New root finding emergence rate

CMakeLists.txt

@@ -20,7 +20,7 @@ if (NOT MSVC)
     set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -msse2 -mfpmath=sse")
   endif (${CMAKE_SYSTEM_PROCESSOR} MATCHES "^arm")
   # We almost always want optimisations enabled:
-  set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O2")
+  set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O2 -g")
 endif (NOT MSVC)
 
 set (OM_STD_LIBS )

model/CMakeLists.txt

@@ -54,6 +54,7 @@ set (Model_CPP
   #Transmission/Anopheles/LifeCycle.cpp
   #Transmission/Anopheles/ResourceFitter.cpp
   Transmission/Anopheles/PerHostAnoph.cpp
+  Transmission/Anopheles/CalcNvO.cpp
 
   WithinHost/WHInterface.cpp
   WithinHost/WHFalciparum.cpp

model/Simulator.cpp

@@ -239,7 +239,7 @@ void Simulator::start(const scnXml::Monitoring& monitoring){
 
         } else if (phase == TRANSMISSION_INIT) {
             // Start or continuation of transmission init cycle (after one life span)
-            SimTime iterate = transmission->initIterate();
+            SimTime iterate = transmission->initIterate(*population);
             if( iterate > SimTime::zero() ){
                 m_phaseEnd += iterate;
                 --phase;        // repeat phase

model/Transmission/Anopheles/AnophelesModel.cpp

@@ -51,6 +51,10 @@ string AnophelesModel::initialise (
 
     mosqSeekingDuration = mosq.getMosqSeekingDuration().getValue();
     probMosqSurvivalOvipositing = mosq.getMosqProbOvipositing().getValue();
+    mosqProbBiting = mosq.getMosqProbBiting().getMean(); //PerHostAnophParams::get(species).ProbMosqbBiting;
+    mosqProbFindRestSite = mosq.getMosqProbFindRestSite().getMean(); //PerHostAnophParams::get(species).ProbMosqbFindRestSite;
+    mosqProbResting = mosq.getMosqProbResting().getMean(); //PerHostAnophParams::get(species).ProbMosqbResting;
+    mosqProbOvipositing = mosq.getMosqProbOvipositing().getValue(); //PerHostAnophParams::get(species).ProbMosqbOvipositing;
 
     transmission.initialise( anoph.getLifeCycle(), anoph.getSimpleMPD(), anoph.getMosq() );
 
@@ -221,6 +225,7 @@ void AnophelesModel::init2 (int nHumans, double meanPopAvail,
     transmission.emergence->init2( initialP_A, initialP_df, initialP_dff,
             nHumans * meanPopAvail / sumPFindBite, transmission );
 
+    meanAvail = meanPopAvail;
     // All set up to drive simulation from forcedS_v
 }
 

model/Transmission/Anopheles/AnophelesModel.h

@@ -29,6 +29,8 @@
 #include "util/SimpleDecayingValue.h"
 #include "util/vectors.h"
 
+#include "CalcNvO.h"
+
 #include <vector>
 #include <limits>
 
@@ -160,8 +162,61 @@ class AnophelesModel
      * so, make necessary changes.
      *
      * @returns true if another iteration is needed. */
-    inline bool initIterate (){
-        return transmission.emergence->initIterate(transmission);
+    inline bool initIterate (size_t species, int populationSize, vector<double> &laggedKappa){
+        //return transmission.emergence->initIterate(species, transmission);
+        double *mosqEmergerateVector = transmission.emergence->getEmergenceRate().internal().data();
+        int daysInYear = transmission.emergence->getEmergenceRate().internal().size(); // 365?
+        int mosqRestDuration = transmission.getMosqRestDuration().inDays();
+        int EIPDuration = transmission.getEIPDuration().inDays();
+        int nHostTypesInit = 1; // + types of non human hosts
+        int nMalHostTypesInit = 1; // ??
+        double popSizeInit = populationSize; // ??
+        double hostAvailabilityRateInit = meanAvail; // ?
+        //double mosqSeekingDuration = mosqSeekingDuration;
+        // double mosqProbBiting = mosq.getMosqProbBiting().getMean(); //PerHostAnophParams::get(species).ProbMosqbBiting;
+        // double mosqProbFindRestSite = mosq.getMosqProbFindRestSite().getMean(); //PerHostAnophParams::get(species).ProbMosqbFindRestSite;
+        // double mosqProbResting = mosq.getMosqProbResting().getMean(); //PerHostAnophParams::get(species).ProbMosqbResting;
+        // double mosqProbOvipositing = mosq.getMosqProbOvipositing().getValue(); //PerHostAnophParams::get(species).ProbMosqbOvipositing;
+
+        vector<double> Kvi(daysInYear, laggedKappa[0]);
+        double *FHumanInfectivityInitVector = Kvi.data();
+        double *FEIRInitVector = transmission.emergence->getEIR().internal().data();
+
+        // check nvo multiplication if all values are 0
+        std::vector<double> & Nv0guessRef = transmission.emergence->getEmergenceRate().internal();
+        std::vector<double> NvOguess(Nv0guessRef.begin(), Nv0guessRef.end());
+        double *FMosqEmergeRateInitEstimateVector = NvOguess.data();
+
+        cout << "daysInYear: " << daysInYear << endl;
+        cout << "mosqRestDuration: " << mosqRestDuration << endl;
+        cout << "EIPDuration: " << EIPDuration << endl;
+        cout << "nHostTypesInit: " << nHostTypesInit << endl;
+        cout << "nMalHostTypesInit: " << nMalHostTypesInit << endl;
+        cout << "popSizeInit: " << popSizeInit << endl;
+        cout << "hostAvailabilityRateInit: " << hostAvailabilityRateInit << endl;
+        cout << "mosqSeekingDuration: " << mosqSeekingDuration << endl;
+        cout << "mosqProbBiting: " << mosqProbBiting << endl;
+        cout << "mosqProbFindRestSite: " << mosqProbFindRestSite << endl;
+        cout << "mosqProbResting: " << mosqProbResting << endl;
+        cout << "mosqProbOvipositing: " << mosqProbOvipositing << endl;
+
+        cout << "FHumanInfectivityInitVector: " << Kvi.size() << endl;
+        cout << "FEIRInitVector: " << transmission.emergence->getEIR().internal().size() << endl;
+        cout << "FMosqEmergeRateInitEstimateVector: " << NvOguess.size() << endl;
+
+        cout << "initNvFromSv: " << transmission.emergence->getinitNvFromSv() << endl;
+        cout << "FEIRInitVector: " << transmission.emergence->getEIR().internal()[365/2.0] << endl;
+
+        CalcInitMosqEmergeRate(mosqEmergerateVector, &daysInYear,
+            &mosqRestDuration, &EIPDuration, &nHostTypesInit,
+            &nMalHostTypesInit, &popSizeInit, 
+            &hostAvailabilityRateInit, &mosqSeekingDeathRate,
+            &mosqSeekingDuration, &mosqProbBiting,
+            &mosqProbFindRestSite, &mosqProbResting,
+            &mosqProbOvipositing, FHumanInfectivityInitVector,
+            FEIRInitVector, FMosqEmergeRateInitEstimateVector, transmission.emergence->getinitNvFromSv());
+
+        return false;
     }
     //@}
 
@@ -380,6 +435,13 @@ class AnophelesModel
     *
     * Doesn't need to be checkpointed (is recalculated each step). */
     vector<double> partialEIR;
+
+    double meanAvail;
+    double mosqProbBiting;
+    double mosqProbFindRestSite;
+    double mosqProbResting;
+    double mosqProbOvipositing;
+
 };
 
 }