Merge remote-tracking branch 'origin/master' into Camille

exploration/nutrients/nutrientFlux.R

+age=3:8
+
+fecundity = function(age){
+  871.72*age +50916
+}
+cbind(age, fecundity(age), fecundity(age) -mean(fecundity(age)))
+# 
+
+
+#===================================================
+# masse des gonades, RGS
+# ===================================================
+# Taverny 1991
+Wt=seq(1000, 3000, 200) # masse totale (g)
+Gn = - 85.5634 + (Wt )*0.166 # masse de la gonade (g)
+plot(Wt,Gn)
+plot(Wt, Gn/Wt)
+
+# ==================================================
+# relation taille poinds
+# =================================================
+LtJuv=30:150 # mm
+LtGen=400:800 #mm
+Minho = function(Lt){
+  # formule avec Lt en cm
+  return(0.0221 * (Lt/10)^2.8147)
+}
+
+
+GirondeJuvenile = function(Lt){
+  # pour année 1985
+  exp(-11.571) * Lt^2.9467
+}
+
+GirondeMale = function(Lt){
+  # Lt en mm
+  # pour l'année  1988 (livre p44)
+  2.4386e-6*Lt^3.2252
+}
+
+GirondeFemale = function(Lt){
+  # Lt en mm
+  # pour l'année  1988 (livre p44)
+  1.2102e-6*Lt^3.3429
+}
+#  =========================================    PB
+LoireMale = function(Lf){
+  # longueur fourche
+  5.5070e-3*Lf^3.114
+}
+LoireFemale = function(Lf){
+  # longueur fourche
+    7.2980e-3* Lf^3.019
+}
+
+SebouMale = function(Lt){
+  2.0705e-6*Lt^3.2587
+}
+SebouFemale = function(Lt){
+  8.2056e-7*Lt^3.4105
+}
+
+          
+plot(LtJuv, GirondeJuvenile(LtJuv), type='l')
+
+
+plot(LtGen, Minho(LtGen), type='l', col='black', ylim=c(0,5000), xlab ='total length (mm)', ylab = 'weight (g)')
+lines(LtGen, GirondeMale(LtGen), col='green')
+lines(LtGen, GirondeFemale(LtGen), col='green', lty=2)
+lines(LtGen, SebouMale(LtGen), col='red')
+lines(LtGen, SebouFemale(LtGen), col='red', lty=2)
+lines(LtGen, LoireMale(LtGen), col='blue')
+lines(LtGen, LoireFemale(LtGen), col='blue', lty=2)
+legend('topleft', legend=c('Minho', 'Gironde Male', 'Gironde Female', 'Sebou Male', 'Sebou Female', 'Loire Male', 'Loire Female'),
+       lty=c(1,1,2, 1,2,1,2, 1,2), 
+       col=c('black', 'green', 'green', 'red', 'red', 'blue', 'blue'))
+
+plot(LtGen, LoireMale(LtGen), col='blue', type='l',xlab ='total length (mm)', ylab = 'weight (g)')
+
+lines(LtGen, LoireFemale(LtGen), col='blue', lty=2)
+points(506, LoireFemale(506), col='blue')

src/main/java/species/DiadromousFish.java

@@ -101,6 +101,13 @@ public class DiadromousFish extends AquaNism<Basin, BasinNetwork> {
 		return birthBasin;
 	}
 		
+	/**
+	 * @return the gender
+	 */
+	public Gender getGender() {
+		return gender;
+	}
+
 	@Override
 	public <ANG extends AquaNismsGroup<?, BasinNetwork>> void moveTo(
 			Pilot pilot, Basin destination, ANG group) {

src/main/java/species/DiadromousFishGroup.java

@@ -39,8 +39,6 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 	public double linfVonBert = 60.;
 	public double dMaxDisp = 300.;
 	public double lFirstMaturity = 40.;
-	public double aLW = 0.02; // param�tre "a" de la relation taille/poids
-	public double bLW = 3.; // param�tre "b" de la relation taille/poids
 	public String fileNameInputForInitialObservation = "data/input/reality/Obs1900.csv";
 	public double centileForRange = 0.95;
 
