From 35254d3c8fa7302b23a813ae2cba04f7e4c46429 Mon Sep 17 00:00:00 2001
From: Poulet Camille <camille.poulet@irstea.priv>
Date: Fri, 12 Jul 2019 14:34:11 +0200
Subject: [PATCH] Weight size relationship to compute gonad weights
The gonad weight was computed in R studio and corresponded to the mean
gonad weight of males and females reprorted in Bruch data base. So,
there was no relationship between the weight in GR3D and the gonad
weight from Bruch.
---
src/main/java/species/FishNutrient.java | 62 +++++++++++++++++++------
1 file changed, 49 insertions(+), 13 deletions(-)
diff --git a/src/main/java/species/FishNutrient.java b/src/main/java/species/FishNutrient.java
index e1befab..337b9c7 100644
--- a/src/main/java/species/FishNutrient.java
+++ b/src/main/java/species/FishNutrient.java
@@ -69,7 +69,7 @@ public class FishNutrient {
* value g
* usually computed as the difference between unspawned gonad (inbound) and spawned gonad (outbound; "spent gonad")
*/
- private Map <DiadromousFish.Gender, Double> spawnedGametesWeight;
+ //private Map <DiadromousFish.Gender, Double> spawnedGametesWeight;
/**
@@ -128,7 +128,7 @@ public class FishNutrient {
Map <String, Double> excretionRate,
Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPreSpawning,
Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPostSpawning,
- Map<DiadromousFish.Gender, Double> gameteSpawned,
+ //Map<DiadromousFish.Gender, Double> gameteSpawned,
Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPreSpawning,
Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPostSpawning,
Map<DiadromousFish.Gender, Map<String, Double>> compoGametes,
@@ -141,7 +141,7 @@ public class FishNutrient {
this.residenceTime = residenceTime;
this.fishFeaturesPreSpawning = fishFeaturesPreSpawning;
this.fishFeaturesPostSpawning = fishFeaturesPostSpawning;
- this.spawnedGametesWeight = gameteSpawned;
+ //this.spawnedGametesWeight = gameteSpawned;
this.compoCarcassPreSpawning = compoCarcassPreSpawning;
this.compoCarcassPostSpawning = compoCarcassPostSpawning;
this.compoGametes = compoGametes;
@@ -202,7 +202,7 @@ public class FishNutrient {
double carcass = totalWeightPost
* compoCarcassPostSpawning.get(fish.getGender()).get(nutrient);
//double gametes = (totalWeightPre - totalWeightPost) FAUX car perte de poids somatique due a la reproduction
- double gametes = spawnedGametesWeight.get(fish.getGender())
+ double gametes = this.getGonadWeight(fish, SpawningPosition.PRE) - this.getGonadWeight(fish, SpawningPosition.POST)
*compoGametes.get(fish.getGender()).get(nutrient);
double excretion = totalWeightPost
* residenceTime
@@ -237,15 +237,15 @@ public class FishNutrient {
//TODO Fix with new data
double totalWeightPost = this.getWeight(fish, SpawningPosition.POST);
//Gamete compositions depends on sex.
- double gametes = spawnedGametesWeight.get(fish.getGender())
+
+ double gametes = this.getGonadWeight(fish, SpawningPosition.PRE) - this.getGonadWeight(fish, SpawningPosition.POST)
* compoGametes.get(fish.getGender()).get(nutrient);
+ // double gametes = spawnedGametesWeight.get(fish.getGender()) * compoGametes.get(fish.getGender()).get(nutrient);
double excretion = totalWeightPost
* residenceTime
* excretionRate.get(nutrient);
double nutrientImport = gametes + excretion;
-
-
nutrientsInput.put(nutrient, nutrientImport);
}
else {
@@ -297,6 +297,7 @@ public class FishNutrient {
return weight;
}
+
/**
* Compute the weight for a fish with length (cm)
@@ -308,9 +309,35 @@ public class FishNutrient {
return getWeight (fish, SpawningPosition.PRE);
}
+ public double getGonadWeight (DiadromousFish fish, SpawningPosition spawningPosition) {
+
+ double gonadWeight = 0.;
+ if (fish.getStage()==Stage.MATURE);
+ if (spawningPosition == SpawningPosition.PRE)
+ gonadWeight = Math.exp(fishFeaturesPreSpawning.get(fish.getGender()).get("aLW_Gonad")
+ + fishFeaturesPreSpawning.get(fish.getGender()).get("bLW_Gonad") * Math.log(fish.getLength()));
+ else
+ gonadWeight = Math.exp(fishFeaturesPostSpawning.get(fish.getGender()).get("aLW_Gonad")
+ + fishFeaturesPostSpawning.get(fish.getGender()).get("bLW_Gonad") * Math.log(fish.getLength()));
+
+ return gonadWeight;
+ }
+
+ /**
+ * Compute the gonad weight for a fish with length (cm) to compute the gamete emission (g).
