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Commit 270faa2b authored by Lambert Patrick's avatar Lambert Patrick
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with groth different between male and female

parent e4859e1f
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data/input/fishTryRealBV_CC.xml
View file @ 270faa2b
......@@ -7,10 +7,12 @@
<blue>0</blue>
<alpha>255</alpha>
</color>
<linfVonBert>70.0</linfVonBert>
<dMaxDisp>300.0</dMaxDisp>
<linfVonBertForFemale>70.0</linfVonBertForFemale>
<linfVonBertForMale>70.0</linfVonBertForMale>
<lFirstMaturityForFemale>55.0</lFirstMaturityForFemale>
<lFirstMaturityForMale>40.0</lFirstMaturityForMale>
<lengthAtHatching>2</lengthAtHatching>
<nutrientRoutine>
<nutrientsOfInterest>
<string>N</string>
......@@ -233,7 +235,7 @@
<species.PopulateBasinNetworkWithANorthLimit>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<nbSIPerBasin>200</nbSIPerBasin>
<initialLength>2.0</initialLength>
<initialLength>20.0</initialLength>
<nbFishPerSI>2500</nbFishPerSI>
<northLimitLatitude>43.54</northLimitLatitude>
</species.PopulateBasinNetworkWithANorthLimit>
......
src/main/java/species/DiadromousFishGroup.java
View file @ 270faa2b
......@@ -36,39 +36,21 @@ import species.DiadromousFish.Gender;
import org.openide.util.lookup.ServiceProvider;
/**
*
*/
@ServiceProvider(service = AquaNismsGroup.class)
public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNetwork> implements Comparable<DiadromousFishGroup> {
public String name = "species A";
public Color color = Color.RED;
/**
* L infinity of the van Bertalanffy growth curve
* L = Linf *(1-exp(-K*(t-t0))
* @unit cm
*/
public double linfVonBert = 60.;
/**
* ????
* @unit
*/
public double dMaxDisp = 300.;
/**
* length at first maturity. At that length the female become Stage.MATURE
* @unit cm
*/
public double lFirstMaturityForFemale = 55.;
/**
* length at first maturity. At that length the female become Stage.MATURE
* @unit cm
*/
public double lFirstMaturityForMale = 40.;
/**
* Routine to compute nutrient fluxes operated by a single individual (TODO by a single super individual).
*
......@@ -127,6 +109,28 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
*/
private transient Map<String, Duo<Double, Double>> basinsToUpdate;
/**
* length when fish hatchs ( when the diadromousFish is created after reproduction)
* no diffrence between gender
* @unit cm
*/
private double lengthAtHatching = 2.;
/**
* L infinity of the van Bertalanffy growth curve for female
* L = Linf *(1-exp(-K*(t-t0))
* @unit cm
*/
public double linfVonBertForFemale = 60.;
/**
* L infinity of the van Bertalanffy growth curve for male
* L = Linf *(1-exp(-K*(t-t0))
* @unit cm
*/
public double linfVonBertForMale = 60.;
/**
* Brody growth coefficient of the von Bertalanffy growth curve for female (calculated from the parameterset file)
* * L = Linf *(1-exp(-K*(t-t0))
......@@ -140,6 +144,20 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
* @unit year-1
*/
private transient double kOptForMale;
/**
* length at first maturity. At that length the female become Stage.MATURE
* @unit cm
*/
public double lFirstMaturityForFemale = 55.;
/**
* length at first maturity. At that length the female become Stage.MATURE
* @unit cm
*/
public double lFirstMaturityForMale = 40.;
/**
* minimum temperature for the reproduction (from the parameterset file)
......@@ -560,28 +578,38 @@ public BufferedWriter getbWForFluxes() {
return color;
}
public double getLinfVonBert() {
return linfVonBert;
public double getLinfVonBert(DiadromousFish fish) {
if ( fish.getGender() == Gender.FEMALE)
return linfVonBertForFemale;
else if (fish.getGender() == Gender.MALE)
return linfVonBertForMale;
else
return (linfVonBertForFemale+linfVonBertForMale)/2.;
}
public void setLinfVonBert(double linfVonBert) {
this.linfVonBert = linfVonBert;
}
public double getdMaxDisp() {
return dMaxDisp;
public double getlFirstMaturity(DiadromousFish fish) {
if ( fish.getGender() == Gender.FEMALE)
return lFirstMaturityForFemale;
else if (fish.getGender() == Gender.MALE)
return lFirstMaturityForMale;
else
return (lFirstMaturityForFemale+lFirstMaturityForFemale)/2.;
}
public double getlFirstMaturityForFemale() {
return lFirstMaturityForFemale;
/**
* @return the lengthAtHatching
*/
public double getLengthAtHatching() {
return lengthAtHatching;
}
public double getlFirstMaturityForMale() {
return lFirstMaturityForMale;
public double getdMaxDisp() {
return dMaxDisp;
}
public NutrientRoutine getNutrientRoutine() {
return nutrientRoutine;
}
......
