add elimination support for nUncomp

model/Clinical/Episode.cpp

@@ -22,6 +22,7 @@
 #include "Clinical/Episode.h"
 #include "Clinical/ClinicalModel.h"
 #include "Host/Human.h"
+#include "Host/WithinHost/WHInterface.h"
 
 namespace OM {
 namespace Clinical {
@@ -40,6 +41,8 @@ void Episode::flush() {
 void Episode::update (const Host::Human& human, Episode::State newState)
 {
     if( time + ClinicalModel::hsMemory() <= sim::ts0() ){
+        infectionType = human.withinHostModel->getInfectionType();
+
         report ();
 
         time = sim::ts0();
@@ -66,6 +69,12 @@ void Episode::report () {
             }
         } else { // UC or UC2
             mon::reportMSACI( mon::MHE_UNCOMPLICATED_EPISODES, surveyPeriod, ageGroup, cohortSet, 1 );
+            if(infectionType == WithinHost::InfectionOrigin::Indigenous)
+                mon::reportMSACI( mon::MHE_UNCOMPLICATED_EPISODES_INDIGENOUS, surveyPeriod, ageGroup, cohortSet, 1 );
+            else if(infectionType == WithinHost::InfectionOrigin::Introduced)
+                mon::reportMSACI( mon::MHE_UNCOMPLICATED_EPISODES_INTRODUCED, surveyPeriod, ageGroup, cohortSet, 1 );
+            else
+                mon::reportMSACI( mon::MHE_UNCOMPLICATED_EPISODES_IMPORTED, surveyPeriod, ageGroup, cohortSet, 1 );
         }
 
         // Report outcomes of malarial fevers

model/Clinical/Episode.h

@@ -24,6 +24,7 @@
 
 #include "Global.h"
 #include "Host/WithinHost/Pathogenesis/State.h"
+#include "Host/WithinHost/Infection/Infection.h"
 #include "mon/AgeGroup.h"
 #include "mon/info.h"
 #include <ostream>
@@ -112,6 +113,8 @@ class Episode{
     /// Descriptor of state, containing reporting info. Not all information will
     /// be reported (e.g. indirect deaths are reported independantly).
     Episode::State state;
+
+    WithinHost::InfectionOrigin infectionType = WithinHost::InfectionOrigin::Indigenous;
 
 private:
     /** Report a clinical episode.

model/Host/WithinHost/CommonWithinHost.cpp

@@ -260,14 +260,30 @@ void CommonWithinHost::update(Host::Human &human, LocalRng& rng, int &nNewInfs_i
         m_y_lag_l[y_lag_i * Genotypes::N() + g] = 0.0;
     }
 
+    int nImported = 0, nIntroduced = 0, nIndigenous = 0;
     for( auto inf = infections.begin(); inf != infections.end(); ++inf )
     {
         if((*inf)->origin() == InfectionOrigin::Imported)
             m_y_lag_i[y_lag_i * Genotypes::N() + (*inf)->genotype()] += (*inf)->getDensity();
         else
             m_y_lag_l[y_lag_i * Genotypes::N() + (*inf)->genotype()] += (*inf)->getDensity();
+
+        if((*inf)->origin() == InfectionOrigin::Indigenous) nIndigenous++;
+        else if((*inf)->origin() == InfectionOrigin::Introduced) nIntroduced++;
+        else nImported++;
     }
 
+    /* The rules are:
+    - Imported only if all infections are imported
+    - Introduced if at least one Introduced
+    - Indigenous otherwise (Imported + Indigenous or just Indigenous infections) */
+    if(nIntroduced > 0)
+        infectionType = InfectionOrigin::Introduced;
+    else if(nIndigenous > 0)
+        infectionType = InfectionOrigin::Indigenous;
+    else
+        infectionType = InfectionOrigin::Imported;
+
     // This is a bug, we keep it this way to be consistent with old simulations
     if(nNewInfsIgnored > 0)
         nNewInfs_l += nNewInfsIgnored;
@@ -294,16 +310,7 @@ bool CommonWithinHost::summarize( Host::Human& human )const{
     pkpdModel.summarize( human );
 
