Merge pull request #238 from dhardy/output

Output EIR by species

.travis.yml

@@ -42,7 +42,7 @@ before_install:
 
 install:
   - mkdir build && pushd build
-  - cmake -DCMAKE_BUILD_TYPE=Release -DOM_COPY_LIBS=1 ..
+  - cmake -DCMAKE_BUILD_TYPE=Release ..
 
 script:
   - make -j4
@@ -60,7 +60,6 @@ script:
   - echo "Using schema ../schema/$SCHEMA"
   - cp ../schema/$SCHEMA example/
   - cp openMalaria example/
-  - cp *.so example/
   - pushd example && strip openMalaria && ./run-example-scenario.sh && popd
   - echo "Running test scenarios"
   - ctest -j4

appveyor.yml

@@ -33,6 +33,7 @@ after_build:
   - cmd: ECHO "build-log:" https://ci.appveyor.com/project/%APPVEYOR_ACCOUNT_NAME%/openmalaria/builds/%APPVEYOR_BUILD_ID% >> %APPVEYOR_BUILD_FOLDER%\OpenMalaria\appveyor.log
   - cmd: ECHO "build-version:" %APPVEYOR_BUILD_VERSION% >> %APPVEYOR_BUILD_FOLDER%\OpenMalaria\appveyor.log
   - cmd: ECHO "worker-image:" %APPVEYOR_BUILD_WORKER_IMAGE% >> %APPVEYOR_BUILD_FOLDER%\OpenMalaria\appveyor.log
+  - cmd: copy %APPVEYOR_BUILD_FOLDER%\version.txt %APPVEYOR_BUILD_FOLDER%\OpenMalaria
   - cmd: copy %APPVEYOR_BUILD_FOLDER%\xsd\bin\xerces-c*.dll %APPVEYOR_BUILD_FOLDER%\OpenMalaria
   - cmd: mkdir %APPVEYOR_BUILD_FOLDER%\OpenMalaria\schema
   - cmd: copy %APPVEYOR_BUILD_FOLDER%\schema\scenario_*.xsd %APPVEYOR_BUILD_FOLDER%\OpenMalaria\schema

model/Transmission/NonVectorModel.cpp

@@ -217,7 +217,7 @@ void NonVectorModel::update () {
 }
 
 
-double NonVectorModel::calculateEIR(Host::Human& human, double ageYears, vector<double>& EIR){
+void NonVectorModel::calculateEIR(Host::Human& human, double ageYears, vector<double>& EIR){
     EIR.resize( 1 );    // no support for per-genotype tracking in this model (possible, but we're lazy)
     // where the full model, with estimates of human mosquito transmission is in use, use this:
     switch (simulationMode) {
@@ -258,7 +258,10 @@ double NonVectorModel::calculateEIR(Host::Human& human, double ageYears, vector<
     }
     #endif
     EIR[0] *= human.perHostTransmission.relativeAvailabilityHetAge (ageYears);
-    return EIR[0];
+
+    auto ag = human.monAgeGroup().i();
+    auto cs = human.cohortSet();
+    mon::reportStatMACGF( mon::MVF_INOCS, ag, cs, 0, EIR[0] );
 }
 
 

model/Transmission/NonVectorModel.h

@@ -73,7 +73,7 @@ class NonVectorModel : public TransmissionModel {
 
   virtual void vectorUpdate () {}
   virtual void update ();
-  virtual double calculateEIR(OM::Host::Human& human, double ageYears, vector< double >& EIR);
+  virtual void calculateEIR(OM::Host::Human& human, double ageYears, vector< double >& EIR);
 
 private:
 

model/Transmission/TransmissionModel.cpp

@@ -40,13 +40,6 @@
 namespace OM { namespace Transmission {
 namespace vectors = util::vectors;
 
-inline size_t survInocsSize(size_t nGenotypes){
-    return mon::AgeGroup::numGroups() * mon::numCohortSets() * nGenotypes; }
-inline size_t survInocsIndex(size_t ageGroup, size_t cohortSet, size_t genotype){
-    return ageGroup + mon::AgeGroup::numGroups() *
-        (cohortSet + mon::numCohortSets() * genotype);
-}
-
 TransmissionModel* TransmissionModel::createTransmissionModel (const scnXml::Entomology& entoData, int populationSize) {
   // Entomology contains either a list of at least one anopheles or a list of at
   // least one EIRDaily.
@@ -125,7 +118,6 @@ TransmissionModel::TransmissionModel(const scnXml::Entomology& entoData,
     tsNumAdults(0)
 {
     initialisationEIR.assign (SimTime::stepsPerYear(), 0.0);
-    surveyInoculations.assign(survInocsSize(nGenotypes), 0.0);
 
   using Monitoring::Continuous;
   Continuous.registerCallback( "input EIR", "\tinput EIR", MakeDelegate( this, &TransmissionModel::ctsCbInputEIR ) );
@@ -201,11 +193,6 @@ double TransmissionModel::getEIR( Host::Human& human, SimTime age,
     calculateEIR( human, ageYears, EIR );
     util::streamValidate( EIR );
 