src/main/java/species/DisperseAndMigrateToRiver.java
View file @ 270faa2b
......@@ -49,26 +49,26 @@ public class DisperseAndMigrateToRiver extends DisperseAndMigrateToRiverBasic {
if (fish.isMature()) {
// fish with homing
amountWithHoming = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), pHoming); // seuil par dfaut fix 50
amountWithHoming = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), pHoming); // seuil par d�faut fix� � 50
// strayed fish
strayedAmount = fish.getAmount() - amountWithHoming;
if (strayedAmount != 0) {
// On rcupre les info du poids des bassin par rapport la position du poisson
// On r�cup�re les info du poids des bassin par rapport � la position du poisson
Map<Basin,Double> accBasOfFish= new TreeMap<Basin, Double>(accessibleBasinsPerBasin.get(fish.getPosition()));
//accBasOfFish = accessibleBasinsPerBasin.get(fish.getPosition());
// On retire certains bassins si on considre une distance max de dispersion
// On retire certains bassins si on consid�re une distance max de dispersion
distBasOfFish = distanceBasinsPerBasin.get(fish.getPosition());
if (group.getdMaxDisp() != 0){
// TODO pourquoi distbasoffish peut tre nul ?
// TODO pourquoi distbasoffish peut �tre nul ?
if (distBasOfFish != null){
dMaxDispFish = (group.getdMaxDisp()/group.getLinfVonBert())*fish.getLength();
dMaxDispFish = (group.getdMaxDisp()/group.getLinfVonBert(fish))*fish.getLength();
// load accessible basins
for (Basin surroundingBasin : distBasOfFish.keySet()){
Double distance = distBasOfFish.get(surroundingBasin);
//System.out.println("pour le poisson " + fish.hashCode() + " situ dans le bassin " + basin.getName() + " et n dans le bassin " + fish.getBirthBasin().getName());
//System.out.println("pour le poisson " + fish.hashCode() + " situ� dans le bassin " + basin.getName() + " et n� dans le bassin " + fish.getBirthBasin().getName());
//System.out.println("la distance vaut " + distance + " pour le bassin " + surroundingBasin.getName());
if (distance >= dMaxDispFish) {
accBasOfFish.remove(surroundingBasin);
......@@ -81,7 +81,7 @@ public class DisperseAndMigrateToRiver extends DisperseAndMigrateToRiverBasic {
double totalWeight = 0.;
double probToGo = 0.;
long amountToGo = 0;
// TODO Qu'est ce qui se passe si AccBasOfFish est vide... a beug pas mais c'est pas trs clair... donc vrifier
// TODO Qu'est ce qui se passe si AccBasOfFish est vide... �a beug pas mais c'est pas tr�s clair... donc � v�rifier
for (Basin accBasin : accBasOfFish.keySet()){
double accBasinWeightLogit = accBasOfFish.get(accBasin) + alpha2Rep * fish.getLength();
double accBasinWeight = 1 / (1 + Math.exp(- accBasinWeightLogit));
......@@ -107,7 +107,7 @@ public class DisperseAndMigrateToRiver extends DisperseAndMigrateToRiverBasic {
if (amountWithHoming > 0){
fish.setAmount(amountWithHoming);
// retour soit dans le bassin de naissance pour les semelpares
// soit dans le dernier bassin de reproduction pour les itropares
// soit dans le dernier bassin de reproduction pour les it�ropares
fish.moveTo(group.getPilot(), bn.getAssociatedRiverBasin(fish.getPosition()), group);
} else {
deadFish.add(fish);
......