@@ -139,7 +137,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 		}
 
 		// charge kopt et temMinRep depuis le fichier de parametre. Sinon (parameterSetLine<=0), ce sont les 
-		// valeur dasn le procoessus de reroduction qui sont utilis
+		// valeur dasn le procoessus de reroduction qui sont utilis�
 		kOpt=Double.NaN;
 		tempMinRep =Double.NaN;
 		if (parameterSetLine>0){
@@ -269,14 +267,6 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 		this.lFirstMaturity = lFirstMaturity;
 	}
 
-	public double getaLW() {
-		return aLW;
-	}
-
-	public double getbLW() {
-		return bLW;
-	}
-
 
 	@Observable(description="Higher Populated Latitude")
 	public double getHigherPopulatedLatitude() {

src/main/java/species/FishNutrient.java

+/**
+ * patrick.lambert
+ * @author Patrick Lambert
+ * @copyright Copyright (c) 2018, Irstea
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+ */
+package species;
+
+import species.DiadromousFish.Gender;
+import species.DiadromousFish.Stage;
+
+/**
+ *
+ */
+public class FishNutrient {
+
+	private double aLWfemalePre = 0.0221; // param�tre "a" de la relation taille/poids avec Lt en cm
+	private double bLWfemalePre  = 2.8147; // param�tre "b" de la relation taille/poids
+	private double GSIfemalePre =.15;	
+	private double aLWmalePre = 0.0221; // param�tre "a" de la relation taille/poids avec Lt en cm
+	private double bLWmalePre  = 2.8147; // param�tre "b" de la relation taille/poids
+	private double GSImalePre =.07;
+
+	// Si on ne possède pas wT post reproduction 
+	
+		private double aLWfemalePost = 0.; // param�tre "a" de la relation taille/poids avec Lt en cm
+		private double bLWfemalePost  = 0.; // param�tre "b" de la relation taille/poids
+		private double GSIfemalePost=0.;	
+		private double aLWmalePost = 0.; // param�tre "a" de la relation taille/poids avec Lt en cm
+		private double bLWmalePost = 0.; // param�tre "b" de la relation taille/poids
+		private double GSImalePost =.07;
+		
+	
+	
+	//Valeurs de Haskell pour A. sapidissima -- A rechercher pour Alosa alosa
+	
+		private double compoNpreMale = 2.921; 
+		private double compoPpreMale = 0.662;
+		private double compoNpreFemale = 2.917;
+		private double compoPpreFemale = 0.725;
+		
+		private double compoNpostMale = 2.790 ;
+		private double compoPpostMale = 0.961;
+		private double compoNpostFemale = 3.216 ;
+		private double compoPpostFemale = 0.997;
+
+
+	/**
+	 * 
+	 */
+	public FishNutrient() {
+		// TODO Auto-generated constructor stub
+	}
+
+	public void computeNP(DiadromousFish fish) {
+		double totalWeightPre, totalWeightPost;
+		
+		if (fish.getStage() == Stage.MATURE) {
+			if (fish.getGender() == Gender.FEMALE ) {
+				totalWeightPre = aLWfemalePre * Math.pow(fish.getLength(), bLWfemalePre);
+				totalWeightPost = aLWfemalePost * Math.pow(fish.getLength(), bLWfemalePost);
+				// totalWeightPost = totalWeightPre * GSIfemalePre;
+			}
+			else if (fish.getGender() == Gender.MALE) {
+				totalWeightPre = aLWmalePre * Math.pow(fish.getLength(), bLWmalePre);
+				totalWeightPost = aLWmalePost * Math.pow(fish.getLength(), bLWmalePost);
+				// totalWeightPost =  totalWeightPre * GSImalePre;
+			}
+			else {
+				totalWeightPre = Double.NaN;
+				totalWeightPost = 0.;
+			}
+			
+		}
+	}
+}
\ No newline at end of file