correction for elegance

src/main/java/species/ReproduceWithDiagnose.java

@@ -25,7 +25,6 @@ import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
 import fr.cemagref.simaqualife.pilot.Pilot;
-import miscellaneous.BinomialForSuperIndividualGen;
 import miscellaneous.Miscellaneous;
 import miscellaneous.Trio;
 import species.DiadromousFish.Gender;
@@ -83,12 +82,12 @@ public class ReproduceWithDiagnose extends AquaNismsGroupProcess<DiadromousFish,
 
 	private transient NormalGen genNormal;
 
-	/**
-	 * the random numbers generator for binomial draws
-	 * 
-	 * @unit --
-	 */
-	private transient BinomialForSuperIndividualGen aleaGen;
+	// /**
+	// * the random numbers generator for binomial draws
+	// *
+	// * @unit --
+	// */
+	// private transient BinomialForSuperIndividualGen aleaGen;
 
 	private transient MortalityFunction mortalityFunction;
 
@@ -111,7 +110,7 @@ public class ReproduceWithDiagnose extends AquaNismsGroupProcess<DiadromousFish,
 		super.initTransientParameters(pilot);
 		genNormal = new NormalGen(pilot.getRandomStream(), new NormalDist(0., 1.));
 
-		aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
+		// aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
 
 		mortalityFunction = new MortalityFunction();
 		stockRecruitmentRelationship = new StockRecruitmentRelationship();
@@ -205,11 +204,11 @@ public class ReproduceWithDiagnose extends AquaNismsGroupProcess<DiadromousFish,
 					amountPerSuperIndividual = alpha / maxNumberOfSuperIndividualPerReproduction;
 
 					// Compute the Allee effect parameters S95 and S50
-					if (Soffset >= 0.) {// Allee effect independant of catchment size (including
+					if (Soffset >= 0.) {// Allee effect independant of catchment size (including no Allee Effect)
 						S95 = Soffset;
 						S50 = Soffset;
 					} else {
-						S95 = eta * riverBasin.getAccessibleSurface(); // corresponds to S* in the rougier publication
+						S95 = eta * riverBasin.getAccessibleSurface(); // corresponds to S* in the rougier etal 2015
 						S50 = S95 / ratioS95_S50;
 					}
 					// initilisation of the stock recruitment relationship
@@ -535,7 +534,7 @@ class StockRecruitmentRelationship implements UnivariateFunction {
 		// BH Stock-Recruitment relationship with logistic depensation
 		double meanNumberOfRecruit = 0.;
 		double effectiveStock = getEffectiveStock(stock);
-		if (stock > 0)
+		if (effectiveStock > 0)
 			meanNumberOfRecruit = Math.round(alpha * effectiveStock) / (beta + effectiveStock);
 		return meanNumberOfRecruit;
 	}