src/main/java/species/DisperseAndMigrateToRiverStandardization.java
View file @ 270faa2b
......@@ -41,7 +41,7 @@ public class DisperseAndMigrateToRiverStandardization extends AquaNismsGroupProc
public void initTransientParameters(Pilot pilot) {
super.initTransientParameters(pilot);
// calcul les poids des bassins voisins qui ne dpendent pas des poissons pour chaque SeaBassin
// calcul les poids des bassins voisins qui ne d�pendent pas des poissons pour chaque SeaBassin
BasinNetwork bn = (BasinNetwork) pilot.getAquaticWorld().getEnvironment();
accessibleBasinsPerBasin = new TreeMap<Basin, Map<Basin,Double>>();
distanceBasinsPerBasin = new TreeMap<Basin, Map<Basin,Double>>();
......@@ -107,26 +107,26 @@ public class DisperseAndMigrateToRiverStandardization extends AquaNismsGroupProc
if (fish.isMature()) {
// fish with homing
amountWithHoming = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), pHoming); // seuil par dfaut fix 50
amountWithHoming = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), pHoming); // seuil par d�faut fix� � 50
// strayed fish
strayedAmount = fish.getAmount() - amountWithHoming;
if (strayedAmount != 0) {
// On rcupre les info du poids des bassin par rapport la position du poisson
// On r�cup�re les info du poids des bassin par rapport � la position du poisson
Map<Basin,Double> accBasOfFish= new TreeMap<Basin, Double>(accessibleBasinsPerBasin.get(fish.getPosition()));
//accBasOfFish = accessibleBasinsPerBasin.get(fish.getPosition());
// On retire certains bassins si on considre une distance max de dispersion
// On retire certains bassins si on consid�re une distance max de dispersion
distBasOfFish = distanceBasinsPerBasin.get(fish.getPosition());
if (group.getdMaxDisp() != 0){
// TODO pourquoi distbasoffish peut tre nul ?
// TODO pourquoi distbasoffish peut �tre nul ?
if (distBasOfFish != null){
dMaxDispFish = (group.getdMaxDisp()/group.getLinfVonBert())*fish.getLength();
dMaxDispFish = (group.getdMaxDisp()/group.getLinfVonBert(fish))*fish.getLength();
// load accessible basins
for (Basin surroundingBasin : distBasOfFish.keySet()){
Double distance = distBasOfFish.get(surroundingBasin);
//System.out.println("pour le poisson " + fish.hashCode() + " situ dans le bassin " + basin.getName() + " et n dans le bassin " + fish.getBirthBasin().getName());
//System.out.println("pour le poisson " + fish.hashCode() + " situ� dans le bassin " + basin.getName() + " et n� dans le bassin " + fish.getBirthBasin().getName());
//System.out.println("la distance vaut " + distance + " pour le bassin " + surroundingBasin.getName());
if (distance >= dMaxDispFish) {
accBasOfFish.remove(surroundingBasin);
......@@ -139,7 +139,7 @@ public class DisperseAndMigrateToRiverStandardization extends AquaNismsGroupProc
double totalWeight = 0.;
double probToGo = 0.;
long amountToGo = 0;
// TODO Qu'est ce qui se passe si AccBasOfFish est vide... a beug pas mais c'est pas trs clair... donc vrifier
// TODO Qu'est ce qui se passe si AccBasOfFish est vide... �a beug pas mais c'est pas tr�s clair... donc � v�rifier
for (Basin accBasin : accBasOfFish.keySet()){
double accBasinWeightLogit = accBasOfFish.get(accBasin) + alpha2Rep*((fish.getLength() - meanLengthOfMatureFishes) / standardDeviationOfMatureFishesLength);
double accBasinWeight = 1 / (1 + Math.exp(- accBasinWeightLogit));
......@@ -165,7 +165,7 @@ public class DisperseAndMigrateToRiverStandardization extends AquaNismsGroupProc
if (amountWithHoming > 0){
fish.setAmount(amountWithHoming);
// retour soit dans le bassin de naissance pour les semelpares
// soit dans le dernier bassin de reproduction pour les itropares
// soit dans le dernier bassin de reproduction pour les it�ropares
fish.moveTo(group.getPilot(), bn.getAssociatedRiverBasin(fish.getPosition()), group);
} else {
deadFish.add(fish);
......
