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Commit df8a3fac authored by Lambert Patrick's avatar Lambert Patrick
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with male and female recruits

parent a02df59d
master BasinImprovement DeplacementBasin SpawnerRunAnalysis atlantic_area develop exploration_GR3D_process hotfix3.2.1 v3.2.1 v3.2.1.b v3.2.0 v3.1 V3.2.1.a
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with 85 additions and 64 deletions
+85 -64
data/input/fishTryRealBV_CC.xml
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View file @ df8a3fac
...@@ -302,6 +302,7 @@ ...@@ -302,6 +302,7 @@
<delta__t>0.33</delta__t> <delta__t>0.33</delta__t>
<survOptRep>0.0017</survOptRep> <survOptRep>0.0017</survOptRep>
<lambda>4.1E-4</lambda> <lambda>4.1E-4</lambda>
<proportionOfFemaleAtBirth>0.5</proportionOfFemaleAtBirth>
<initialLength>2.0</initialLength> <initialLength>2.0</initialLength>
<sigmaRecruitment>0.2</sigmaRecruitment> <sigmaRecruitment>0.2</sigmaRecruitment>
<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction> <survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
......
src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
+ 84
− 64
View file @ df8a3fac
...@@ -60,6 +60,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -60,6 +60,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
private double survivalRateAfterReproduction = 0.1; private double survivalRateAfterReproduction = 0.1;
private double maxNumberOfSuperIndividualPerReproduction = 50.; private double maxNumberOfSuperIndividualPerReproduction = 50.;
private boolean withDiagnose = true; private boolean withDiagnose = true;
private double proportionOfFemaleAtBirth =0.5;
private boolean displayFluxesOnConsole = true; private boolean displayFluxesOnConsole = true;
...@@ -98,7 +99,8 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -98,7 +99,8 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
for(RiverBasin riverBasin : group.getEnvironment().getRiverBasins()){ for(RiverBasin riverBasin : group.getEnvironment().getRiverBasins()){
double b, c, alpha, beta, amountPerSuperIndividual , S95, S50 ; double b, c, alpha, beta, amountPerSuperIndividual , S95, S50 ;
double numberOfFemaleGenitors = 0.; double numberOfFemaleSpawners = 0.;
double numberOfMaleSpawners = 0.;
double numberOfAutochtones = 0.; double numberOfAutochtones = 0.;
double numberOfFemaleSpawnerForFirstTime = 0.; double numberOfFemaleSpawnerForFirstTime = 0.;
double femaleSpawnersForFirstTimeAgesSum = 0.; double femaleSpawnersForFirstTimeAgesSum = 0.;
...@@ -169,25 +171,30 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -169,25 +171,30 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// age of autochnonous spawnser // age of autochnonous spawnser
Map<Integer, Long> ageOfNativeSpawners = new TreeMap<Integer, Long>(); Map<Integer, Long> ageOfNativeSpawners = new TreeMap<Integer, Long>();
// compute the number of female spawners and keep the origine of the female spawners
// compute the number of spawners and keep the origines of the spawners
for (DiadromousFish fish : fishInBasin){ for (DiadromousFish fish : fishInBasin){
if (fish.getGender() == Gender.FEMALE & fish.isMature()){ if (fish.isMature()) {
//System.out.println(fish.getAge() + " -> "+ fish.getLength() + " ("+fish.getStage()+")"); // number of spawners per gender
if (fish.getNumberOfReproduction() < 1) { if (fish.getGender() == Gender.FEMALE) {
numberOfFemaleSpawnerForFirstTime++; //System.out.println(fish.getAge() + " -> "+ fish.getLength() + " ("+fish.getStage()+")");
femaleSpawnersForFirstTimeAgesSum += fish.getAge(); 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 // spawner per origine
String basinName = fish.getBirthBasin().getName(); String basinName = fish.getBirthBasin().getName();
spawnerOriginsDuringReproduction.put(basinName, spawnerOriginsDuringReproduction.get(basinName) + fish.getAmount() ); spawnerOriginsDuringReproduction.put(basinName, spawnerOriginsDuringReproduction.get(basinName) + fish.getAmount() );
// number of autochtonous fish per age // number of autochtonous fish per age
if (riverBasin == fish.getBirthBasin()){ if (riverBasin == fish.getBirthBasin()){
numberOfAutochtones += fish.getAmount(); numberOfAutochtones += fish.getAmount();
Integer age = (int) Math.floor(fish.getAge()); //ASK floor() or ceil() Integer age = (int) Math.floor(fish.getAge()); //ASK floor() or ceil()
if (ageOfNativeSpawners.containsKey(age)) if (ageOfNativeSpawners.containsKey(age))
