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688 Add Symptomatic State to ABM #1539

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6 changes: 3 additions & 3 deletions cpp/benchmarks/abm.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -72,8 +72,8 @@ mio::abm::Simulation<> make_simulation(size_t num_persons, std::initializer_list
//some % of people are infected, large enough to have some infection activity without everyone dying
auto pct_infected = 0.05;
if (mio::UniformDistribution<ScalarType>::get_instance()(prng, 0.0, 1.0) < pct_infected) {
auto state = mio::abm::InfectionState(
mio::UniformIntDistribution<int>::get_instance()(prng, 1, int(mio::abm::InfectionState::Count) - 1));
auto state = mio::abm::SymptomState(
mio::UniformIntDistribution<int>::get_instance()(prng, 1, int(mio::abm::SymptomState::Count) - 1));
auto infection = mio::abm::Infection(prng, mio::abm::VirusVariant::Wildtype, person.get_age(),
model.parameters, mio::abm::TimePoint(0), state);
person.add_new_infection(std::move(infection));
Expand Down Expand Up @@ -107,7 +107,7 @@ mio::abm::Simulation<> make_simulation(size_t num_persons, std::initializer_list
});
auto random_criteria = [&]() {
auto random_ages = sample(ages, 2);
auto random_states = std::vector<mio::abm::InfectionState>(0);
auto random_states = std::vector<mio::abm::SymptomState>(0);
return mio::abm::TestingCriteria(random_ages, random_states);
};

Expand Down
10 changes: 5 additions & 5 deletions cpp/examples/abm_history_object.cpp
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Expand Up @@ -73,7 +73,7 @@ int main()
auto model = mio::abm::Model(num_age_groups);
mio::ParameterDistributionLogNormal log_norm(4., 1.);
// Set same infection parameter for all age groups. For example, the incubation period is log normally distributed with parameters 4 and 1.
model.parameters.get<mio::abm::TimeExposedToNoSymptoms>() = mio::ParameterDistributionLogNormal(4., 1.);
model.parameters.get<mio::abm::TimeInfectedNoSymptomsToModerate>() = mio::ParameterDistributionLogNormal(4., 1.);

// Set the age group the can go to school is AgeGroup(1) (i.e. 5-14)
model.parameters.get<mio::abm::AgeGroupGotoSchool>()[age_group_5_to_14] = true;
Expand Down Expand Up @@ -144,11 +144,11 @@ int main()
auto persons = model.get_persons();
for (auto& person : persons) {
auto rng = mio::abm::PersonalRandomNumberGenerator(model.get_rng(), person);
mio::abm::InfectionState infection_state =
(mio::abm::InfectionState)(rand() % ((uint32_t)mio::abm::InfectionState::Count - 1));
if (infection_state != mio::abm::InfectionState::Susceptible)
mio::abm::SymptomState symptom_state =
(mio::abm::SymptomState)(rand() % ((uint32_t)mio::abm::SymptomState::Count));
if (symptom_state != mio::abm::SymptomState::Count)
person.add_new_infection(mio::abm::Infection(rng, mio::abm::VirusVariant::Wildtype, person.get_age(),
model.parameters, start_date, infection_state));
model.parameters, start_date, symptom_state));
}

// Assign locations to the people
Expand Down
2 changes: 1 addition & 1 deletion cpp/examples/graph_abm.cpp
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Expand Up @@ -20,7 +20,7 @@

#include "abm/household.h"
#include "abm/model.h"
#include "abm/infection_state.h"
#include "abm/symptom_state.h"
#include "abm/location_type.h"
#include "abm/time.h"
#include "abm/person_id.h"
Expand Down
2 changes: 1 addition & 1 deletion cpp/models/abm/CMakeLists.txt
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Expand Up @@ -29,7 +29,7 @@ add_library(abm
lockdown_rules.h
infection.cpp
infection.h
infection_state.h
symptom_state.h
virus_variant.h
protection_event.h
mask.h
Expand Down
29 changes: 14 additions & 15 deletions cpp/models/abm/common_abm_loggers.h
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Expand Up @@ -21,7 +21,7 @@
#ifndef ABM_COMMON_LOGGERS_H
#define ABM_COMMON_LOGGERS_H

