diff --git a/data/input/fishTryRealBV_CC.xml b/data/input/fishTryRealBV_CC.xml
index b112bc6c38c45fb5fe07b32d991a0069d2898579..11b8cc2c32260553c016f7aeb2494377ea332c4b 100644
--- a/data/input/fishTryRealBV_CC.xml
+++ b/data/input/fishTryRealBV_CC.xml
@@ -302,6 +302,7 @@
<delta__t>0.33</delta__t>
<survOptRep>0.0017</survOptRep>
<lambda>4.1E-4</lambda>
+ <proportionOfFemaleAtBirth>0.5</proportionOfFemaleAtBirth>
<initialLength>2.0</initialLength>
<sigmaRecruitment>0.2</sigmaRecruitment>
<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
diff --git a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
index 3d54e84fe305847ebcdcc4ea97fe8656ff2d37d6..6d33cce2e47e9f18653b239fcf9c8f460aaf0091 100644
--- a/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
+++ b/src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
@@ -60,6 +60,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
private double survivalRateAfterReproduction = 0.1;
private double maxNumberOfSuperIndividualPerReproduction = 50.;
private boolean withDiagnose = true;
+ private double proportionOfFemaleAtBirth =0.5;
private boolean displayFluxesOnConsole = true;
@@ -98,7 +99,8 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
for(RiverBasin riverBasin : group.getEnvironment().getRiverBasins()){
double b, c, alpha, beta, amountPerSuperIndividual , S95, S50 ;
- double numberOfFemaleGenitors = 0.;
+ double numberOfFemaleSpawners = 0.;
+ double numberOfMaleSpawners = 0.;
double numberOfAutochtones = 0.;
double numberOfFemaleSpawnerForFirstTime = 0.;
double femaleSpawnersForFirstTimeAgesSum = 0.;
@@ -169,25 +171,30 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// age of autochnonous spawnser
Map<Integer, Long> ageOfNativeSpawners = new TreeMap<Integer, Long>();
-
- // compute the number of spawners and keep the origines of the spawners
+ // compute the number of female spawners and keep the origine of the female spawners
for (DiadromousFish fish : fishInBasin){
- if (fish.getGender() == Gender.FEMALE & fish.isMature()){
-
- //System.out.println(fish.getAge() + " -> "+ fish.getLength() + " ("+fish.getStage()+")");
- if (fish.getNumberOfReproduction() < 1) {
- numberOfFemaleSpawnerForFirstTime++;
- femaleSpawnersForFirstTimeAgesSum += fish.getAge();
+ if (fish.isMature()) {
+
+ // number of spawners per gender
+ if (fish.getGender() == Gender.FEMALE) {
+ //System.out.println(fish.getAge() + " -> "+ fish.getLength() + " ("+fish.getStage()+")");
+ if (fish.getNumberOfReproduction() < 1) {
+ numberOfFemaleSpawnerForFirstTime++;
+ femaleSpawnersForFirstTimeAgesSum += fish.getAge();
+ }
+ numberOfFemaleSpawners += fish.getAmount() ; // on ajoute a chaque fois le fish.getAmount (CcumSum)
}
- numberOfFemaleGenitors += 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)
+ }
+
// spawner per origine
String basinName = fish.getBirthBasin().getName();
spawnerOriginsDuringReproduction.put(basinName, spawnerOriginsDuringReproduction.get(basinName) + fish.getAmount() );
// number of autochtonous fish per age
- if (riverBasin == fish.getBirthBasin()){
+ if (riverBasin == fish.getBirthBasin()){
numberOfAutochtones += fish.getAmount();
Integer age = (int) Math.floor(fish.getAge()); //ASK floor() or ceil()
if (ageOfNativeSpawners.containsKey(age))
@@ -195,18 +202,24 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
else
ageOfNativeSpawners.put(age, fish.getAmount());
}
-
+
// increment number of reproduction (for possible iteroparty)
fish.incNumberOfReproduction();
+ // origin of the spwaner
+ fluxOrigin spawnerOrigin;
+ if (fish.getBirthBasin() == riverBasin)
+ spawnerOrigin = fluxOrigin.AUTOCHTONOUS;
+ else
+ spawnerOrigin = fluxOrigin.ALLOCHTONOUS;
+
// survival after reproduction (semelparity or iteroparity) of SI (change the amount of the SI)
- survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction);
double biomass = 0.;
- fluxOrigin origin;
- if(fish.getBirthBasin()== riverBasin)
- origin = fluxOrigin.AUTOCHTONOUS;
- else
- origin = fluxOrigin.ALLOCHTONOUS;
+ survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction);
+
+
+ // update the amount of fish or kill the fish if survival amount = 0
+ // compute nutrient fluxes
if (survivalAmount > 0) {// SUperindividu est encore vivant mais il perd des effectifs
//Export for fishes survived after spawning (survivalAmount) : excretion + gametes
@@ -217,15 +230,15 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
for (String nutrient: aFluxAfterSurvival.keySet()) {
//For survival fish
- totalInputFluxes.get(origin).put(nutrient,totalInputFluxes.get(origin).get(nutrient) + aFluxAfterSurvival.get(nutrient) * survivalAmount);
