Merge branch 'develop' of gitlab-ssh.irstea.fr:SimAquaLife/GR3D into exploration_GR3D_process

data/input/northeastamerica/fishRIOBasin_Sapidissima.xml

@@ -289,6 +289,7 @@
 					<tempMinRep>10</tempMinRep>
 					<tempOptRep>17</tempOptRep>
 					<tempMaxRep>30</tempMaxRep>
+					<Soffset>-1.0</Soffset>
 					<eta>2.4</eta>
 					<ratioS95__S50>1.9</ratioS95__S50>
 					<a>270000</a>

data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml

@@ -296,12 +296,13 @@
 					<minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
 				</analysis.AnalyseFishDistribution>
 
-				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
+				<species.ReproduceWithDiagnose>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<reproductionSeason>SPRING</reproductionSeason>
 					<tempMinRep>10</tempMinRep>
 					<tempOptRep>17</tempOptRep>
 					<tempMaxRep>30</tempMaxRep>
+					<Soffset>-1.0</Soffset>
 					<eta>2.4</eta>
 					<ratioS95__S50>1.9</ratioS95__S50>
 					<a>270000</a>
@@ -311,13 +312,17 @@
 					<proportionOfFemaleAtBirth>0.5</proportionOfFemaleAtBirth>
 					<initialLength>2.8</initialLength>
 					<sigmaRecruitment>0.2</sigmaRecruitment>
-					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
 					<maxNumberOfSuperIndividualPerReproduction>100.0
 					</maxNumberOfSuperIndividualPerReproduction>
 					<withDiagnose>false</withDiagnose>
 					<displayFluxesOnConsole>false</displayFluxesOnConsole>
-				</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
+				</species.ReproduceWithDiagnose>
 
+				<species.SurviveAfterReproduction>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<afterReproductionSeason>SPRING</afterReproductionSeason>
+					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
+				</species.SurviveAfterReproduction>
 
 				<species.MigrateFromRiverToInshore>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>

exploration/scriptR/temperatureEffects.R

@@ -185,6 +185,13 @@ modifiedMasterReaction = function(temperature, par){
   return(rate)
 }
 
+# DeucthEtal 
+# Deutsch, Curtis A., Joshua J. Tewksbury, Raymond B. Huey, Kimberly S. Sheldon, Cameron K. Ghalambor, David C. Haak, et Paul R. Martin. « Impacts of Climate Warming on Terrestrial Ectotherms across Latitude ». Proceedings of the National Academy of Sciences 105, nᵒ 18 (5 juin 2008): 6668‑72. https://doi.org/10.1073/pnas.0709472105.
+# Huey, Raymond B., et R. D. Stevenson. « Integrating Thermal Physiology and Ecology of Ectotherms: A Discussion of Approaches ». American Zoologist 19, nᵒ 1 (1 février 1979): 357‑66. https://doi.org/10.1093/icb/19.1.357.
+
+# Payne, Nicholas L., James A. Smith, Dylan E. van der Meulen, Matthew D. Taylor, Yuuki Y. Watanabe, Akinori Takahashi, Teagan A. Marzullo, Charles A. Gray, Gwenael Cadiou, et Iain M. Suthers. « Temperature Dependence of Fish Performance in the Wild: Links with Species Biogeography and Physiological Thermal Tolerance ». Functional Ecology 30, nᵒ 6 (2016): 903‑12. https://doi.org/10.1111/1365-2435.12618.
+
+
 
 temperature = seq(0,100,.1)
 plot(temperature, modifiedMasterReaction(temperature, par = c(48.6, 49.7, 388, 1)), type = 'l', ylab = 'rate', main = "modifiedMasterReaction", 
@@ -250,3 +257,17 @@ plot(temperature, modifiedThorntonLessem(temperature, par = c(Tmin, 14, 27, Tmax
 temperature[which.max(modifiedThorntonLessem(temperature, par = c(Tmin, 14, 27, Tmax)))]
 
 lines(temperature, modifiedLehman(temperature,  par = c(Tmin, 21.3, Tmax)), col = 'red')
+
+StrabakaGnauck = function(temperature, par){
+  # in Lefrançois, C., et G. Claireaux (2003). Influence of Ambient Oxygenation and Temperature on Metabolic Scope and 
+  #   Scope for Heart Rate in the Common Sole Solea Solea. Marine Ecology Progress Series 259 : 273‑84.
+
+  Topt = par[1]
+  Tmax = par[2]
+  omega = par[3]
+  
+  rate = ((Tmax - temperature) / (Tmax - Topt))^omega * exp(-omega * (Tmax - temperature) / (Tmax - Topt) )
+return(rate)
+}
+
+plot(temperature, StrabakaGnauck(temperature, par = c(19.74, 30.48, 1.87)))
\ No newline at end of file

src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java

@@ -47,10 +47,11 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 	private double tempOptRep = 20.;
 	private double eta = 2.4; // parameter linking surface of a basin and S_etoile
 	private double ratioS95_S50 = 2.;
+	private double Soffset = -1.;
 	private double a = 270000.; // Parameter of fecndity (number of eggs per individual) Modifié depuis la valeur
-								// initial de tHibault, qui était 135000
+	// initial de tHibault, qui était 135000
 	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)
+	// to juvenile in estuary for alosa alosa = 0.33)
 	private double survOptRep = 0.0017;
 	private double lambda = 0.00041;
 	private double initialLength = 2.;
@@ -95,6 +96,9 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 
 		mortalityFunction = new MortalityFunction();
 		stockRecruitmentRelationship = new StockRecruitmentRelationship();
+
+		if (Double.isNaN(Soffset))
+			Soffset = -1.;
 	}
 
