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Commit e2c7bf24 authored by Poulet Camille's avatar Poulet Camille
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Merge remote-tracking branch 'origin/Camille' into Camille

parents 30b99661 efa18237
master BasinImprovement Camille DeplacementBasin Script 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 28 additions and 21 deletions
+28 -21
src/main/java/species/PopulateBasinNetwork.java
+ 1
− 1
View file @ e2c7bf24
......@@ -23,7 +23,7 @@ public class PopulateBasinNetwork extends AquaNismsGroupProcess<DiadromousFish,
public void doProcess(DiadromousFishGroup group) {
for (Basin basin : group.getEnvironment().getRiverBasins()){
for (int i=0; i < nbSIPerBasin; i++){
group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbFishPerSI, Gender.UNDIFFERENCIED));
group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbFishPerSI, Gender.FEMALE));
}
}
}
......
src/main/java/species/PopulateBasinNetworkWithANorthLimit.java
+ 1
− 1
View file @ e2c7bf24
......@@ -47,7 +47,7 @@ public class PopulateBasinNetworkWithANorthLimit extends AquaNismsGroupProcess<D
for (RiverBasin basin : group.getEnvironment().getRiverBasins()){
if (basin.getLatitude()<=northLimitLatitude){
for (int i=0; i < nbSIPerBasin; i++){
group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbFishPerSI, Gender.UNDIFFERENCIED));
group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbFishPerSI, Gender.FEMALE));
}
}
}
......
src/main/java/species/PopulateWithASinglePopulation.java
+ 1
− 1
View file @ e2c7bf24
......@@ -25,7 +25,7 @@ public class PopulateWithASinglePopulation extends AquaNismsGroupProcess<Diadrom
Basin basin = group.getEnvironment().getRiverBasins()[bassinInd];
for (int i=0; i < nbSIPerBasin; i++){
group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbIndPerSI, Gender.UNDIFFERENCIED));
group.addAquaNism(new DiadromousFish(group.getPilot(), basin, initialLength, nbIndPerSI, Gender.FEMALE));
}
}
}
......
src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java
+ 25
− 18
View file @ e2c7bf24
......@@ -61,6 +61,12 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
private transient NormalGen genNormal;
private transient MortalityFunction mortalityFunction;
/**
* relationship between
* recruitment in number of juvenile on spawning grounds
* stock in number of FEMALES
* @unit
*/
private transient StockRecruitmentRelationship stockRecruitmentRelationship;
// private transient UniformGen genUniform;
......@@ -85,10 +91,10 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
for(RiverBasin riverBasin : group.getEnvironment().getRiverBasins()){
double b, c, alpha, beta, amountPerSuperIndividual , S95, S50 ;
double numberOfGenitors = 0.;
double numberOfFemaleGenitors = 0.;
double numberOfAutochtones = 0.;
double numberOfSpawnerForFirstTime = 0.;
double spawnersForFirstTimeAgesSum = 0.;
double numberOfFemaleSpawnerForFirstTime = 0.;
double femaleSpawnersForFirstTimeAgesSum = 0.;
long survivalAmount;
double muRecruitment = 0.;
//double weightOfGenitors = 0.;
......@@ -145,15 +151,16 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
Map<Integer, Long> ageOfNativeSpawners = new TreeMap<Integer, Long>();
// compute the number of spawners and keep the origines of the spawners
for( DiadromousFish fish : fishInBasin){
if( fish.isMature()){
for (DiadromousFish fish : fishInBasin){
if (fish.getGender() == Gender.FEMALE & fish.isMature()){
//System.out.println(fish.getAge() + " -> "+ fish.getLength() + " ("+fish.getStage()+")");
if (fish.getNumberOfReproduction() < 1) {
numberOfSpawnerForFirstTime++;
spawnersForFirstTimeAgesSum += fish.getAge();
numberOfFemaleSpawnerForFirstTime++;
femaleSpawnersForFirstTimeAgesSum += fish.getAge();
}
numberOfGenitors += fish.getAmount() ;
numberOfFemaleGenitors += fish.getAmount() ;
// spawner per origine
String basinName = fish.getBirthBasin().getName();
......@@ -182,7 +189,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
}
// keep the spawner number
riverBasin.setLastSpawnerNumber(numberOfGenitors);
riverBasin.setLastSpawnerNumber(numberOfFemaleGenitors);
// --------------------------------------------------------------------------------------------------
// Diagnose of the population dynamics in the basin
......@@ -193,7 +200,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// 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 (numberOfGenitors > 0.) {
if (numberOfFemaleGenitors > 0.) {
List<Trio<Integer, Long, Long>> mortalityData= new ArrayList<Trio<Integer, Long, Long>>();
// first age
// second effective of native spwaner
......@@ -224,7 +231,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
"\tZcrash="+ stockRecruitmentRelationship.getSigmaZcrash() +
"\tZ="+ riverBasin.getNativeSpawnerMortality());
System.out.println("\tStrap="+stockRecruitmentRelationship.getStockTrap(riverBasin.getNativeSpawnerMortality())+
"\tStotal="+numberOfGenitors+"\tSautochthonous="+
"\tStotal="+numberOfFemaleGenitors+"\tSautochthonous="+
spawnerOriginsDuringReproduction.get(riverBasin.getName()));
......@@ -236,7 +243,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
if (riverBasin.getNativeSpawnerMortality()>stockRecruitmentRelationship.getSigmaZcrash())
message="overZcrash";
else {
if (numberOfGenitors < stockTrap)
if (numberOfFemaleGenitors < stockTrap)
message = "inTrapWithStrayers";
else {
if (spawnerOriginsDuringReproduction.get(riverBasin.getName()) < stockTrap)
......@@ -253,10 +260,10 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
// Reproduction process (number of recruits)
// --------------------------------------------------------------------------------------------------
if (numberOfGenitors > 0.) {
if (numberOfFemaleGenitors > 0.) {
//BH Stock-Recruitment relationship with logistic depensation
double meanNumberOfRecruit = stockRecruitmentRelationship.getRecruitment(numberOfGenitors);
double meanNumberOfRecruit = stockRecruitmentRelationship.getRecruitment(numberOfFemaleGenitors);
// lognormal random draw
muRecruitment = Math.log(meanNumberOfRecruit) - (Math.pow(sigmaRecruitment,2))/2;
......@@ -265,11 +272,11 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
//System.out.println(group.getPilot().getCurrentTime()+" "+Time.getSeason(group.getPilot())+" "+ riverBasin.getName()+": " + numberOfGenitors + " spwaners \tgive "+ numberOfRecruit + " recruits");
// keep last % of autochtone
riverBasin.getLastPercentagesOfAutochtones().push(numberOfAutochtones * 100 / numberOfGenitors);
riverBasin.getLastPercentagesOfAutochtones().push(numberOfAutochtones * 100 / numberOfFemaleGenitors);
// keep the number of spawners for the firt time in the basin
if (numberOfSpawnerForFirstTime>0){
riverBasin.getSpawnersForFirstTimeMeanAges().push(spawnersForFirstTimeAgesSum/numberOfSpawnerForFirstTime);
if (numberOfFemaleSpawnerForFirstTime>0){
riverBasin.getSpawnersForFirstTimeMeanAges().push(femaleSpawnersForFirstTimeAgesSum/numberOfFemaleSpawnerForFirstTime);
}else{
riverBasin.getSpawnersForFirstTimeMeanAges().push(0.);
}
......@@ -286,7 +293,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
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, initialLength, effectiveAmount, Gender.FEMALE));
}
// stock the first year when recruitment is non nul
......
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