-    for( size_t g = 0, nG = EIR.size(); g < nG; ++g ){
-        size_t index = survInocsIndex(human.monAgeGroup().i(), human.cohortSet(), g);
-        surveyInoculations[index] += EIR[g];
-    }
-
     double allEIR = vectors::sum( EIR );
     if( age >= adultAge ){
         tsAdultEntoInocs += allEIR;
@@ -220,19 +207,6 @@ void TransmissionModel::summarize () {
 
     if( !mon::isReported() ) return;    // cannot use counters below when not reporting
 
-    for( size_t ag = 0, nAg = mon::AgeGroup::numGroups(), cs = 0,
-        nCS = mon::numCohortSets(), g = 0, nG = surveyInoculations.size() / (nAg * nCS);
-        ag < nAg; ++ag )
-    {
-        for( cs = 0; cs < nCS; ++cs ){
-            for( g = 0; g < nG; ++ g ){
-                size_t index = survInocsIndex(ag, cs, g);
-                mon::reportStatMACGF( mon::MVF_INOCS, ag, cs, g, surveyInoculations[index] );
-            }
-        }
-    }
-    surveyInoculations.assign( surveyInoculations.size(), 0.0 );
-
     double duration = (sim::now() - lastSurveyTime).inSteps();
     if( duration == 0.0 ){
         assert( surveyInputEIR == 0.0 && surveySimulatedEIR == 0.0 );
@@ -265,7 +239,6 @@ void TransmissionModel::checkpoint (istream& stream) {
     lastSurveyTime & stream;
     numTransmittingHumans & stream;
     tsNumAdults & stream;
-    surveyInoculations & stream;
 }
 void TransmissionModel::checkpoint (ostream& stream) {
     simulationMode & stream;
@@ -283,7 +256,6 @@ void TransmissionModel::checkpoint (ostream& stream) {
     lastSurveyTime & stream;
     numTransmittingHumans & stream;
     tsNumAdults & stream;
-    surveyInoculations & stream;
 }
 
 } }

model/Transmission/TransmissionModel.h

@@ -215,7 +215,7 @@ class TransmissionModel {
    * @param EIR Out-vector. Set to the age- and heterogeneity-specific EIR an
    *    individual human is exposed to, per parasite genotype, in units of
    *    inoculations per day. Length set by callee. */
-  virtual double calculateEIR(Host::Human& human, double ageYears,
+  virtual void calculateEIR(Host::Human& human, double ageYears,
         vector<double>& EIR ) = 0; 
 
   /** Needs to be called each time-step after Human::update() to update summary
@@ -307,10 +307,6 @@ class TransmissionModel {
 
   /// accumulator for time step adults requesting EIR
   int tsNumAdults;
-
-    /// Total inoculations since last survey (multidimensional).
-    /// See survInocsSize, survInocsIndex in cpp file.
-    vector<double> surveyInoculations;
 };
 
 } }

model/Transmission/VectorModel.cpp

@@ -414,16 +414,18 @@ SimTime VectorModel::initIterate () {
     }
 }
 
-double VectorModel::calculateEIR(Host::Human& human, double ageYears,
+void VectorModel::calculateEIR(Host::Human& human, double ageYears,
         vector<double>& EIR)
 {
+    auto ag = human.monAgeGroup().i();
+    auto cs = human.cohortSet();
     PerHost& host = human.perHostTransmission;
     host.update( human );
     if (simulationMode == forcedEIR){
         double eir = initialisationEIR[sim::ts0().moduloYearSteps()] *
                 host.relativeAvailabilityHetAge (ageYears);
+        mon::reportStatMACGF( mon::MVF_INOCS, ag, cs, 0, eir );
         EIR.assign( 1, eir );
-        return eir;
     }else{
         assert( simulationMode == dynamicEIR );
         EIR.assign( WithinHost::Genotypes::N(), 0.0 );
@@ -441,10 +443,11 @@ double VectorModel::calculateEIR(Host::Human& human, double ageYears,
              * See comment in AnophelesModel::advancePeriod for method. */
             double entoFactor = ageFactor * host.availBite(species[i].getHumanBaseParams(), i);
             for( size_t g = 0; g < EIR.size(); ++g ){
-                EIR[g] += partialEIR[g] * entoFactor;
+                auto eir = partialEIR[g] * entoFactor;
+                mon::reportStatMACSGF( mon::MVF_INOCS, ag, cs, i, g, eir );
+                EIR[g] += eir;
             }
         }
-        return vectors::sum( EIR );
     }
 }
 

