with calibration statistic for male and female

src/main/java/environment/RiverBasin.java

 package environment;
 
-import org.jfree.data.time.MovingAverage;
+import java.util.Hashtable;
+import java.util.Map;
 
 import miscellaneous.QueueMemory;
 import miscellaneous.QueueMemoryMap;
@@ -8,6 +9,7 @@ import fr.cemagref.observation.kernel.Observable;
 import fr.cemagref.observation.kernel.ObservablesHandler;
 import fr.cemagref.simaqualife.pilot.Pilot;
 import species.DiadromousFish;
+import species.DiadromousFish.Gender;
 import species.DiadromousFishGroup;
 
 /**
@@ -35,7 +37,7 @@ public class RiverBasin extends Basin {
 	private QueueMemory<Double> lastRecsOverProdCaps;
 	private QueueMemory<Double> lastPercentagesOfAutochtones;
 	private QueueMemory<Double> numberOfNonNulRecruitmentDuringLastYears; // Prob of non nul recruitment during the last "memorySize" years... if 10 non nul recruitment during the last 10 year, p=0.999... if 8 non nul recruitment during the last 10 years, p = 0.8... if 0 recruitment, p = 0.001
-	private QueueMemory<Double> femaleSpawnersForFirstTimeMeanAges;
+	private Map<DiadromousFish.Gender, QueueMemory<Double>> spawnersForFirstTimeMeanAges;;
 	private QueueMemory<Double> numberOfNonNulRecruitmentForFinalProbOfPres;
 	
 	private double nativeSpawnerMortality; // mortality coefficient between recruitement and spawning for fish born in this basin
@@ -98,7 +100,11 @@ public class RiverBasin extends Basin {
 		this.lastRecsOverProdCaps = new QueueMemory<Double>(memorySize);
 		this.lastPercentagesOfAutochtones = new QueueMemory<Double>(memorySize);
 		this.numberOfNonNulRecruitmentDuringLastYears = new QueueMemory<Double>(memorySize);
-		this.femaleSpawnersForFirstTimeMeanAges = new QueueMemory<Double>(memorySize);
+		
+		this.spawnersForFirstTimeMeanAges = new Hashtable<DiadromousFish.Gender, QueueMemory<Double>>();
+		this.spawnersForFirstTimeMeanAges.put( DiadromousFish.Gender.FEMALE, new QueueMemory<Double>(memorySize) );
+		this.spawnersForFirstTimeMeanAges.put( DiadromousFish.Gender.MALE, new QueueMemory<Double>(memorySize) );
+		
 		this.numberOfNonNulRecruitmentForFinalProbOfPres = new QueueMemory<Double>(memorySizeLongQueue);
 
 		if (cobservable == null) {
@@ -189,8 +195,12 @@ public class RiverBasin extends Basin {
 		return numberOfNonNulRecruitmentDuringLastYears;
 	}
 
-	public QueueMemory<Double> getFemaleSpawnersForFirstTimeMeanAges() {
-		return femaleSpawnersForFirstTimeMeanAges;
+	/*public QueueMemory<Double> getFemaleSpawnersForFirstTimeMeanAges() {
+		return spawnersForFirstTimeMeanAges.get(Gender.FEMALE);
+	}*/
+	
+	public QueueMemory<Double> getSpawnersForFirstTimeMeanAges(DiadromousFish.Gender gender) {
+		return spawnersForFirstTimeMeanAges.get(gender);
 	}
 
 	public QueueMemory<Double> getNumberOfNonNulRecruitmentForFinalProbOfPres(){

src/main/java/species/DiadromousFishGroup.java

@@ -46,8 +46,8 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 	public Color color = Color.RED;
 
 	/**
-	 *  ????
-	 * @unit
+	 *  distance maximum of dispersion
+	 * @unit km
 	 */
 	public double dMaxDisp = 300.;
 	
@@ -60,7 +60,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 	public String fileNameInputForInitialObservation = "data/input/reality/Obs1900.csv";
 
 	/**
-	 *  centile to calucale the range of species distribution
+	 *  centile to calcucale the range of species distribution
 	 * @unit
 	 */
 	public double centileForRange = 0.95;
@@ -491,6 +491,7 @@ public BufferedWriter getbWForFluxes() {
 		return tempMinRep;
 	}
 
+	
 	@Observable(description = "Nb of SI")
 	public int getNbSI() {
 		int nbSI = 0;
@@ -501,6 +502,7 @@ public BufferedWriter getbWForFluxes() {
 		return nbSI;
 	}
 
+	
 	@Observable(description = "Sizes mean of SI")
 	public double getSizesMeanOfSI() {
 		double totalEffective = 0;
@@ -518,6 +520,7 @@ public BufferedWriter getbWForFluxes() {
 		else
 			return Double.NaN;
 	}
+	
 
 	@Observable(description = "# of SI with ind < 10")
 	public double getNbLittleSI() {
@@ -533,6 +536,7 @@ public BufferedWriter getbWForFluxes() {
 		return nb;
 	}
 
