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Merge branch 'gh152_BloodCapacity_Calculation_Fix' into New_Pyrogenic_Threshold_And_MSP1_Antibody_Capacity_Fix
# Conflicts: # Eradication/SusceptibilityMalaria.cpp # Regression/Malaria/113_Malaria_AntibodyLongTermDecay/output/InsetChart.json # Regression/Malaria/114_Malaria_Serialization_AntibodyLongTermDecay/output/InsetChart.json
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‎Eradication/SusceptibilityMalaria.cpp‎

Lines changed: 17 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -260,7 +260,6 @@ namespace Kernel
260260
}
261261
else if(SusceptibilityMalariaConfig::innate_immune_variation_type != InnateImmuneVariationType::NONE)
262262
{
263-
264263
const NodeDemographics& r_demographics = parent->GetEventContext()->GetNodeEventContext()->GetDemographics();
265264
if(!r_demographics["IndividualAttributes"].Contains( "InnateImmuneDistributionFlag" ) ||
266265
!r_demographics["IndividualAttributes"].Contains( "InnateImmuneDistribution1" ) ||
@@ -306,22 +305,22 @@ namespace Kernel
306305

307306
void SusceptibilityMalaria::Update(float dt)
308307
{
309-
release_assert( params() );
308+
// dt = 0.125 when infected, 1.0 otherwise
309+
release_assert(params());
310310

311311
age += dt; // age in days
312312
m_age_dependent_biting_risk = BitingRiskAgeFactor(age);
313313

314-
if( age <= (20 * DAYSPERYEAR) ) // recalculate kids every day
314+
if(age < ( 20 * DAYSPERYEAR )) // recalculate under-20 year olds every time step
315315
{
316-
recalculateBloodCapacity( age );
316+
recalculateBloodCapacity( age );
317317
}
318-
else if(age <= 20 * DAYSPERYEAR + dt) // recalculate once when they turn 20
318+
else if(age < ( 20 * DAYSPERYEAR + dt )) // recalculate once when they turn 20
319319
{
320320
// set adult blood capacity once when they turn 20, it remains constant after that, no need to update again
321-
recalculateBloodCapacity( age );
321+
recalculateBloodCapacity( age );
322322
}
323323

324-
325324
// approximately every 3 months, within the first timestep once three months have passed
326325
if(SusceptibilityMalariaConfig::innate_immune_variation_type == InnateImmuneVariationType::PYROGENIC_THRESHOLD_VS_AGE_CONCAVE ||
327326
SusceptibilityMalariaConfig::innate_immune_variation_type == InnateImmuneVariationType::PYROGENIC_THRESHOLD_VS_AGE_INCREASING_AND_CYTOKINE_KILLING_INVERSE)
@@ -566,24 +565,21 @@ namespace Kernel
566565
void SusceptibilityMalaria::recalculateBloodCapacity( float _age )
567566
{
568567
// How many RBCs a person should have determined by age.
569-
// This sets the daily production of red blood cells for adults to maintain
570-
// standard equilibrium RBC concentrations given RBC lifetime
571-
if ( _age > (20 * DAYSPERYEAR) )
568+
// Sets daily production of red blood cells for people to set their equilibrium RBC concentrations and blood volume given an RBC lifetime
569+
// Only approximate due to linear increase in blood volume from 0.5 to 5 liters with age, a better growth model would be nonlinear
570+
if (_age >= 20 * DAYSPERYEAR) // 20 years = 7300 days, keeping this separate for initializing the population
572571
{
573-
// This initializes the daily production of red blood cells for adults to maintain standard equilibrium RBC concentrations given RBC lifetime
574-
// N.B. Heavily caveated, because not all adults are same size. However, this keeps consistent equilibrium RBC densities, allowing study of anemia, etc...
575-
m_RBCproduction = ADULT_RBC_PRODUCTION; // 2.0*10^11 (RBCs/day)*(120 days) = 2.4x10^13 RBCs ~= 5 liters * 5x10^6 RBCs/microliter
576-
// This equation tracks the blood volume separately from the equilibrium number of RBCs, allowing for non-constant RBC concentration.
577-
// m_inv_microliters_blood is 1/(microliters of blood in body)--this allows easy calculation of pathogen densities from pathogen numbers
578-
m_inv_microliters_blood = float(1 / ( (0.225 * (7300/DAYSPERYEAR) + 0.5) * 1e6 ));
572+
m_RBCproduction = ADULT_RBC_PRODUCTION;
573+
m_inv_microliters_blood = float( 1 / ( ( 0.225 * ( 7300 / DAYSPERYEAR ) + 0.5 ) * 1e6 ) );// adult blood volume 5 liters
579574
}
580575
else
581576
{
582-
// Update children
583-
// Sets daily production of red blood cells for children to set their equilibrium RBC concentrations and blood volume given an RBC lifetime
584-
// Only approximate due to linear increase in blood volume from 0.5 to 5 liters with age, a better growth model would be nonlinear
585-
m_RBCproduction = int64_t(INFANT_RBC_PRODUCTION + (_age * .000137) * (ADULT_RBC_PRODUCTION - INFANT_RBC_PRODUCTION)); //*.000137==/(20*DAYSPERYEAR)
586-
m_inv_microliters_blood = float(1 / ( (0.225 * (_age/DAYSPERYEAR) + 0.5 ) * 1e6 ));
577+
m_RBCproduction = int64_t( INFANT_RBC_PRODUCTION + ( _age * .000137 ) * ( ADULT_RBC_PRODUCTION - INFANT_RBC_PRODUCTION ) );
578+
if(m_RBCproduction > ADULT_RBC_PRODUCTION)
579+
{
580+
m_RBCproduction = ADULT_RBC_PRODUCTION; // cap at adult production, overrun happens to infected people at age 7299.375-7300 days
581+
}
582+
m_inv_microliters_blood = float( 1 / ( ( 0.225 * ( _age / DAYSPERYEAR ) + 0.5 ) * 1e6 ) );
587583
}
588584
m_RBCcapacity = m_RBCproduction * AVERAGE_RBC_LIFESPAN; // Health equilibrium of RBC is production*lifetime
589585
}

‎Regression/Malaria/101_Malaria_ReportInterventionData/output/InsetChart.json‎

Lines changed: 1 addition & 1 deletion
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‎Regression/Malaria/104_Malaria_Household_5x5_Serialization/output/InsetChart.json‎

Lines changed: 3 additions & 3 deletions
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‎Regression/Malaria/105_Malaria_Innate_Immune_Variation/output/InsetChart.json‎

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‎Regression/Malaria/106_Malaria_ReportInterventionData_GH4629/output/InsetChart.json‎

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‎Regression/Malaria/107_Malaria_Serialization_DelayedIntervention/output/InsetChart.json‎

Lines changed: 7 additions & 7 deletions
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‎Regression/Malaria/108_Malaria_Serialization_GH4791/output/InsetChart.json‎

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‎Regression/Malaria/109_Malaria_FPG_WorkflowOutput/output/InsetChart.json‎

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