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Commit 1b615869 authored by Lambert Patrick's avatar Lambert Patrick
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targeted age for calibration as a field

parent 7ca61607
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src/main/java/species/DiadromousFishGroup.java
View file @ 1b615869
......@@ -172,6 +172,12 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
*/
private transient List<Duo<Double, Double>> parameterSets;
// =================================================
// calibration
// =================================================
private Double targetedAgeForFemaleSpawnerForFirstTime = 5.5;
private Double targetedAgeForMaleSpawnerForFirstTime = 4.5;
/**
* map of observedoccurence in 1900
......@@ -491,6 +497,12 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
} catch (IOException ex) {
Logger.getLogger(DiadromousFishGroup.class.getName()).log(Level.SEVERE, null, ex);
}
// defaut values
if (targetedAgeForFemaleSpawnerForFirstTime == null)
targetedAgeForFemaleSpawnerForFirstTime = 5.5;
if (targetedAgeForMaleSpawnerForFirstTime == null)
targetedAgeForMaleSpawnerForFirstTime = 4.5;
}
......@@ -666,7 +678,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
@Observable(description="Female spawners For First Time Summary Statistic")
public double computeFemaleSpawnerForFirstTimeSummaryStatistic() {
return computeFemaleSpawnerForFirstTimeSummaryStatisticWithTarget(5.5);
return computeFemaleSpawnerForFirstTimeSummaryStatisticWithTarget(targetedAgeForFemaleSpawnerForFirstTime);
}
......@@ -712,7 +724,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
@Observable(description="Male spawners For First Time Summary Statistic")
public double computeMaleSpawnerForFirstTimeSummaryStatistic() {
return computeMaleSpawnerForFirstTimeSummaryStatisticWithTarget(4.5);
return computeMaleSpawnerForFirstTimeSummaryStatisticWithTarget(targetedAgeForFemaleSpawnerForFirstTime);
}
@Observable(description="mean age of first reprodution for male")
......
src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
View file @ 1b615869
......@@ -89,7 +89,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
mortalityFunction=new MortalityFunction();
stockRecruitmentRelationship= new StockRecruitmentRelationship();
}
/**
* @return the tempMinRep
......@@ -105,20 +105,22 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
List<DiadromousFish> deadFish = new ArrayList<DiadromousFish>();
for(RiverBasin riverBasin : group.getEnvironment().getRiverBasins()){
// before the party !!!!
double fluxBefore =riverBasin.getSpawnerNumber();
double b, c, alpha, beta, amountPerSuperIndividual , S95, S50 ;
double numberOfFemaleSpawners = 0.;
double numberOfMaleSpawners = 0.;
double numberOfAutochtones = 0.;
double numberOfFemaleSpawnerForFirstTime = 0.;
double femaleSpawnersForFirstTimeAgesSum = 0.;
double femaleSpawnersForFirstTimeLengthsSum = 0.;
double numberOfMaleSpawnerForFirstTime = 0.;
double maleSpawnersForFirstTimeAgesSum = 0.;
double maleSpawnersForFirstTimeLengthsSum = 0.;
long survivalAmount;
double muRecruitment = 0.;
//double weightOfGenitors = 0.;
......@@ -190,24 +192,26 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
for (DiadromousFish fish : fishInBasin){
if (fish.isMature()) {
// 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();
numberOfFemaleSpawnerForFirstTime += fish.getAmount();
femaleSpawnersForFirstTimeAgesSum += fish.getAge() * fish.getAmount();
femaleSpawnersForFirstTimeLengthsSum += fish.getLength() * fish.getAmount();
}
}
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();
numberOfMaleSpawnerForFirstTime += fish.getAmount();
maleSpawnersForFirstTimeAgesSum += fish.getAge() * fish.getAmount();
maleSpawnersForFirstTimeLengthsSum += fish.getLength() * fish.getAmount();
}
}
// spawner per origine
String basinName = fish.getBirthBasin().getName();
spawnerOriginsDuringReproduction.put(basinName, spawnerOriginsDuringReproduction.get(basinName) + fish.getAmount() );