+	
 	public double getMeanLengthOfMatureFish(){
 		double sumOfLength = 0.;
 		double numberOfMatureFish = 0.;
@@ -618,20 +622,33 @@ public  NutrientRoutine getNutrientRoutine() {
 	// ================================================================
 	// statictis for calibration
 	// ================================================================
-	@Observable(description="Spawners For First Time Summary Statistic")
+	@Observable(description="Female spawners For First Time Summary Statistic")
 	public double computeFemaleSpawnerForFirstTimeSummaryStatistic() {
 		double sum = 0;
 		//TODO move TARGET to the right place
 		double TARGET = 5.0;
 		for (RiverBasin riverBasin : getEnvironment().getRiverBasins()) {
-			if (riverBasin.getFemaleSpawnersForFirstTimeMeanAges().getMeanWithoutZero() > 0.) {
-				double val = riverBasin.getFemaleSpawnersForFirstTimeMeanAges().getMeanWithoutZero()  - TARGET;
+			if (riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).getMeanWithoutZero() > 0.) {
+				double val = riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).getMeanWithoutZero()  - TARGET;
 				sum += val * val;
 			}
 		}
 		return sum;
 	}
 
+	@Observable(description="Male spawners For First Time Summary Statistic")
+	public double computeMaleSpawnerForFirstTimeSummaryStatistic() {
+		double sum = 0;
+		//TODO move TARGET to the right place
+		double TARGET = 5.0;
+		for (RiverBasin riverBasin : getEnvironment().getRiverBasins()) {
+			if (riverBasin.getSpawnersForFirstTimeMeanAges(Gender.MALE).getMeanWithoutZero() > 0.) {
+				double val = riverBasin.getSpawnersForFirstTimeMeanAges(Gender.MALE).getMeanWithoutZero()  - TARGET;
+				sum += val * val;
+			}
+		}
+		return sum;
+	}
 
 	@Observable(description = "Likelihood Summary stat")
 	public double computeLikelihood() throws IOException {

src/main/java/species/ReproduceAndSurviveAfterReproduction.java

@@ -219,9 +219,9 @@ public class ReproduceAndSurviveAfterReproduction extends AquaNismsGroupProcess<
 
 						// keep the number of spawners for the firt time in the basin
 						if (numberOfSpawnerForFirstTime>0){
-							riverBasin.getFemaleSpawnersForFirstTimeMeanAges().push(spawnersForFirstTimeAgesSum/numberOfSpawnerForFirstTime);
+							riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).push(spawnersForFirstTimeAgesSum/numberOfSpawnerForFirstTime);
 						}else{
-							riverBasin.getFemaleSpawnersForFirstTimeMeanAges().push(0.);
+							riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).push(0.);
 						}
 
 						//System.out.println("nb spawners in basin " + riverBasin.getName() + " : " + numberOfGenitors);

src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java

@@ -102,8 +102,12 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 				double numberOfFemaleSpawners = 0.;
 				double numberOfMaleSpawners = 0.;
 				double numberOfAutochtones = 0.;
+				
 				double numberOfFemaleSpawnerForFirstTime = 0.;
 				double femaleSpawnersForFirstTimeAgesSum = 0.;
+				double numberOfMaleSpawnerForFirstTime = 0.;
+				double maleSpawnersForFirstTimeAgesSum = 0.;
+				
 				long survivalAmount;
 				double muRecruitment = 0.;
 				//double weightOfGenitors = 0.;
@@ -179,14 +183,18 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 							// number of spawners per gender
 							if (fish.getGender() == Gender.FEMALE) {
 								//System.out.println(fish.getAge() + " -> "+ fish.getLength() + " ("+fish.getStage()+")");
+								numberOfFemaleSpawners += fish.getAmount() ; // on ajoute a chaque fois le fish.getAmount (CcumSum)		
 								if (fish.getNumberOfReproduction() < 1) {
 									numberOfFemaleSpawnerForFirstTime++;
 									femaleSpawnersForFirstTimeAgesSum += fish.getAge();
 								}
-								numberOfFemaleSpawners += fish.getAmount() ; // on ajoute a chaque fois le fish.getAmount (CcumSum)								
 							}
 							else if (fish.getGender() == Gender.MALE) {
 								numberOfMaleSpawners += fish.getAmount() ; // on ajoute a chaque fois le fish.getAmount (CcumSum)
+								if (fish.getNumberOfReproduction() < 1) {
+									numberOfMaleSpawnerForFirstTime++;
+									maleSpawnersForFirstTimeAgesSum += fish.getAge();
+								}
 							}
 							
 							// spawner per origine
@@ -333,12 +341,17 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 						riverBasin.getLastPercentagesOfAutochtones().push(numberOfAutochtones * 100 / numberOfFemaleSpawners);
 
 						// keep the number of spawners for the first time in the basin
-						if (numberOfFemaleSpawnerForFirstTime>0){
-							riverBasin.getFemaleSpawnersForFirstTimeMeanAges().push(femaleSpawnersForFirstTimeAgesSum/numberOfFemaleSpawnerForFirstTime);
-						}else{
-							riverBasin.getFemaleSpawnersForFirstTimeMeanAges().push(0.);
-						}
-
+						if (numberOfFemaleSpawnerForFirstTime>0)
+							riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).push(femaleSpawnersForFirstTimeAgesSum/numberOfFemaleSpawnerForFirstTime);
+						else
+							riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).push(0.);
+						if (numberOfMaleSpawnerForFirstTime>0)
+							riverBasin.getSpawnersForFirstTimeMeanAges(Gender.MALE).push(maleSpawnersForFirstTimeAgesSum/numberOfMaleSpawnerForFirstTime);
+						else
+							riverBasin.getSpawnersForFirstTimeMeanAges(Gender.MALE).push(0.);
+
+						//TODO the same with male
+						
 						//System.out.println("nb spawners in basin " + riverBasin.getName() + " : " + numberOfGenitors);
 						//System.out.println("nb recruit in basin " + riverBasin.getName() + " : " + numberOfRecruit);