float Susceptibility::getModAcquire() const
{
float susceptibility_correction = 1.0f;
if(SusceptibilityConfig::maternal_protection && SusceptibilityConfig::susceptibility_type == SusceptibilityType::FRACTIONAL)
{
if(SusceptibilityConfig::maternal_protection_type == MaternalProtectionType::LINEAR)
{
susceptibility_correction *= SusceptibilityConfig::matlin_slope*age+
SusceptibilityConfig::matlin_suszero;
}
else if(SusceptibilityConfig::maternal_protection_type == MaternalProtectionType::SIGMOID)
{
susceptibility_correction *= SusceptibilityConfig::matsig_susinit +
(1.0f - SusceptibilityConfig::matsig_susinit)/
(1.0f + exp((SusceptibilityConfig::matsig_halfmax-age)/
SusceptibilityConfig::matsig_steepfac));
}
}
// Reduces mod_acquire to zero if age is less than calculated immunity failure day.
if(age < immune_failage)
{
susceptibility_correction = 0.0f;
}
BOUND_RANGE(susceptibility_correction, 0.0f, 1.0f);
LOG_VALID_F("id = %d, age = %f, mod_acquire = %f, immune_failage = %f\n", parent->GetSuid().data, age, mod_acquire*susceptibility_correction, immune_failage);
return mod_acquire * susceptibility_correction;
}
void
ReportEnvironmental::LogIndividualData( IIndividualHuman * individual )
{
Report::LogIndividualData( individual );
if( individual->IsInfected() )
{
// Get infection incidence by route
NewInfectionState::_enum nis = individual->GetNewInfectionState();
LOG_VALID_F( "nis = %d\n", ( nis ) );
auto mcw = individual->GetMonteCarloWeight();
if ( nis == NewInfectionState::NewAndDetected ||
nis == NewInfectionState::NewInfection /*||
nis == NewInfectionState::NewlyDetected*/ )
{
auto inf = individual->GetInfections().back();
StrainIdentity strain;
inf->GetInfectiousStrainID( &strain );
if( strain.GetGeneticID() == 0 )
{
enviro_infections_counter += mcw;
}
else if( strain.GetGeneticID() == 1 )
{
contact_infections_counter += mcw;
}
}
}
}
void VectorSpeciesReport::LogNodeData( Kernel::INodeContext * pNC )
{
LOG_DEBUG( "VectorSpeciesReport::LogNodeData.\n" );
int bin_index = 0;
Kernel::INodeVector * pNV = nullptr;
if( pNC->QueryInterface( GET_IID( Kernel::INodeVector ), (void**) &pNV ) != Kernel::s_OK )
{
throw Kernel::QueryInterfaceException( __FILE__, __LINE__, __FUNCTION__, "pNC", "INodeVector", "INodeContext" );
}
// reverse order, since push_front is used in NodeVector::SetVectorPopulations(), why??
const VectorPopulationReportingList_t& population_list = pNV->GetVectorPopulationReporting();
for (auto iterator = population_list.rbegin(); iterator != population_list.rend(); iterator++)
{
const auto vectorpopulation = *iterator;
LOG_VALID_F( "bin_index = %d \t species name = %s\n", bin_index, vectorpopulation->get_SpeciesID().c_str() );
adult_vectors[bin_index] += (float)( vectorpopulation->getAdultCount() + vectorpopulation->getInfectedCount() + vectorpopulation->getInfectiousCount() );
infectious_vectors[bin_index] += (float)( vectorpopulation->getInfectiousCount() );
daily_eir[bin_index] += vectorpopulation->GetEIRByPool(Kernel::VectorPoolIdEnum::BOTH_VECTOR_POOLS);
daily_hbr[bin_index] += vectorpopulation->GetHBRByPool(Kernel::VectorPoolIdEnum::BOTH_VECTOR_POOLS);
bin_index++;
}
}
void SusceptibilityTyphoid::Update(float dt)
{
age += dt; // tracks age for immune purposes
// if cross N year age boundary
//end of maternal antibodies at 6 months
float age_boundary = 0.5f * DAYSPERYEAR;
if( ( age >= age_boundary ) && ( ( age - dt ) < age_boundary ) && ( mod_acquire == 0 ) )
{
if( parent->GetRng()->SmartDraw( IndividualHumanTyphoidConfig::typhoid_6month_susceptible_fraction ) )
{
LOG_DEBUG_F("id %lu 6-month old being made susceptible.\n", parent->GetSuid().data);
mod_acquire = 1.0f;
}
}
float age_boundary_2 = 3 * DAYSPERYEAR;
if( ( age >= age_boundary_2 ) && ( ( age - dt ) < age_boundary_2 ) && ( mod_acquire == 0 ) )
{
if( parent->GetRng()->SmartDraw( IndividualHumanTyphoidConfig::typhoid_3year_susceptible_fraction ) )
{
LOG_DEBUG_F("id %lu 3-yo being made susceptible.\n", parent->GetSuid().data);
mod_acquire = 1.0f;
}
}
float age_boundary_3 = 6 * DAYSPERYEAR;
if( ( age >= age_boundary_3 ) && ( ( age - dt ) < age_boundary_3 ) && ( mod_acquire == 0 ) )
{
if( parent->GetRng()->SmartDraw( IndividualHumanTyphoidConfig::typhoid_6year_susceptible_fraction ) )
{
LOG_DEBUG_F("id %lu 6-yo being made susceptible.\n", parent->GetSuid().data);
mod_acquire = 1.0f;
}
}
#define SUSPCEPT_INTRO_YEAR (20)
#define LAMBDA_THRESHOLD (1000)
if (IndividualHumanTyphoidConfig::typhoid_exposure_lambda < LAMBDA_THRESHOLD )
{
float twenty_years_old_days = SUSPCEPT_INTRO_YEAR*DAYSPERYEAR;
if( ( age < twenty_years_old_days ) && mod_acquire == 0 )
{
double perc = 0.0f;
double perc1 = 0.0f;
double perc2 = 0.0f;
double num = 0.0f;
double denom = 0.0f;
float lambda = IndividualHumanTyphoidConfig::typhoid_exposure_lambda;
perc2 = 1.0f - ((twenty_years_old_days - age) / (age*lambda + twenty_years_old_days ));
perc1 = 1.0f - ((twenty_years_old_days - (age-1)) / ((age-1)*lambda + twenty_years_old_days ));
perc = (perc2 - perc1) / (1 - perc1);
if( parent->GetRng()->SmartDraw( perc ) )
{
mod_acquire = 1.0f;
LOG_VALID_F("id %lu , age %f being made susceptible.\n", parent->GetSuid().data, age);
//LOG_INFO_F("SUSCEPTIBLE %f %f\n", perc, mod_acquire);
}
}
}
float intro_year = 10; // magic number?
if (IndividualHumanTyphoidConfig::typhoid_exposure_lambda < LAMBDA_THRESHOLD )
{
intro_year = SUSPCEPT_INTRO_YEAR;
}
float age_boundary_4 = intro_year * DAYSPERYEAR;
if (age >= age_boundary_4 && age - dt < age_boundary_4 && mod_acquire == 0)
{
LOG_DEBUG_F("id %lu Schoolkids being made susceptible.\n", parent->GetSuid().data);
mod_acquire = 1.0f;
}
if( ( age > age_boundary_4 + dt ) && ( mod_acquire == 0 ) )
{
LOG_INFO_F("SOMEONE WAS MISSED AGE %f CUTOFF DAY %f MODACQUIRE %f\n", age, age_boundary_4 + dt, mod_acquire);
}
}