 
@@ -195,10 +199,13 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 					amountPerSuperIndividual = alpha / maxNumberOfSuperIndividualPerReproduction;
 
 					// Compute the Allee effect parameters S95 and S50
-
-					S95 = eta * riverBasin.getAccessibleSurface(); // corresponds to S* in the rougier publication
-					S50 = S95 / ratioS95_S50;
-
+					if (Soffset >= 0.) {
+						S95 = Soffset;
+						S50 = Soffset;
+					} else {
+						S95 = eta * riverBasin.getAccessibleSurface(); // corresponds to S* in the rougier publication
+						S50 = S95 / ratioS95_S50;
+					}
 					// initilisation of the stock recruitment relationship
 					stockRecruitmentRelationship.init(alpha, beta, S50, S95);
 
@@ -223,7 +230,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 								// System.out.println(fish.getAge() + " -> "+ fish.getLength() + "
 								// ("+fish.getStage()+")");
 								numberOfFemaleSpawners += fish.getAmount(); // on ajoute a chaque fois le fish.getAmount
-																			// (CcumSum)
+								// (CcumSum)
 								if (fish.getNumberOfReproduction() < 1) {
 									numberOfFemaleSpawnerForFirstTime += fish.getAmount();
 									femaleSpawnersForFirstTimeAgesSum += fish.getAge() * fish.getAmount();
@@ -231,7 +238,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 								}
 							} else if (fish.getGender() == Gender.MALE) {
 								numberOfMaleSpawners += fish.getAmount(); // on ajoute a chaque fois le fish.getAmount
-																			// (CcumSum)
+								// (CcumSum)
 								if (fish.getNumberOfReproduction() < 1) {
 									numberOfMaleSpawnerForFirstTime += fish.getAmount();
 									maleSpawnersForFirstTimeAgesSum += fish.getAge() * fish.getAmount();
@@ -657,7 +664,11 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 
 
 		public double getEffectiveStock(double stock) {
-			return stock / (1 + Math.exp(-log19 * (stock - S50) / (S95 - S50)));
+
+			if (S50 == S95) // catchment size independant Allee effect (including no Allee effect when S95 = 0)
+				return (stock < S95 ? 0. : stock);
+			else // catchment size dependant Allee effect
+				return stock / (1 + Math.exp(-log19 * (stock - S50) / (S95 - S50)));
 		}
 
 

