICU) in the ABM #1100

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1075 Let persons die from hospital (non ICU) in the ABM #1100

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afc78a9
Add mobility rule so a person can go to hospital when they have Infec…
khoanguyen-dev Aug 8, 2024
fd74351
Add test case for when mobility rules are not applied
khoanguyen-dev Aug 8, 2024
7e0ea0a
Add possibility so a person can go from severe infection to dead
khoanguyen-dev Oct 7, 2024
2bfe7af
Merge branch 'main' into 1075-let-persons-die-from-hospital-non-icu-i…
khoanguyen-dev Oct 7, 2024
5aca0fc
Improve tests for personCanDieInHospital
khoanguyen-dev Oct 14, 2024
134f8d8
Add test for Severe to Dead in draw_infection_course()
khoanguyen-dev Oct 18, 2024
05d8f56
Merge branch 'main' into 1075-let-persons-die-from-hospital-non-icu-i…
DavidKerkmann Nov 18, 2024
6c2a212
Merge branch 'main' into 1075-let-persons-die-from-hospital-non-icu-i…
DavidKerkmann Dec 6, 2024
1b97796
Improvements according to review
DavidKerkmann Dec 6, 2024
7a9f84a
Mock targets infections specifically
DavidKerkmann Jan 6, 2025
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16 changes: 13 additions & 3 deletions cpp/models/abm/infection.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -180,7 +180,10 @@ void Infection::draw_infection_course_forward(PersonalRandomNumberGenerator& rng
case InfectionState::InfectedSevere:
// roll out next infection step
v = uniform_dist(rng);
if (v < 0.5) { // TODO: subject to change
if (v < 0.25) { // TODO: subject to change
time_period = days(params.get<SevereToDead>()[{m_virus_variant, age}]); // TODO: subject to change
next_state = InfectionState::Dead;
} else if (v < 0.5) { // TODO: subject to change
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time_period = days(params.get<SevereToCritical>()[{m_virus_variant, age}]); // TODO: subject to change
next_state = InfectionState::InfectedCritical;
}
Expand Down Expand Up @@ -271,8 +274,15 @@ TimePoint Infection::draw_infection_course_backward(PersonalRandomNumberGenerato
break;

case InfectionState::Dead:
time_period = days(params.get<CriticalToDead>()[{m_virus_variant, age}]); // TODO: subject to change
previous_state = InfectionState::InfectedCritical;
v = uniform_dist(rng);
if (v < 0.5) {
time_period = days(params.get<SevereToDead>()[{m_virus_variant, age}]); // TODO: subject to change
previous_state = InfectionState::InfectedSevere;
}
else {
time_period = days(params.get<CriticalToDead>()[{m_virus_variant, age}]); // TODO: subject to change
previous_state = InfectionState::InfectedCritical;
}
break;

default:
Expand Down
20 changes: 19 additions & 1 deletion cpp/models/abm/parameters.h
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Expand Up @@ -132,6 +132,18 @@ struct SevereToRecovered {
}
};

struct SevereToDead {
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using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
static Type get_default(AgeGroup size)
{
return Type({VirusVariant::Count, size}, 1.);
}
static std::string name()
{
return "SevereToDead";
}
};

struct CriticalToRecovered {
using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
static Type get_default(AgeGroup size)
Expand Down Expand Up @@ -549,7 +561,7 @@ struct AgeGroupGotoWork {

using ParametersBase =
ParameterSet<IncubationPeriod, InfectedNoSymptomsToSymptoms, InfectedNoSymptomsToRecovered,
InfectedSymptomsToRecovered, InfectedSymptomsToSevere, SevereToCritical, SevereToRecovered,
InfectedSymptomsToRecovered, InfectedSymptomsToSevere, SevereToCritical, SevereToRecovered, SevereToDead,
CriticalToDead, CriticalToRecovered, RecoveredToSusceptible, ViralLoadDistributions,
InfectivityDistributions, DetectInfection, MaskProtection, AerosolTransmissionRates, LockdownDate,
QuarantineDuration, SocialEventRate, BasicShoppingRate, WorkRatio, SchoolRatio, GotoWorkTimeMinimum,
Expand Down Expand Up @@ -688,6 +700,12 @@ class Parameters : public ParametersBase
return true;
}

if (this->get<SevereToDead>()[{VirusVariant::Wildtype, i}] < 0.0) {
log_error("Constraint check: Parameter SevereToDead of age group {:.0f} smaller than {:d}",
(size_t)i, 0);
return true;
}

if (this->get<CriticalToDead>()[{VirusVariant::Wildtype, i}] < 0.0) {
log_error("Constraint check: Parameter CriticalToDead of age group {:.0f} smaller than {:d}", (size_t)i,
0);
Expand Down
12 changes: 12 additions & 0 deletions cpp/simulations/abm.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -480,6 +480,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.001;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.186;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.015;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.001;
params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.143;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.001;

Expand All @@ -491,6 +492,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.001;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.186;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.015;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.001;
params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.143;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.001;
params.get<mio::abm::RecoveredToSusceptible>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.;
Expand All @@ -504,6 +506,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.003;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.157;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.013;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.021;
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params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.126;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.021;

Expand All @@ -516,6 +519,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.009;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.113;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.02;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.008;
params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.05;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.008;
params.get<mio::abm::RecoveredToSusceptible>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.;
Expand All @@ -529,6 +533,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.024;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.083;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.035;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.023;
params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.035;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.023;
params.get<mio::abm::RecoveredToSusceptible>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.;
Expand All @@ -541,6 +546,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.033;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.055;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.036;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.052;
params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.035;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.052;
params.get<mio::abm::RecoveredToSusceptible>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.;
Expand All @@ -555,6 +561,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.001;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.186;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.015;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.001;
params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.143;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.001;
params.get<mio::abm::RecoveredToSusceptible>()[{mio::abm::VirusVariant::Wildtype, age_group_0_to_4}] = 0.0;
Expand All @@ -567,6 +574,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.001;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.186;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.015;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.001;
params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.143;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.001;
params.get<mio::abm::RecoveredToSusceptible>()[{mio::abm::VirusVariant::Wildtype, age_group_5_to_14}] = 0.0;
Expand All @@ -580,6 +588,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.001;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.157;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.013;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.021;
params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.126;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.021;
params.get<mio::abm::RecoveredToSusceptible>()[{mio::abm::VirusVariant::Wildtype, age_group_15_to_34}] = 0.0;
Expand All @@ -593,6 +602,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.003;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.113;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.02;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.008;
params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.05;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.008;
params.get<mio::abm::RecoveredToSusceptible>()[{mio::abm::VirusVariant::Wildtype, age_group_35_to_59}] = 0.0;
Expand All @@ -606,6 +616,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.009;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.083;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.035;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.023;
params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.035;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.023;
params.get<mio::abm::RecoveredToSusceptible>()[{mio::abm::VirusVariant::Wildtype, age_group_60_to_79}] = 0.0;
Expand All @@ -618,6 +629,7 @@ void set_parameters(mio::abm::Parameters params)
params.get<mio::abm::InfectedSymptomsToSevere>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.012;
params.get<mio::abm::SevereToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.055;
params.get<mio::abm::SevereToCritical>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.036;
params.get<mio::abm::SevereToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.052;
params.get<mio::abm::CriticalToRecovered>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.035;
params.get<mio::abm::CriticalToDead>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.052;
params.get<mio::abm::RecoveredToSusceptible>()[{mio::abm::VirusVariant::Wildtype, age_group_80_plus}] = 0.0;
Expand Down
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