#include "abm/infection_state.h"
#include "abm/symptom_state.h"
#include "abm/person_id.h"
#include "abm/simulation.h"
#include "memilio/io/history.h"
Expand All @@ -48,7 +48,7 @@ struct mobility_data {
mio::abm::TimePoint end_time;
mio::abm::TransportMode transport_mode;
mio::abm::ActivityType activity_type;
mio::abm::InfectionState infection_state;
mio::abm::SymptomState symptom_state;
};

constexpr mio::abm::ActivityType guess_activity_type(mio::abm::LocationType current_location)
Expand Down Expand Up @@ -138,7 +138,7 @@ struct LogPersonInformation : mio::LogOnce {
*/
struct LogDataForMobility : mio::LogAlways {
using Type = std::vector<std::tuple<mio::abm::PersonId, mio::abm::LocationId, mio::abm::TimePoint,
mio::abm::TransportMode, mio::abm::ActivityType, mio::abm::InfectionState>>;
mio::abm::TransportMode, mio::abm::ActivityType, mio::abm::SymptomState>>;
/**
* @brief Log the mobility data of the agents in the simulation.
* @param[in] sim The simulation of the ABM.
Expand All @@ -148,41 +148,40 @@ struct LogDataForMobility : mio::LogAlways {
* -# The time point.
* -# The transport mode.
* -# The activity type.
* -# The infection state.
* -# The symptom state.
*/
static Type log(const mio::abm::Simulation<>& sim)
{
Type mobility_data{};
for (Person p : sim.get_model().get_persons()) {
mobility_data.push_back(
std::make_tuple(p.get_id(), p.get_location(), sim.get_time(), p.get_last_transport_mode(),
guess_activity_type(p.get_location_type()), p.get_infection_state(sim.get_time())));
guess_activity_type(p.get_location_type()), p.get_symptom_state(sim.get_time())));
}
return mobility_data;
}
};

/**
* @brief Logger to log the TimeSeries of the number of Person%s in an #InfectionState.
* @brief Logger to log the TimeSeries of the number of Person%s in an #SymptomState.
*/
struct LogInfectionState : mio::LogAlways {
struct LogSymptomState : mio::LogAlways {
using Type = std::pair<mio::abm::TimePoint, Eigen::VectorX<ScalarType>>;
/**
* @brief Log the TimeSeries of the number of Person%s in an #InfectionState.
* @brief Log the TimeSeries of the number of Person%s in an #SymptomState.
* @param[in] sim The simulation of the abm.
* @return A pair of the TimePoint and the TimeSeries of the number of Person%s in an #InfectionState.
* @return A pair of the TimePoint and the TimeSeries of the number of Person%s in an #SymptomState.
*/
static Type log(const mio::abm::Simulation<>& sim)
{

Eigen::VectorX<ScalarType> sum =
Eigen::VectorX<ScalarType>::Zero(Eigen::Index(mio::abm::InfectionState::Count));
auto curr_time = sim.get_time();
Eigen::VectorX<ScalarType> sum = Eigen::VectorX<ScalarType>::Zero(Eigen::Index(mio::abm::SymptomState::Count));
auto curr_time = sim.get_time();
PRAGMA_OMP(for)
for (auto& location : sim.get_model().get_locations()) {
for (uint32_t inf_state = 0; inf_state < (int)mio::abm::InfectionState::Count; inf_state++) {
sum[inf_state] += sim.get_model().get_subpopulation(location.get_id(), curr_time,
mio::abm::InfectionState(inf_state));
for (uint32_t inf_state = 0; inf_state < (int)mio::abm::SymptomState::Count; inf_state++) {
sum[inf_state] +=
sim.get_model().get_subpopulation(location.get_id(), curr_time, mio::abm::SymptomState(inf_state));
}
}
return std::make_pair(curr_time, sum);
Expand Down
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