src/main/java/species/Grow.java
View file @ 270faa2b
......@@ -94,22 +94,20 @@ public class Grow extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGr
// 2) Update the fish length with a lognormal normal draw of increment
// limit the fish length to Linf
if (fish.getLength() < group.getLinfVonBert()){
muDeltaLVonBert = Math.log((group.getLinfVonBert() - fish.getLength()) * (1 - Math.exp(-kVonBert * Time.getSeasonDuration()))) - (sigmaDeltaLVonBert*sigmaDeltaLVonBert)/2;
if (fish.getLength() < group.getLinfVonBert(fish)){
muDeltaLVonBert = Math.log((group.getLinfVonBert(fish) - fish.getLength()) * (1 - Math.exp(-kVonBert * Time.getSeasonDuration()))) - (sigmaDeltaLVonBert*sigmaDeltaLVonBert)/2;
growthIncrement = Math.exp(genNormal.nextDouble()*sigmaDeltaLVonBert + muDeltaLVonBert);
fish.setLength(Math.min(group.getLinfVonBert(), fish.getLength() + growthIncrement));
fish.setLength(Math.min(group.getLinfVonBert(fish), fish.getLength() + growthIncrement));
}
else {
fish.setLength(group.getLinfVonBert());
fish.setLength(group.getLinfVonBert(fish));
}
//System.out.println(fish.getAge() + " -> "+ fish.getLength() + " ("+fish.getStage()+"): "+ growthIncrement);
// test if fish become mature
if (fish.getStage() == Stage.IMMATURE){
if (fish.getLength() > group.getlFirstMaturityForFemale()){
if (fish.getStage() == Stage.IMMATURE && fish.getLength() > group.getlFirstMaturity(fish)){
fish.setStage(Stage.MATURE);
}
}
//System.out.println("la temp�rature du lieu de vie du poisson est :" + fish.getPosition().getCurrentTemperature() + ", la saison est :" + Time.getSeason() + " et sa nouvelle taille est :" + fish.getLength());
}
......
src/main/java/species/ReproduceAndSurviveAfterReproduction.java
View file @ 270faa2b
......@@ -44,7 +44,6 @@ public class ReproduceAndSurviveAfterReproduction extends AquaNismsGroupProcess<
private double delta_t=0.33; // duration of the mortality considered in the reproduction process (ex.: from eggs to juvenile in estuary for alosa alosa = 0.33)
private double survOptRep = 0.0017;
private double lambda = 0.00041;
private double initialLength = 2.;
private double sigmaRecruitment = 0.3;
private double survivalRateAfterReproduction = 0.1;
private double maxNumberOfSuperIndividualPerReproduction = 50.;
......@@ -237,7 +236,7 @@ public class ReproduceAndSurviveAfterReproduction extends AquaNismsGroupProcess<
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, group.getLengthAtHatching(), effectiveAmount, Gender.UNDIFFERENCIED));
}
// stock the first year when recruitment is non nul
......
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