+ totalInputFluxes.get(spawnerOrigin).put(nutrient,totalInputFluxes.get(spawnerOrigin).get(nutrient) + aFluxAfterSurvival.get(nutrient) * survivalAmount);
//For dead fish
- totalInputFluxes.get(origin).put(nutrient,totalInputFluxes.get(origin).get(nutrient) + aFluxForDeadFish.get(nutrient) * (fish.getAmount() - survivalAmount));
+ totalInputFluxes.get(spawnerOrigin).put(nutrient,totalInputFluxes.get(spawnerOrigin).get(nutrient) + aFluxForDeadFish.get(nutrient) * (fish.getAmount() - survivalAmount));
}
//compute biomass for dead fish
biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount() - survivalAmount);
- totalInputFluxes.get(origin).put("biomass", totalInputFluxes.get(origin).get("biomass") + biomass);
+ totalInputFluxes.get(spawnerOrigin).put("biomass", totalInputFluxes.get(spawnerOrigin).get("biomass") + biomass);
//update the amount of individual in the super-individual
fish.setAmount(survivalAmount);
@@ -238,27 +251,27 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
Map<String, Double> aFlux = group.getNutrientRoutine().computeNutrientsInputForDeathAfterSpawning(fish); //
for (String nutrient: aFlux.keySet()) {
- totalInputFluxes.get(origin).put(nutrient,totalInputFluxes.get(origin).get(nutrient) + aFlux.get(nutrient) * fish.getAmount()); //Fish.getAmount - survivalAmount = total fishes died.
+ totalInputFluxes.get(spawnerOrigin).put(nutrient,totalInputFluxes.get(spawnerOrigin).get(nutrient) + aFlux.get(nutrient) * fish.getAmount()); //Fish.getAmount - survivalAmount = total fishes died.
}
biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount());
- totalInputFluxes.get(origin).put("biomass", totalInputFluxes.get(origin).get("biomass") + biomass);
+ totalInputFluxes.get(spawnerOrigin).put("biomass", totalInputFluxes.get(spawnerOrigin).get("biomass") + biomass);
}
}
}
- // keep the spawner number
- riverBasin.setLastSpawnerNumber(numberOfFemaleGenitors);
+ // keep the number of female spawner
+ riverBasin.setLastFemaleSpawnerNumber(numberOfFemaleSpawners);
// --------------------------------------------------------------------------------------------------
// Diagnose of the population dynamics in the basin
// --------------------------------------------------------------------------------------------------
- if (withDiagnose==true) {
+ if (withDiagnose == true) {
// calculate and keep the features of the stock recruitment relationships
riverBasin.setMortalityCrash(stockRecruitmentRelationship.getSigmaZcrash());
// 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 (numberOfFemaleGenitors > 0.) {
+ if (numberOfFemaleSpawners > 0.) {
List<Trio<Integer, Long, Long>> mortalityData= new ArrayList<Trio<Integer, Long, Long>>();
// first age
// second effective of native spwaner
@@ -289,50 +302,37 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
"\tZcrash="+ stockRecruitmentRelationship.getSigmaZcrash() +
"\tZ="+ riverBasin.getNativeSpawnerMortality());
System.out.println("\tStrap="+stockRecruitmentRelationship.getStockTrap(riverBasin.getNativeSpawnerMortality())+
- "\tStotal="+numberOfFemaleGenitors+"\tSautochthonous="+
+ "\tStotal="+numberOfFemaleSpawners+"\tSautochthonous="+
spawnerOriginsDuringReproduction.get(riverBasin.getName()));
-
- String message;
- if (Double.isNaN(riverBasin.getNativeSpawnerMortality()))
- message="noSense";
- else {
- double stockTrap=stockRecruitmentRelationship.getStockTrap(riverBasin.getNativeSpawnerMortality());
- if (riverBasin.getNativeSpawnerMortality()>stockRecruitmentRelationship.getSigmaZcrash())
- message="overZcrash";
- else {
- if (numberOfFemaleGenitors < stockTrap)
- message = "inTrapWithStrayers";
- else {
- if (spawnerOriginsDuringReproduction.get(riverBasin.getName()) < stockTrap)
- message = "inTrapWithOnlyNatives";
- else
- message = "sustain";
- }
- }
- }
- //System.out.println("\t"+message);
+ // System.out.println("\t"+ riverBasin.getPopulationStatus());
}
// --------------------------------------------------------------------------------------------------
- // Reproduction process (number of recruits)
+ // Reproduction process (compute the number of recruits)
+ // need to have at least one female and one male
+ // use the proportion of female at birth to compute the number of recruits of each gender
// --------------------------------------------------------------------------------------------------
- if (numberOfFemaleGenitors > 0.) {
+ if (numberOfFemaleSpawners > 0. && numberOfMaleSpawners >0.) {
//BH Stock-Recruitment relationship with logistic depensation
- double meanNumberOfRecruit = stockRecruitmentRelationship.getRecruitment(numberOfFemaleGenitors);
