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

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Merged
DavidKerkmann merged 12 commits into from
Jan 22, 2025
Merged

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
f32856a
Merge branch 'main' into 1075-let-persons-die-from-hospital-non-icu-i…
DavidKerkmann Jan 20, 2025
a338810
Increase code coverage
DavidKerkmann Jan 20, 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
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
21 changes: 17 additions & 4 deletions cpp/models/abm/infection.h
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Expand Up @@ -141,33 +141,46 @@ class Infection
Infection() = default;

/**
* @brief Determine ViralLoad course and Infection course based on init_state.
* @brief Determine Infection course based on #InfectionState init_state.
* Calls draw_infection_course_backward for all #InfectionState%s prior and draw_infection_course_forward for all
* subsequent #InfectionState%s.
* @param[inout] rng PersonalRandomNumberGenerator of the Person.
* @param[in] age AgeGroup of the Person.
* @param[in] params Parameters of the Model.
* @param[in] init_date Date of initializing the Infection.
* @param[in] init_state #InfectionState at time of initializing the Infection.
* @param[in] latest_protection Latest protection against Infection, has an influence on transition probabilities.
* @return The starting date of the Infection.
*/
TimePoint draw_infection_course(PersonalRandomNumberGenerator& rng, AgeGroup age, const Parameters& params,
TimePoint init_date, InfectionState start_state, ProtectionEvent latest_protection);

/**
* @brief Determine ViralLoad course and Infection course prior to the given start_state.
* @brief Determine Infection course subsequent to the given #InfectionState start_state.
* From the start_state, a random path through the #InfectionState tree is chosen, that is
* Susceptible -> InfectedNoSymptoms,
* InfectedNoSymptoms -> InfectedSymptoms or InfectedNoSymptoms -> Recovered,
* InfectedSymptoms -> Infected_Severe or InfectedSymptoms -> Recovered,
* InfectedSevere -> InfectedCritical or InfectedSevere -> Recovered or InfectedSevere -> Dead,
* InfectedCritical -> Recovered or InfectedCritical -> Dead,
* with artifical, hardcoded probabilites, until either Recoverd or Dead is reached.
* This is subject to change when parameter distributions for these transitions are implemented.
* The duration in each #InfectionState is taken from the respective parameter.
* @param[inout] rng PersonalRandomNumberGenerator of the Person.
* @param[in] age AgeGroup of the Person.
* @param[in] params Parameters of the Model.
* @param[in] init_date Date of initializing the Infection.
* @param[in] init_state #InfectionState at time of initializing the Infection.
* @param[in] latest_protection Latest protection against Infection, has an influence on transition probabilities.
*/
void draw_infection_course_forward(PersonalRandomNumberGenerator& rng, AgeGroup age, const Parameters& params,
TimePoint init_date, InfectionState start_state,
TimePoint init_date, InfectionState init_state,
ProtectionEvent latest_protection);

/**
* @brief Determine ViralLoad course and Infection course subsequent to the given start_state.
* @brief Determine Infection course prior to the given #InfectionState start_state.
* From the start_state, a random path through the #InfectionState tree is chosen backwards, until Susceptible is reached.
* For more detailed information, refer to draw_infection_course_forward.
* @param[inout] rng PersonalRandomNumberGenerator of the Person.
* @param[in] age AgeGroup of the person.
* @param[in] params Parameters of the Model.
Expand Down
20 changes: 19 additions & 1 deletion cpp/models/abm/parameters.h
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Expand Up @@ -133,6 +133,18 @@ struct SevereToRecovered {
}
};

struct SevereToDead {
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 @@ -551,7 +563,7 @@ 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 @@ -692,6 +704,12 @@ class Parameters : public ParametersBase
return true;
}

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

if (this->get<CriticalToDead>()[{virus_variant, age_group}] < 0.0) {
log_error("Constraint check: Parameter CriticalToDead of age group {:.0f} smaller than {:d}",
(size_t)age_group, 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 @@ -475,6 +475,7 @@ 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 @@ -486,6 +487,7 @@ 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 @@ -499,6 +501,7 @@ 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;
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 @@ -511,6 +514,7 @@ 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 @@ -524,6 +528,7 @@ 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 @@ -536,6 +541,7 @@ 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 @@ -550,6 +556,7 @@ 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 @@ -562,6 +569,7 @@ 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 @@ -575,6 +583,7 @@ 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 @@ -588,6 +597,7 @@ 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 @@ -601,6 +611,7 @@ 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 @@ -613,6 +624,7 @@ 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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