     // If the number of infections is 0 and parasite density is positive we default to Indigenous
-    InfectionOrigin infectionType = InfectionOrigin::Indigenous;
     if( infections.size() > 0 ){
-        int nImported = 0, nIntroduced = 0, nIndigenous = 0;
-        for(const auto infection : infections)
-        {
-            if(infection->origin() == InfectionOrigin::Indigenous) nIndigenous++;
-            else if(infection->origin() == InfectionOrigin::Introduced) nIntroduced++;
-            else nImported++;
-        }
-
         mon::reportStatMHI( mon::MHR_INFECTED_HOSTS, human, 1 );
         if(infectionType == InfectionOrigin::Indigenous)
             mon::reportStatMHI( mon::MHR_INFECTED_HOSTS_INDIGENOUS, human, 1 );

model/Host/WithinHost/DescriptiveWithinHost.cpp

@@ -151,7 +151,7 @@ void DescriptiveWithinHostModel::update(Host::Human &human, LocalRng& rng, int &
 
     bool treatmentLiver = treatExpiryLiver > sim::ts0();
     bool treatmentBlood = treatExpiryBlood > sim::ts0();
-    
+
     for(auto inf = infections.begin(); inf != infections.end();) {
         //NOTE: it would be nice to combine this code with that in
         // CommonWithinHost.cpp, but a few changes would be needed:
@@ -207,14 +207,30 @@ void DescriptiveWithinHostModel::update(Host::Human &human, LocalRng& rng, int &
         m_y_lag_l[y_lag_i * Genotypes::N() + g] = 0.0;
     }
 
+    int nImported = 0, nIntroduced = 0, nIndigenous = 0;
     for( auto inf = infections.begin(); inf != infections.end(); ++inf )
     {
         if(inf->origin() == InfectionOrigin::Imported)
             m_y_lag_i[y_lag_i * Genotypes::N() + inf->genotype()] += inf->getDensity();
         else
             m_y_lag_l[y_lag_i * Genotypes::N() + inf->genotype()] += inf->getDensity();
+
+        if(inf->origin() == InfectionOrigin::Indigenous) nIndigenous++;
+        else if(inf->origin() == InfectionOrigin::Introduced) nIntroduced++;
+        else nImported++;
     }
 
+    /* The rules are:
+    - Imported only if all infections are imported
+    - Introduced if at least one Introduced
+    - Indigenous otherwise (Imported + Indigenous or just Indigenous infections) */
+    if(nIntroduced > 0)
+        infectionType = InfectionOrigin::Introduced;
+    else if(nIndigenous > 0)
+        infectionType = InfectionOrigin::Indigenous;
+    else
+        infectionType = InfectionOrigin::Imported;
+
     // This is a bug, we keep it this way to be consistent with old simulations
     if(opt_vaccine_genotype == false)
     {
@@ -230,27 +246,7 @@ bool DescriptiveWithinHostModel::summarize( Host::Human& human )const{
     pathogenesisModel->summarize( human );
 
     // If the number of infections is 0 and parasite density is positive we default to Indigenous
-    InfectionOrigin infectionType = InfectionOrigin::Indigenous;
     if( infections.size() > 0 ){
-        int nImported = 0, nIntroduced = 0, nIndigenous = 0;
-        for(const auto& infection : infections)
-        {
-            if(infection.origin() == InfectionOrigin::Indigenous) nIndigenous++;
-            else if(infection.origin() == InfectionOrigin::Introduced) nIntroduced++;
-            else nImported++;
-        }
-
-        /* The rules are:
-        - Imported only if all infections are imported
-        - Introduced if at least one Introduced
-        - Indigenous otherwise (Imported + Indigenous or just Indigenous infections) */
-        if(nIntroduced > 0)
-            infectionType = InfectionOrigin::Introduced;
-        else if(nIndigenous > 0)
-            infectionType = InfectionOrigin::Indigenous;
-        else
-            infectionType = InfectionOrigin::Imported;
-
         mon::reportStatMHI( mon::MHR_INFECTED_HOSTS, human, 1 );
         if(infectionType == InfectionOrigin::Indigenous)
             mon::reportStatMHI( mon::MHR_INFECTED_HOSTS_INDIGENOUS, human, 1 );
@@ -259,6 +255,14 @@ bool DescriptiveWithinHostModel::summarize( Host::Human& human )const{
         else
             reportStatMHI( mon::MHR_INFECTED_HOSTS_IMPORTED, human, 1 );
 
+        int nImported = 0, nIntroduced = 0, nIndigenous = 0;
+        for( auto inf = infections.begin(); inf != infections.end(); ++inf )
+        {
+            if(inf->origin() == InfectionOrigin::Indigenous) nIndigenous++;
+            else if(inf->origin() == InfectionOrigin::Introduced) nIntroduced++;
+            else nImported++;
+        }
+
         // (patent) infections are reported by genotype, even though we don't have
         // genotype in this model
         mon::reportStatMHGI( mon::MHR_INFECTIONS, human, 0, infections.size() );

model/Host/WithinHost/WHFalciparum.h

@@ -70,6 +70,10 @@ class WHFalciparum : public WHInterface {
 
     virtual Pathogenesis::StatePair determineMorbidity( Host::Human& human, double ageYears, bool isDoomed );
 