+ double meanNumberOfRecruit = stockRecruitmentRelationship.getRecruitment(numberOfFemaleSpawners);
// lognormal random draw
muRecruitment = Math.log(meanNumberOfRecruit) - (Math.pow(sigmaRecruitment,2))/2;
long numberOfRecruit = Math.round(Math.exp(genNormal.nextDouble()*sigmaRecruitment + muRecruitment));
-
+ long numberOfFemaleRecruit = Math.round(numberOfRecruit * proportionOfFemaleAtBirth);
+ long numberOfMaleRecruit = numberOfRecruit - numberOfFemaleRecruit;
+
//System.out.println(group.getPilot().getCurrentTime()+" "+Time.getSeason(group.getPilot())+" "+ riverBasin.getName()+": " + numberOfGenitors + " spwaners \tgive "+ numberOfRecruit + " recruits");
+ // ----------------------------------------------
+ // keep information when reproduction
// keep last % of autochtone
- riverBasin.getLastPercentagesOfAutochtones().push(numberOfAutochtones * 100 / numberOfFemaleGenitors);
+ riverBasin.getLastPercentagesOfAutochtones().push(numberOfAutochtones * 100 / numberOfFemaleSpawners);
- // keep the number of spawners for the firt time in the basin
+ // keep the number of spawners for the first time in the basin
if (numberOfFemaleSpawnerForFirstTime>0){
riverBasin.getSpawnersForFirstTimeMeanAges().push(femaleSpawnersForFirstTimeAgesSum/numberOfFemaleSpawnerForFirstTime);
}else{
@@ -345,15 +345,34 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// Creation of new superFish
if (numberOfRecruit > 0){
+ long numberOfsuperIndividual, effectiveAmount, remainingFish;
+
// features of the super individuals
- int numberOfsuperIndividual = Math.max(1,
- (int) Math.round(numberOfRecruit / amountPerSuperIndividual));
- long effectiveAmount = numberOfRecruit / numberOfsuperIndividual;
-
- for (int i = 0; i < numberOfsuperIndividual; i++){
+ // for female
+ numberOfsuperIndividual = Math.max(1L,
+ Math.round(numberOfFemaleRecruit / amountPerSuperIndividual));
+ effectiveAmount = (long) Math.floor(numberOfFemaleRecruit / numberOfsuperIndividual);
+ for (long i = 0; i < (numberOfsuperIndividual-1); i++){
group.addAquaNism(new DiadromousFish(group.getPilot(), riverBasin, initialLength, effectiveAmount, Gender.FEMALE));
}
-
+ // the last Super indivial could be larger to include remainging fish
+ remainingFish = numberOfFemaleRecruit - numberOfsuperIndividual * effectiveAmount;
+ group.addAquaNism(new DiadromousFish(group.getPilot(), riverBasin, initialLength, effectiveAmount + remainingFish, Gender.FEMALE));
+
+
+ // for male
+ numberOfsuperIndividual = Math.max(1L,
+ Math.round(numberOfMaleRecruit / amountPerSuperIndividual));
+ effectiveAmount = (long) Math.floor(numberOfMaleRecruit / numberOfsuperIndividual);
+ for (long i = 0; i < (numberOfsuperIndividual-1); i++){
+ group.addAquaNism(new DiadromousFish(group.getPilot(), riverBasin, initialLength, effectiveAmount, Gender.MALE));
+ }
+ // the last Super indivial could be larger to include remainging fish
+ remainingFish = numberOfMaleRecruit - numberOfsuperIndividual * effectiveAmount;
+ group.addAquaNism(new DiadromousFish(group.getPilot(), riverBasin, initialLength, effectiveAmount + remainingFish, Gender.FEMALE));
+
+ // ----------------------------------------------
+ // keep information when reproduction with success
// stock the first year when recruitment is non nul
if (riverBasin.getYearOfFirstNonNulRep() == 0){
riverBasin.setYearOfFirstNonNulRep(Time.getYear(group.getPilot()));
@@ -386,6 +405,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
}
else {
// stock information when no spawners reproduce
+ System.out.println(riverBasin.getName()+ "\tF:"+numberOfFemaleSpawners+ " M:"+numberOfMaleSpawners);
riverBasin.setYearOfLastNulRep(Time.getYear(group.getPilot()));
riverBasin.getLastRecruitmentExpectations().push((long) 0);
riverBasin.getLastRecruitments().push((long) 0);
@@ -412,7 +432,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot())
+";"+ riverBasin.getName() + ";" + riverBasin.getSpawnerNumber() + ";" + ";IMPORT;"+origin);
bW.write(";" + totalInputFluxes.get(origin).get("biomass"));
-
+
for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
bW.write(";" + totalInputFluxes.get(origin).get(nutrient));
}
@@ -434,8 +454,8 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
riverBasin.getSpawnerOrigins().push(spawnerOriginsDuringReproduction);
//System.out.println(" AFTER " +riverBasin.getSpawnerOrigins().keySet());
}
-
-
+
+
// --------------------------------------------------------------------------------------------------
// update the observers
// --------------------------------------------------------------------------------------------------