diff --git a/src/main/java/species/PopulateBasinNetwork.java b/src/main/java/species/PopulateBasinNetwork.java
index aae4046c03976a067b46a4d38f1d837cd471c95e..a6c0ee94bef49796c68abb12172889ee59b205e9 100644
--- a/src/main/java/species/PopulateBasinNetwork.java
+++ b/src/main/java/species/PopulateBasinNetwork.java
@@ -23,7 +23,7 @@ public class PopulateBasinNetwork extends AquaNismsGroupProcess<DiadromousFish,
public void doProcess(DiadromousFishGroup group) {
for (Basin basin : group.getEnvironment().getRiverBasins()){
for (int i=0; i < nbSIPerBasin; i++){
- group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbFishPerSI, Gender.UNDIFFERENCIED));
+ group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbFishPerSI, Gender.FEMALE));
}
}
}
diff --git a/src/main/java/species/PopulateBasinNetworkWithANorthLimit.java b/src/main/java/species/PopulateBasinNetworkWithANorthLimit.java
index c1ea61d092aed0ddb4c90da8fe6272c8b40cabfe..a11504f25dc1ded0cbf1337965c350434931e602 100644
--- a/src/main/java/species/PopulateBasinNetworkWithANorthLimit.java
+++ b/src/main/java/species/PopulateBasinNetworkWithANorthLimit.java
@@ -47,7 +47,7 @@ public class PopulateBasinNetworkWithANorthLimit extends AquaNismsGroupProcess<D
for (RiverBasin basin : group.getEnvironment().getRiverBasins()){
if (basin.getLatitude()<=northLimitLatitude){
for (int i=0; i < nbSIPerBasin; i++){
- group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbFishPerSI, Gender.UNDIFFERENCIED));
+ group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbFishPerSI, Gender.FEMALE));
}
}
}
diff --git a/src/main/java/species/PopulateWithASinglePopulation.java b/src/main/java/species/PopulateWithASinglePopulation.java
index 5af2db3d2a432d09a4b4fa924b88be98825299c0..de93c702a43c91c73091d00d51e5f21a5663a5a0 100644
--- a/src/main/java/species/PopulateWithASinglePopulation.java
+++ b/src/main/java/species/PopulateWithASinglePopulation.java
@@ -25,7 +25,7 @@ public class PopulateWithASinglePopulation extends AquaNismsGroupProcess<Diadrom
Basin basin = group.getEnvironment().getRiverBasins()[bassinInd];
for (int i=0; i < nbSIPerBasin; i++){
- group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbIndPerSI, Gender.UNDIFFERENCIED));
+ group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbIndPerSI, Gender.FEMALE));
}
}
}
diff --git a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
index 63f83c7bcd6002dd403b266a9c83e3ed9faa51eb..a7ffa89871d199929d0aafed7c7045b47b3719f9 100644
--- a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
+++ b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
@@ -61,6 +61,12 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
private transient NormalGen genNormal;
private transient MortalityFunction mortalityFunction;
+ /**
+ * relationship between
+ * recruitment in number of juvenile on spawning grounds
+ * stock in number of FEMALES
+ * @unit
+ */
private transient StockRecruitmentRelationship stockRecruitmentRelationship;
// private transient UniformGen genUniform;
@@ -85,10 +91,10 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
for(RiverBasin riverBasin : group.getEnvironment().getRiverBasins()){
double b, c, alpha, beta, amountPerSuperIndividual , S95, S50 ;
- double numberOfGenitors = 0.;
+ double numberOfFemaleGenitors = 0.;
double numberOfAutochtones = 0.;
- double numberOfSpawnerForFirstTime = 0.;
- double spawnersForFirstTimeAgesSum = 0.;
+ double numberOfFemaleSpawnerForFirstTime = 0.;
+ double femaleSpawnersForFirstTimeAgesSum = 0.;
long survivalAmount;
double muRecruitment = 0.;
//double weightOfGenitors = 0.;
@@ -145,15 +151,16 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
Map<Integer, Long> ageOfNativeSpawners = new TreeMap<Integer, Long>();
// compute the number of spawners and keep the origines of the spawners
- for( DiadromousFish fish : fishInBasin){
- if( fish.isMature()){
+ for (DiadromousFish fish : fishInBasin){
+
+ if (fish.getGender() == Gender.FEMALE & fish.isMature()){
//System.out.println(fish.getAge() + " -> "+ fish.getLength() + " ("+fish.getStage()+")");
