From 270faa2bbc7556d81a50a7c0104069d2b5b30cc3 Mon Sep 17 00:00:00 2001
From: Lambert Patrick <patrick.lambert@irstea.fr>
Date: Wed, 28 Aug 2019 16:48:10 +0200
Subject: [PATCH] with groth different between male and female
---
data/input/fishTryRealBV_CC.xml | 6 +-
.../java/species/DiadromousFishGroup.java | 98 ++++++++++++-------
.../species/DisperseAndMigrateToRiver.java | 16 +--
...perseAndMigrateToRiverStandardization.java | 18 ++--
src/main/java/species/Grow.java | 12 +--
.../ReproduceAndSurviveAfterReproduction.java | 3 +-
6 files changed, 90 insertions(+), 63 deletions(-)
diff --git a/data/input/fishTryRealBV_CC.xml b/data/input/fishTryRealBV_CC.xml
index 604bc07..097a228 100644
--- a/data/input/fishTryRealBV_CC.xml
+++ b/data/input/fishTryRealBV_CC.xml
@@ -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>
diff --git a/src/main/java/species/DiadromousFishGroup.java b/src/main/java/species/DiadromousFishGroup.java
index 497bf91..e07e8d3 100644
--- a/src/main/java/species/DiadromousFishGroup.java
+++ b/src/main/java/species/DiadromousFishGroup.java
@@ -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;
}
diff --git a/src/main/java/species/DisperseAndMigrateToRiver.java b/src/main/java/species/DisperseAndMigrateToRiver.java
index fe7c1ff..db6d184 100644
--- a/src/main/java/species/DisperseAndMigrateToRiver.java
+++ b/src/main/java/species/DisperseAndMigrateToRiver.java
@@ -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 défaut fixé à 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 récupère les info du poids des bassin par rapport à 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 considère 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 être 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() + " situé dans le bassin " + basin.getName() + " et né 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... ça beug pas mais c'est pas très clair... donc à vérifier
+ // 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 itéropares
+ // soit dans le dernier bassin de reproduction pour les it�ropares
fish.moveTo(group.getPilot(), bn.getAssociatedRiverBasin(fish.getPosition()), group);
} else {
deadFish.add(fish);
diff --git a/src/main/java/species/DisperseAndMigrateToRiverStandardization.java b/src/main/java/species/DisperseAndMigrateToRiverStandardization.java
index 9aa8357..d810e41 100644
--- a/src/main/java/species/DisperseAndMigrateToRiverStandardization.java
+++ b/src/main/java/species/DisperseAndMigrateToRiverStandardization.java
@@ -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 dépendent 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 défaut fixé à 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 récupère les info du poids des bassin par rapport à 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 considère 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 être 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() + " situé dans le bassin " + basin.getName() + " et né 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... ça beug pas mais c'est pas très clair... donc à vérifier
+ // 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 itéropares
+ // soit dans le dernier bassin de reproduction pour les it�ropares
fish.moveTo(group.getPilot(), bn.getAssociatedRiverBasin(fish.getPosition()), group);
} else {
deadFish.add(fish);
diff --git a/src/main/java/species/Grow.java b/src/main/java/species/Grow.java
index 8a7638b..902d3ca 100644
--- a/src/main/java/species/Grow.java
+++ b/src/main/java/species/Grow.java
@@ -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());
}
diff --git a/src/main/java/species/ReproduceAndSurviveAfterReproduction.java b/src/main/java/species/ReproduceAndSurviveAfterReproduction.java
index 21007cc..11755b4 100644
--- a/src/main/java/species/ReproduceAndSurviveAfterReproduction.java
+++ b/src/main/java/species/ReproduceAndSurviveAfterReproduction.java
@@ -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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