...@@ -195,18 +202,24 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -195,18 +202,24 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
else else
ageOfNativeSpawners.put(age, fish.getAmount()); ageOfNativeSpawners.put(age, fish.getAmount());
} }
// increment number of reproduction (for possible iteroparty) // increment number of reproduction (for possible iteroparty)
fish.incNumberOfReproduction(); 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) // 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.; double biomass = 0.;
fluxOrigin origin; survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction);
if(fish.getBirthBasin()== riverBasin)
origin = fluxOrigin.AUTOCHTONOUS;
else // update the amount of fish or kill the fish if survival amount = 0
origin = fluxOrigin.ALLOCHTONOUS; // compute nutrient fluxes
if (survivalAmount > 0) {// SUperindividu est encore vivant mais il perd des effectifs if (survivalAmount > 0) {// SUperindividu est encore vivant mais il perd des effectifs
//Export for fishes survived after spawning (survivalAmount) : excretion + gametes //Export for fishes survived after spawning (survivalAmount) : excretion + gametes
...@@ -217,15 +230,15 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -217,15 +230,15 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
for (String nutrient: aFluxAfterSurvival.keySet()) { for (String nutrient: aFluxAfterSurvival.keySet()) {
//For survival fish //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 //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 //compute biomass for dead fish
biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount() - survivalAmount); 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 //update the amount of individual in the super-individual
fish.setAmount(survivalAmount); fish.setAmount(survivalAmount);
...@@ -238,27 +251,27 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -238,27 +251,27 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
Map<String, Double> aFlux = group.getNutrientRoutine().computeNutrientsInputForDeathAfterSpawning(fish); // Map<String, Double> aFlux = group.getNutrientRoutine().computeNutrientsInputForDeathAfterSpawning(fish); //
for (String nutrient: aFlux.keySet()) { 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()); 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 // keep the number of female spawner
riverBasin.setLastSpawnerNumber(numberOfFemaleGenitors); riverBasin.setLastFemaleSpawnerNumber(numberOfFemaleSpawners);
// -------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------
// Diagnose of the population dynamics in the basin // Diagnose of the population dynamics in the basin
// -------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------
if (withDiagnose==true) { if (withDiagnose == true) {
// calculate and keep the features of the stock recruitment relationships // calculate and keep the features of the stock recruitment relationships
riverBasin.setMortalityCrash(stockRecruitmentRelationship.getSigmaZcrash()); riverBasin.setMortalityCrash(stockRecruitmentRelationship.getSigmaZcrash());
// initialise the mortality function for the autochnous spawners // 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 // 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>>(); List<Trio<Integer, Long, Long>> mortalityData= new ArrayList<Trio<Integer, Long, Long>>();
// first age // first age
// second effective of native spwaner // second effective of native spwaner
...@@ -289,50 +302,37 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -289,50 +302,37 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
"\tZcrash="+ stockRecruitmentRelationship.getSigmaZcrash() + "\tZcrash="+ stockRecruitmentRelationship.getSigmaZcrash() +
"\tZ="+ riverBasin.getNativeSpawnerMortality()); "\tZ="+ riverBasin.getNativeSpawnerMortality());
System.out.println("\tStrap="+stockRecruitmentRelationship.getStockTrap(riverBasin.getNativeSpawnerMortality())+ System.out.println("\tStrap="+stockRecruitmentRelationship.getStockTrap(riverBasin.getNativeSpawnerMortality())+
"\tStotal="+numberOfFemaleGenitors+"\tSautochthonous="+ "\tStotal="+numberOfFemaleSpawners+"\tSautochthonous="+
spawnerOriginsDuringReproduction.get(riverBasin.getName())); spawnerOriginsDuringReproduction.get(riverBasin.getName()));
// System.out.println("\t"+ riverBasin.getPopulationStatus());
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);
} }
// -------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------