src/main/java/species/SurviveAfterReproduction.java

+package species;
+
+import java.util.Hashtable;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Map;
+
+import org.openide.util.lookup.ServiceProvider;
+
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.DomDriver;
+
+import environment.RiverBasin;
+import environment.Time;
+import environment.Time.Season;
+import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
+import fr.cemagref.simaqualife.pilot.Pilot;
+import miscellaneous.BinomialForSuperIndividualGen;
+import species.DiadromousFish.SpawnerOrigin;
+import umontreal.iro.lecuyer.probdist.NormalDist;
+import umontreal.iro.lecuyer.randvar.NormalGen;
+
+@ServiceProvider(service = AquaNismsGroupProcess.class)
+
+public class SurviveAfterReproduction extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
+
+	private Season afterReproductionSeason = Season.SUMMER;
+
+	private double survivalRateAfterReproduction = 0.1;
+
+	private transient NormalGen genNormal;
+
+	/**
+	 * the random numbers generator for binomial draws
+	 * 
+	 * @unit --
+	 */
+	private transient BinomialForSuperIndividualGen aleaGen;
+
+	public static void main(String[] args) {
+		System.out.println((new XStream(new DomDriver())).toXML(new SurviveAfterReproduction()));
+	}
+
+
+	@Override
+	@InitTransientParameters
+	public void initTransientParameters(Pilot pilot) {
+		super.initTransientParameters(pilot);
+		genNormal = new NormalGen(pilot.getRandomStream(), new NormalDist(0., 1.));
+
+		aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
+
+	}
+
+
+	@Override
+	public void doProcess(DiadromousFishGroup group) {
+		Time time = group.getEnvironment().getTime();
+		if (time.getSeason(group.getPilot()) == afterReproductionSeason) {
+
+			for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
+
+				long survivalAmount;
+
+				List<DiadromousFish> fishInBasin = riverBasin.getFishs(group);
+				if (fishInBasin != null) {
+
+					// Initiate the total fluxes for this basin
+					Map<SpawnerOrigin, Map<String, Double>> totalInputFluxes = new Hashtable<SpawnerOrigin, Map<String, Double>>(); // On
+					totalInputFluxes.put(SpawnerOrigin.AUTOCHTONOUS, new Hashtable<String, Double>());
+					totalInputFluxes.put(SpawnerOrigin.ALLOCHTONOUS, new Hashtable<String, Double>());
+					for (SpawnerOrigin origin : totalInputFluxes.keySet()) {
+						for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
+							totalInputFluxes.get(origin).put(nutrient, 0.); // ON MET A JOUR NOTRE map
+						}
+						totalInputFluxes.get(origin).put("biomass", 0.);
+					}
+
+					// iterate on the fish
+					ListIterator<DiadromousFish> fishIterator = fishInBasin.listIterator();
+					while (fishIterator.hasNext()) {
+						DiadromousFish fish = fishIterator.next();
+
+						if (fish.isMature()) {
+
+							// origin of the spwaner
+							SpawnerOrigin spawnerOrigin = (fish.getBirthBasin() == riverBasin ? SpawnerOrigin.AUTOCHTONOUS
+									: SpawnerOrigin.ALLOCHTONOUS);
+
+							// survival amount of fish
+							double biomass = 0.;
+							survivalAmount = aleaGen.getSuccessNumber(fish.getAmount(), survivalRateAfterReproduction);
+
+							// at least one fish in the SI survive, the other die
+							if (survivalAmount > 0) {
+
+								// ---------------------------------------------------------- start of nutrient routine
+								// nutrient fluxes for one fish surviving after spawning (fish.getAmount):
+								// excretion + gametes
+								Map<String, Double> aFluxAfterSurvival = group.getNutrientRoutine()
+										.computeNutrientsInputForSurvivalAfterSpawning(fish);
+
+								// nutrient fluxes for one fish dying after spawning (fish.getAmount):
+								// carcasses + excretion + gametes
+								Map<String, Double> aFluxForDeadFish = group.getNutrientRoutine()
+										.computeNutrientsInputForDeathAfterSpawning(fish);
+
+								for (String nutrient : aFluxAfterSurvival.keySet()) {
+									// For all survival fish in the SI
+									group.getNutrientRoutine().getNutrientImportFluxesCollection().put(
+											time.getYear(group.getPilot()), nutrient, fish.getBirthBasin().getName(),
+											riverBasin.getName(), aFluxAfterSurvival.get(nutrient) * survivalAmount);
+
+									// For all dead fish in the SI
+									group.getNutrientRoutine().getNutrientImportFluxesCollection().put(
+											time.getYear(group.getPilot()), nutrient, fish.getBirthBasin().getName(),
+											riverBasin.getName(),
+											aFluxForDeadFish.get(nutrient) * (fish.getAmount() - survivalAmount));
+								}
+
+								// take into account the fish origine
+								for (String nutrient : aFluxAfterSurvival.keySet()) {
+									// For all survival fish
+									totalInputFluxes.get(spawnerOrigin).put(nutrient,
+											totalInputFluxes.get(spawnerOrigin).get(nutrient)
+													+ aFluxAfterSurvival.get(nutrient) * survivalAmount);
+
+									// For all dead fish
+									totalInputFluxes.get(spawnerOrigin).put(nutrient,
+											totalInputFluxes.get(spawnerOrigin).get(nutrient)
+													+ aFluxForDeadFish.get(nutrient) * (fish.getAmount() - survivalAmount));
+								}
+								// compute biomass for dead fish
+								biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount() - survivalAmount);
+								totalInputFluxes.get(spawnerOrigin).put("biomass",
+										totalInputFluxes.get(spawnerOrigin).get("biomass") + biomass);
+								// ------------------------------------------------------ end of nutrient routine
+
+								// update the amount of individual in the super-individual
+								fish.setAmount(survivalAmount);
+
+							} else { // the superindividual dies !!!
+								// ------------------------------------------------------ start of nutrient routine
+								// nutrient fluxes for one fish dying after spawning (fish.getAmount):
+								// carcasses + excretion + gametes
+								Map<String, Double> aFluxForDeadFish = group.getNutrientRoutine()
+										.computeNutrientsInputForDeathAfterSpawning(fish); //
+
+								for (String nutrient : aFluxForDeadFish.keySet()) {
+									group.getNutrientRoutine().getNutrientImportFluxesCollection().put(
+											time.getYear(group.getPilot()), nutrient, fish.getBirthBasin().getName(),
+											riverBasin.getName(),
+											aFluxForDeadFish.get(nutrient) * (fish.getAmount() - survivalAmount));
+								}
+								biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount());
+								totalInputFluxes.get(spawnerOrigin).put("biomass",
+										totalInputFluxes.get(spawnerOrigin).get("biomass") + biomass);
+								// ------------------------------------------------------ end of nutrient routine
+
+								// remove fish because fish is dead
+								fishIterator.remove();
+							}
+						}
+					}
+				}
+			}
+		}
+	}
+}