model/Transmission/VectorModel.h

@@ -62,7 +62,7 @@ class VectorModel : public TransmissionModel {
   virtual void vectorUpdate ();
   virtual void update ();
 
-  virtual double calculateEIR( Host::Human& human, double ageYears,
+  virtual void calculateEIR( Host::Human& human, double ageYears,
         vector<double>& EIR );
 
   virtual const map<string,size_t>& getSpeciesIndexMap();

model/mon/OutputMeasures.h

@@ -236,8 +236,8 @@ void defineOutMeasures(){
     /// Kappa (human infectiousness) weighted by availability per day-of-year for the last year.
     /// (Reporting removed.)
     namedOutMeasures["kappaPerDayOfYear"] = OutMeasure::obsolete( 29 );
-    /** The total number of inoculations, by age group and cohort, summed over
-     * the reporting period. */
+    /** The total number of inoculations, by age group, cohort and parasite
+     * genotype, summed over the reporting period. */
     namedOutMeasures["innoculationsPerAgeGroup"] =
         OutMeasure::humanACG( 30, MVF_INOCS, true );
     /// N_v0: emergence of feeding vectors during the last time step. Units: mosquitoes/day
@@ -450,6 +450,10 @@ void defineOutMeasures(){
      */
     namedOutMeasures["expectedSevere"] =
         OutMeasure::humanAC( 78, MHF_EXPECTED_SEVERE, true );
+    /** The total number of inoculations, by mosquito species, summed over
+     * the reporting period. */
+    namedOutMeasures["innoculationsPerVector"] =
+        OutMeasure::species( 79, MVF_INOCS, false );
 
     // Now initialise valid condition measures:
     foreach( const NamedMeasureMapT::value_type& v, namedOutMeasures ){

model/mon/mon.cpp

@@ -655,6 +655,12 @@ void reportStatMACGF( Measure measure, size_t ageIndex, uint32_t cohortSet,
     const size_t survey = impl::survNumStat;
     storeF.report( val, measure, survey, ageIndex, cohortSet, 0, genotype, 0 );
 }
+void reportStatMACSGF( Measure measure, size_t ageIndex, uint32_t cohortSet,
+                  size_t species, size_t genotype, double val )
+{
+    const size_t survey = impl::survNumStat;
+    storeF.report( val, measure, survey, ageIndex, cohortSet, species, genotype, 0 );
+}
 void reportStatMHPF( Measure measure, const Host::Human& human, size_t drug, double val ){
     const size_t survey = impl::survNumStat;
     const size_t ageIndex = human.monAgeGroup().i();

model/mon/reporting.h

@@ -227,7 +227,7 @@ void reportStatMHF( Measure measure, const Host::Human& human, double val );
 /// Report some value (floating point) for the current survey and some age
 /// group and cohort set
 void reportStatMACGF( Measure measure, size_t ageIndex, uint32_t cohortSet,
-                  size_t genotpye, double val );
+                  size_t genotype, double val );
 /// Report some value (floating point) for some human and genotype to the current survey.
 void reportStatMHGF( Measure measure, const Host::Human& human, size_t genotype,
                  double val );
@@ -237,6 +237,10 @@ void reportStatMHPF( Measure measure, const Host::Human& human, size_t drugIndex
 void reportStatMSF( Measure measure, size_t species, double val );
 /// Report some value (floating point) by genotype to the current survey.
 void reportStatMSGF( Measure measure, size_t species, size_t genotype, double val );
+/// Report some value (floating point) for the current survey and some age
+/// group, cohort set, genotype and vector species
+void reportStatMACSGF( Measure measure, size_t ageIndex, uint32_t cohortSet,
+                  size_t species, size_t genotype, double val );
 
 /// Query whether an output measure is used.
 /// This function is not fast, so it is recommended to cache the result.