// 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 //BH Stock-Recruitment relationship with logistic depensation
double meanNumberOfRecruit = stockRecruitmentRelationship.getRecruitment(numberOfFemaleGenitors); double meanNumberOfRecruit = stockRecruitmentRelationship.getRecruitment(numberOfFemaleSpawners);
// lognormal random draw // lognormal random draw
muRecruitment = Math.log(meanNumberOfRecruit) - (Math.pow(sigmaRecruitment,2))/2; muRecruitment = Math.log(meanNumberOfRecruit) - (Math.pow(sigmaRecruitment,2))/2;
long numberOfRecruit = Math.round(Math.exp(genNormal.nextDouble()*sigmaRecruitment + muRecruitment)); 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"); //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 // 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){ if (numberOfFemaleSpawnerForFirstTime>0){
riverBasin.getSpawnersForFirstTimeMeanAges().push(femaleSpawnersForFirstTimeAgesSum/numberOfFemaleSpawnerForFirstTime); riverBasin.getSpawnersForFirstTimeMeanAges().push(femaleSpawnersForFirstTimeAgesSum/numberOfFemaleSpawnerForFirstTime);
}else{ }else{
...@@ -345,15 +345,34 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -345,15 +345,34 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// Creation of new superFish // Creation of new superFish
if (numberOfRecruit > 0){ if (numberOfRecruit > 0){
long numberOfsuperIndividual, effectiveAmount, remainingFish;
// features of the super individuals // features of the super individuals
int numberOfsuperIndividual = Math.max(1, // for female
(int) Math.round(numberOfRecruit / amountPerSuperIndividual)); numberOfsuperIndividual = Math.max(1L,
long effectiveAmount = numberOfRecruit / numberOfsuperIndividual; Math.round(numberOfFemaleRecruit / amountPerSuperIndividual));
effectiveAmount = (long) Math.floor(numberOfFemaleRecruit / numberOfsuperIndividual);
for (int i = 0; i < numberOfsuperIndividual; i++){ for (long i = 0; i < (numberOfsuperIndividual-1); i++){
group.addAquaNism(new DiadromousFish(group.getPilot(), riverBasin, initialLength, effectiveAmount, Gender.FEMALE)); 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 // stock the first year when recruitment is non nul
if (riverBasin.getYearOfFirstNonNulRep() == 0){ if (riverBasin.getYearOfFirstNonNulRep() == 0){
riverBasin.setYearOfFirstNonNulRep(Time.getYear(group.getPilot())); riverBasin.setYearOfFirstNonNulRep(Time.getYear(group.getPilot()));
...@@ -386,6 +405,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -386,6 +405,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
} }
else { else {
// stock information when no spawners reproduce // stock information when no spawners reproduce
System.out.println(riverBasin.getName()+ "\tF:"+numberOfFemaleSpawners+ " M:"+numberOfMaleSpawners);
riverBasin.setYearOfLastNulRep(Time.getYear(group.getPilot())); riverBasin.setYearOfLastNulRep(Time.getYear(group.getPilot()));
riverBasin.getLastRecruitmentExpectations().push((long) 0); riverBasin.getLastRecruitmentExpectations().push((long) 0);
riverBasin.getLastRecruitments().push((long) 0); riverBasin.getLastRecruitments().push((long) 0);
...@@ -412,7 +432,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -412,7 +432,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot())
+";"+ riverBasin.getName() + ";" + riverBasin.getSpawnerNumber() + ";" + ";IMPORT;"+origin); +";"+ riverBasin.getName() + ";" + riverBasin.getSpawnerNumber() + ";" + ";IMPORT;"+origin);
bW.write(";" + totalInputFluxes.get(origin).get("biomass")); bW.write(";" + totalInputFluxes.get(origin).get("biomass"));
for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) { for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
bW.write(";" + totalInputFluxes.get(origin).get(nutrient)); bW.write(";" + totalInputFluxes.get(origin).get(nutrient));
} }
...@@ -434,8 +454,8 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG ...@@ -434,8 +454,8 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
riverBasin.getSpawnerOrigins().push(spawnerOriginsDuringReproduction); riverBasin.getSpawnerOrigins().push(spawnerOriginsDuringReproduction);
//System.out.println(" AFTER " +riverBasin.getSpawnerOrigins().keySet()); //System.out.println(" AFTER " +riverBasin.getSpawnerOrigins().keySet());
} }
// -------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------
// update the observers // update the observers
// -------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------
......
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