bool IndividualHumanTB::HasEverRelapsedAfterTreatment() const
{
// Query for intervention container
IIndividualHumanInterventionsContext *context = GetInterventionsContext();
ITBInterventionsContainer * itbivc = nullptr;
if (s_OK != context->QueryInterface(GET_IID(ITBInterventionsContainer), (void**)&itbivc) )
{
throw QueryInterfaceException( __FILE__, __LINE__, __FUNCTION__, "context", "ITBInterventionsContainer", "IIndividualHumanInterventionsContext" );
}
return itbivc->GetTxEverRelapsedStatus();
}
bool IndividualHumanTB::IsTreatmentNaive() const
{
// Query for intervention container, in future cache TB Intervention container when we create it
IIndividualHumanInterventionsContext *context = GetInterventionsContext();
ITBInterventionsContainer * itbivc = nullptr;
if (s_OK != context->QueryInterface(GET_IID(ITBInterventionsContainer), (void**)&itbivc) )
{
throw QueryInterfaceException( __FILE__, __LINE__, __FUNCTION__, "context", "ITBInterventionsContainer", "IIndividualHumanInterventionsContext" );
}
return itbivc->GetTxNaiveStatus();
}
bool IndividualHumanTB::IsOnTreatment() const
{
// Query for intervention container
IIndividualHumanInterventionsContext *context = GetInterventionsContext();
ITBInterventionsContainer * itbivc = nullptr;
if (s_OK != context->QueryInterface(GET_IID(ITBInterventionsContainer), (void**)&itbivc) )
{
throw QueryInterfaceException( __FILE__, __LINE__, __FUNCTION__, "context", "ITBInterventionsContainer", "IIndividualHumanInterventionsContext" );
}
if ( itbivc->GetNumTBDrugsActive() > 0 )
{
return true;
}
else
{
return false;
}
}
void IndividualHumanMalaria::UpdateGametocyteCounts(float dt)
{
// Check for mature gametocyte drug killing
float drugGametocyteKill = 0;
IMalariaDrugEffects* imde = nullptr;
if (s_OK == GetInterventionsContext()->QueryInterface(GET_IID(IMalariaDrugEffects), (void **)&imde))
{
drugGametocyteKill = imde->get_drug_gametocyteM();
}
else
{
throw QueryInterfaceException( __FILE__, __LINE__, __FUNCTION__, "GetInterventionsContext()", "IMalariaDrugEffects", "IIndividualHumanInterventionsContext" );
}
// Older mature gametocytes die; then add in the newly matured ones
double pkill = 0;
double numkilled = 0;
// Decay half-life--Sinden, R. E., G. A. Butcher, et al. (1996). "Regulation of Infectivity of Plasmodium to the Mosquito Vector." Advances in Parasitology 38: 53-117.
// Smalley, M. E. and R. E. Sinden (1977). "Plasmodium falciparum gametocytes: their longevity and infectivity." Parasitology 74(01): 1-8.
pkill = EXPCDF(-dt * (0.277 + drugGametocyteKill));// half-life of 2.5 days corresponds to a decay time constant of 3.6 days, 0.277 = 1/3.6
m_male_gametocytes = 0;
for( gametocytes_strain_map_t::iterator gc = m_male_gametocytes_by_strain.begin(); gc != m_male_gametocytes_by_strain.end(); )
{
// Gaussian approximation of binomial errors for each strain that is present
numkilled = (randgen->eGauss() * sqrt(pkill * gc->second * (1.0 - pkill)) + pkill * gc->second); // halflife of 2.5 days
numkilled = max(0.0, numkilled); //can't add by killing
gc->second = int64_t(gc->second - numkilled);
gc->second = max(0L, gc->second);
if ( gc->second == 0 )
{
gc = m_male_gametocytes_by_strain.erase(gc); // remove empty strains from map
}
else
{
m_male_gametocytes += gc->second;
++gc;
}
}
m_female_gametocytes = 0;
for( gametocytes_strain_map_t::iterator gc = m_female_gametocytes_by_strain.begin(); gc != m_female_gametocytes_by_strain.end(); )
{
numkilled = (randgen->eGauss() * sqrt(pkill * gc->second * (1.0 - pkill)) + pkill * gc->second); // halflife of 2.5 days
numkilled = max(0.0, numkilled); //can't add by killing
gc->second = int64_t(gc->second - numkilled);
gc->second = max(0L, gc->second);
if ( gc->second == 0 )
{
gc = m_female_gametocytes_by_strain.erase(gc); // remove empty strains from map
}
else
{
m_female_gametocytes += gc->second;
++gc;
}
}
infectiousness = 0;
int64_t tmp_male_gametocytes = 0;
int64_t tmp_female_gametocytes = 0;
StrainIdentity tmp_strainIDs;
// Loop over infections and add newly matured male and female gametocytes by strain
for (auto infection : infections)
{
// Cast from Infection --> InfectionMalaria
IInfectionMalaria *tempinf = nullptr;
if( infection->QueryInterface( GET_IID(IInfectionMalaria), (void**)&tempinf ) != s_OK )
{
throw QueryInterfaceException( __FILE__, __LINE__, __FUNCTION__, "Infection", "IInfectionMalaria", "tempinf" );
}
//InfectionMalaria *tempinf = static_cast<InfectionMalaria *>(infection);
// Get gametocytes that have matured in this timestep
// N.B. malariaCycleGametocytes is called once per asexual cycle (several days),
// so the stage-5 counter is reset to avoid multiple counting.
tmp_male_gametocytes = tempinf->get_MaleGametocytes(5);
tempinf->reset_MaleGametocytes(/* stage */5);
tmp_female_gametocytes = tempinf->get_FemaleGametocytes(5);
tempinf->reset_FemaleGametocytes(/* stage */5);
// No new gametocytes
if ( tmp_male_gametocytes==0 && tmp_female_gametocytes==0 ) continue;
// Add new gametocytes to those carried over (and not killed) from the previous time steps
infection->GetInfectiousStrainID(&tmp_strainIDs);
m_male_gametocytes_by_strain[tmp_strainIDs] += tmp_male_gametocytes;
m_male_gametocytes += tmp_male_gametocytes;
m_female_gametocytes_by_strain[tmp_strainIDs] += tmp_female_gametocytes;
m_female_gametocytes += tmp_female_gametocytes;
}
}