......@@ -231,12 +235,12 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
spawnerOrigin = fluxOrigin.AUTOCHTONOUS;
else
spawnerOrigin = fluxOrigin.ALLOCHTONOUS;
// survival after reproduction (semelparity or iteroparity) of SI (change the amount of the SI)
double biomass = 0.;
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
......@@ -323,8 +327,8 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
System.out.println("\tStrap="+stockRecruitmentRelationship.getStockTrap(riverBasin.getNativeSpawnerMortality())+
"\tStotal="+numberOfFemaleSpawners+"\tSautochthonous="+
spawnerOriginsDuringReproduction.get(riverBasin.getName()));
/* // display effective from each catchment
/* // display effective from each catchment
System.out.print(riverBasin.getName());
for (String natalBasinName : group.getEnvironment().getRiverBasinNames()){
System.out.print("\t"+natalBasinName);
......@@ -335,9 +339,9 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
System.out.print("\t"+spawnerOriginsDuringReproduction.get(natalBasinName));
}
System.out.println();*/
// System.out.println("\t"+ riverBasin.getPopulationStatus());
String message;
if (Double.isNaN(riverBasin.getNativeSpawnerMortality()))
message="noSense";
......@@ -375,7 +379,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
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");
// ----------------------------------------------
......@@ -384,16 +388,24 @@ 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.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).push(femaleSpawnersForFirstTimeAgesSum/numberOfFemaleSpawnerForFirstTime);
else
if (numberOfFemaleSpawnerForFirstTime>0) {
riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).push(femaleSpawnersForFirstTimeAgesSum / numberOfFemaleSpawnerForFirstTime);
riverBasin.getSpawnersForFirstTimeMeanLengths(Gender.FEMALE).push(femaleSpawnersForFirstTimeLengthsSum / numberOfFemaleSpawnerForFirstTime);
}
else {
riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).push(0.);
if (numberOfMaleSpawnerForFirstTime>0)
riverBasin.getSpawnersForFirstTimeMeanLengths(Gender.MALE).push(0.);
}
if (numberOfMaleSpawnerForFirstTime>0) {
riverBasin.getSpawnersForFirstTimeMeanAges(Gender.MALE).push(maleSpawnersForFirstTimeAgesSum/numberOfMaleSpawnerForFirstTime);
else
riverBasin.getSpawnersForFirstTimeMeanLengths(Gender.MALE).push(maleSpawnersForFirstTimeLengthsSum / numberOfMaleSpawnerForFirstTime);
}
else {
riverBasin.getSpawnersForFirstTimeMeanAges(Gender.MALE).push(0.);
riverBasin.getSpawnersForFirstTimeMeanLengths(Gender.MALE).push(0.);
}
//System.out.println("nb spawners in basin " + riverBasin.getName() + " : " + numberOfGenitors);
//System.out.println("nb recruit in basin " + riverBasin.getName() + " : " + numberOfRecruit);
......@@ -401,31 +413,31 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
if (numberOfRecruit > 0){
long numberOfsuperIndividual, effectiveAmount, remainingFish;
// features of the super individuals
// for female
numberOfsuperIndividual = Math.max(1L,
Math.round(numberOfFemaleRecruit / amountPerSuperIndividual));
effectiveAmount = (long) Math.floor(numberOfFemaleRecruit / numberOfsuperIndividual);
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;
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);
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
......@@ -476,12 +488,12 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
group.removeAquaNism(fish);
}
deadFish.clear();
// -------------------------------------------------------
// display information
// -----------------------------------------------------
if (displayFluxesOnConsole)
System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";IMPORT;"
+ riverBasin.getName() + ";" + fluxBefore + ";" + riverBasin.getSpawnerNumberPerGroup(group)+ "; " + totalInputFluxes);
BufferedWriter bW = group.getbWForFluxes();
......
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