if (fish.getNumberOfReproduction() < 1) {
- numberOfSpawnerForFirstTime++;
- spawnersForFirstTimeAgesSum += fish.getAge();
+ numberOfFemaleSpawnerForFirstTime++;
+ femaleSpawnersForFirstTimeAgesSum += fish.getAge();
}
- numberOfGenitors += fish.getAmount() ;
+ numberOfFemaleGenitors += fish.getAmount() ;
// spawner per origine
String basinName = fish.getBirthBasin().getName();
@@ -182,7 +189,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
}
// keep the spawner number
- riverBasin.setLastSpawnerNumber(numberOfGenitors);
+ riverBasin.setLastSpawnerNumber(numberOfFemaleGenitors);
// --------------------------------------------------------------------------------------------------
// Diagnose of the population dynamics in the basin
@@ -193,7 +200,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// initialise the mortality function for the autochnous spawners
// use to approximate the mortality of all the spawners to give a proxy of the Allee trap
- if (numberOfGenitors > 0.) {
+ if (numberOfFemaleGenitors > 0.) {
List<Trio<Integer, Long, Long>> mortalityData= new ArrayList<Trio<Integer, Long, Long>>();
// first age
// second effective of native spwaner
@@ -224,7 +231,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
"\tZcrash="+ stockRecruitmentRelationship.getSigmaZcrash() +
"\tZ="+ riverBasin.getNativeSpawnerMortality());
System.out.println("\tStrap="+stockRecruitmentRelationship.getStockTrap(riverBasin.getNativeSpawnerMortality())+
- "\tStotal="+numberOfGenitors+"\tSautochthonous="+
+ "\tStotal="+numberOfFemaleGenitors+"\tSautochthonous="+
spawnerOriginsDuringReproduction.get(riverBasin.getName()));
@@ -236,7 +243,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
if (riverBasin.getNativeSpawnerMortality()>stockRecruitmentRelationship.getSigmaZcrash())
message="overZcrash";
else {
- if (numberOfGenitors < stockTrap)
+ if (numberOfFemaleGenitors < stockTrap)
message = "inTrapWithStrayers";
else {
if (spawnerOriginsDuringReproduction.get(riverBasin.getName()) < stockTrap)
@@ -253,10 +260,10 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// Reproduction process (number of recruits)
// --------------------------------------------------------------------------------------------------
- if (numberOfGenitors > 0.) {
+ if (numberOfFemaleGenitors > 0.) {
//BH Stock-Recruitment relationship with logistic depensation
- double meanNumberOfRecruit = stockRecruitmentRelationship.getRecruitment(numberOfGenitors);
+ double meanNumberOfRecruit = stockRecruitmentRelationship.getRecruitment(numberOfFemaleGenitors);
// lognormal random draw
muRecruitment = Math.log(meanNumberOfRecruit) - (Math.pow(sigmaRecruitment,2))/2;
@@ -265,11 +272,11 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
//System.out.println(group.getPilot().getCurrentTime()+" "+Time.getSeason(group.getPilot())+" "+ riverBasin.getName()+": " + numberOfGenitors + " spwaners \tgive "+ numberOfRecruit + " recruits");
// keep last % of autochtone
- riverBasin.getLastPercentagesOfAutochtones().push(numberOfAutochtones * 100 / numberOfGenitors);
+ riverBasin.getLastPercentagesOfAutochtones().push(numberOfAutochtones * 100 / numberOfFemaleGenitors);
// keep the number of spawners for the firt time in the basin
- if (numberOfSpawnerForFirstTime>0){
- riverBasin.getSpawnersForFirstTimeMeanAges().push(spawnersForFirstTimeAgesSum/numberOfSpawnerForFirstTime);
+ if (numberOfFemaleSpawnerForFirstTime>0){
+ riverBasin.getSpawnersForFirstTimeMeanAges().push(femaleSpawnersForFirstTimeAgesSum/numberOfFemaleSpawnerForFirstTime);
}else{
riverBasin.getSpawnersForFirstTimeMeanAges().push(0.);
}
@@ -286,7 +293,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
long effectiveAmount = numberOfRecruit / numberOfsuperIndividual;
for (int i = 0; i < numberOfsuperIndividual; i++){
- group.addAquaNism(new DiadromousFish(group.getPilot(), riverBasin, initialLength, effectiveAmount, Gender.UNDIFFERENCIED));
+ group.addAquaNism(new DiadromousFish(group.getPilot(), riverBasin, initialLength, effectiveAmount, Gender.FEMALE));
}
// stock the first year when recruitment is non nul