+    virtual InfectionOrigin getInfectionType() const {
+        return infectionType;
+    }
+
     inline double getCumulative_h() const {
         return m_cumulative_h;
     }
@@ -136,6 +140,8 @@ class WHFalciparum : public WHInterface {
 
     /// End of step on which treatment expires = start of first step after expiry
     SimTime treatExpiryLiver, treatExpiryBlood;
+
+    InfectionOrigin infectionType = InfectionOrigin::Indigenous;
 
     virtual void checkpoint (istream& stream);
     virtual void checkpoint (ostream& stream);

model/Host/WithinHost/WHInterface.h

@@ -26,6 +26,8 @@
 #include "util/random.h"
 #include "Host/WithinHost/Diagnostic.h"
 #include "Host/WithinHost/Pathogenesis/State.h"
+#include "Host/WithinHost/Infection/Infection.h"
+
 #include "Parameters.h"
 
 using namespace std;
@@ -192,6 +194,8 @@ class WHInterface {
     virtual double getCumulative_h() const =0;
     virtual double getCumulative_Y() const =0;
 
+    virtual InfectionOrigin getInfectionType() const =0;
+
     /** The maximum number of infections a human can have. The only real reason
      * for this limit is to prevent incase bad input from causing the number of
      * infections to baloon stupidly.

model/Host/WithinHost/WHVivax.h

@@ -164,6 +164,10 @@ class WHVivax : public WHInterface {
     virtual Pathogenesis::StatePair determineMorbidity( Host::Human& human, double ageYears, bool );
 
     virtual void clearImmunity();
+
+    virtual InfectionOrigin getInfectionType() const {
+        return InfectionOrigin::Indigenous;
+    }
 
 protected:
     virtual void treatment( Host::Human& human, TreatmentId treatId );

model/mon/OutputMeasures.h

@@ -188,8 +188,10 @@ void defineOutMeasures(){
     /// number of blood-stage treatments (inpatient)
     namedOutMeasures["nTreatments3"] = OutMeasure::humanAC( 13, MHT_TREATMENTS_3, false );
     /// number of episodes (uncomplicated)
-    namedOutMeasures["nUncomp"] =
-        OutMeasure::humanAC( 14, MHE_UNCOMPLICATED_EPISODES, false );
+    namedOutMeasures["nUncomp"] = OutMeasure::humanAC( 14, MHE_UNCOMPLICATED_EPISODES, false );
+        namedOutMeasures["nUncomp_Imported"] = OutMeasure::humanAC( 1014, MHE_UNCOMPLICATED_EPISODES_IMPORTED, false );
+        namedOutMeasures["nUncomp_Introduced"] = OutMeasure::humanAC( 2014, MHE_UNCOMPLICATED_EPISODES_INTRODUCED, false );
+        namedOutMeasures["nUncomp_Indigenous"] = OutMeasure::humanAC( 3014, MHE_UNCOMPLICATED_EPISODES_INDIGENOUS, false );
     /// Number of severe episodes (severe malaria or malaria + coinfection)
     namedOutMeasures["nSevere"] =
         OutMeasure::humanAC( 15, MHE_SEVERE_EPISODES, false );

model/mon/reporting.h

@@ -81,7 +81,7 @@ enum Measure{
 
     // ———  MHE: measures for human episodes (integers)  ———
     // Number of uncomplicated fever episodes in humans. Units: cases
-    MHE_UNCOMPLICATED_EPISODES,
+    MHE_UNCOMPLICATED_EPISODES, MHE_UNCOMPLICATED_EPISODES_IMPORTED, MHE_UNCOMPLICATED_EPISODES_INTRODUCED, MHE_UNCOMPLICATED_EPISODES_INDIGENOUS,
     // Number of severe fever episodes in humans. Units: cases
     MHE_SEVERE_EPISODES,
     // Number of severe fever episodes without counting episodes due to comorbidities in humans. Units: cases

unittest/WHMock.cpp

@@ -94,6 +94,10 @@ double WHMock::getCumulative_Y() const{
     throw util::unimplemented_exception( "not needed in unit test" );
 }
 
+InfectionOrigin WHMock::getInfectionType() const{
+    return InfectionOrigin::Indigenous;
+}
+
 void WHMock::checkpoint (istream& stream){
     throw util::unimplemented_exception( "not needed in unit test" );
 }

unittest/WHMock.h

@@ -59,6 +59,7 @@ class WHMock : public WHInterface {
     virtual void clearImmunity();
     virtual double getCumulative_h() const;
     virtual double getCumulative_Y() const;
+    virtual InfectionOrigin getInfectionType() const;
 
     // This mock class does not have actual infections. Just set this as you please.
     double totalDensity;