+ * @param fish
+ * @return weight (g)
+ */
+ public double getGonadWeight (DiadromousFish fish) {
+
+ return getGonadWeight (fish, SpawningPosition.PRE);
+ }
-public ArrayList<String> getNutrientsOfInterest() {
+
+
+
+ public ArrayList<String> getNutrientsOfInterest() {
return nutrientsOfInterest;
}
@@ -349,6 +376,8 @@ public static void main(String[] args) {
aFeature.put("aLW", Math.exp(-4.9078)); //weight size relationship computed from BDalosesBruch
aFeature.put("bLW", 3.147);
+ aFeature.put("aLW_Gonad", -5.2425); // issu de la relation taille - poids des gonades Bruch
+ aFeature.put("bLW_Gonad", 2.6729); // issu de la relation taille - poids des gonades Bruch
//aFeature.put("bLW",3.3429);// parametre "b" de la relation taille/poids - Coefficient d'allometrie
//aFeature.put("aLW",1.2102E-6 * Math.pow(10., aFeature.get("bLW"))); // parametre "a" de la relation taille/poids en kg/cm- Traduit la condition
//aFeature.put("GSI",0.15);
@@ -360,6 +389,8 @@ public static void main(String[] args) {
aFeature = new Hashtable<String,Double>();
aFeature.put("aLW", Math.exp(-1.304));
aFeature.put("bLW", 2.1774);
+ aFeature.put("aLW_Gonad", -8.8744);
+ aFeature.put("bLW_Gonad", 3.3838);
//aFeature.put("aLW",2.4386E-6 * Math.pow(10, aFeature.get("bLW"))); // Conversion des g/mm en g.cm (from Taverny, 1991)
//aFeature.put("GSI",.08);
aFeaturePreSpawning.put(Gender.MALE,aFeature);
@@ -377,6 +408,8 @@ public static void main(String[] args) {
aFeature = new Hashtable<String,Double>();
aFeature.put("aLW", Math.exp(-4.3276)); //weight size relationship computed from BDalosesBruch
aFeature.put("bLW", 2.9418);
+ aFeature.put("aLW_Gonad", -6.6234); // issu de la relation taille - poids des gonades Bruch
+ aFeature.put("bLW_Gonad", 2.8545); // issu de la relation taille - poids des gonades Bruch
//aFeature.put("GSI",0.10); //From BDalosesBruch
//aFeature.put("aLW",aFeaturePreSpawning.get(Gender.FEMALE).get("aLW")/(1+aFeature.get("GSI"))); // parametre "a" de la relation taille/poids avec Lt en cm - Traduit la condition
//aFeature.put("bLW",aFeaturePreSpawning.get(Gender.FEMALE).get("bLW"));// parametre "b" de la relation taille/poids - Coefficient d'allometrie
@@ -389,6 +422,8 @@ public static void main(String[] args) {
aFeature.put("aLW", Math.exp(-4.5675));// parametre "a" de la relation taille/poids - Coefficient d'allometrie
aFeature.put("bLW", 2.9973);
+ aFeature.put("aLW_Gonad", -11.285); // issu de la relation taille - poids des gonades Bruch
+ aFeature.put("bLW_Gonad", 3.8331); // issu de la relation taille - poids des gonades Bruch
//aFeature.put("GSI",.05); From BDalosesBruch
//aFeature.put("aLW",aFeaturePreSpawning.get(Gender.MALE).get("aLW")/(1+aFeature.get("GSI")));
//aFeature.put("bLW",aFeaturePreSpawning.get(Gender.MALE).get("bLW"));
@@ -396,11 +431,12 @@ public static void main(String[] args) {
System.out.println("aFeaturePostSpawning: " + aFeaturePostSpawning.toString());
- Map<Gender, Double> aGameteSpawned = new Hashtable <DiadromousFish.Gender,Double>();
- aGameteSpawned.put(Gender.FEMALE, 131.); // Compute from the difference between spawned and unspawned ovaries ie correspond to a mean weight of eggs spawned
- aGameteSpawned.put(Gender.MALE, 44.8); // Compute from the difference between spawned and unspawned testes ie correspond to a mean weight of sperm spawned
- System.out.println("aGameteSpawned: " + aGameteSpawned.toString());
+ //Map<Gender, Double> aGameteSpawned = new Hashtable <DiadromousFish.Gender,Double>();
+ //aGameteSpawned.put(Gender.FEMALE, 131.); // Compute from the difference between spawned and unspawned ovaries ie correspond to a mean weight of eggs spawned
+ //aGameteSpawned.put(Gender.MALE, 44.8); // Compute from the difference between spawned and unspawned testes ie correspond to a mean weight of sperm spawned
+
+ //System.out.println("aGameteSpawned: " + aGameteSpawned.toString());
// carcass composition for fish before spawning
Map<Gender, Map<String, Double>> aCompoCarcassPreSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
@@ -466,7 +502,7 @@ public static void main(String[] args) {
System.out.println("nutrientsOfInterest: " + nutrientsOfInterest);
- FishNutrient fn = new FishNutrient(nutrientsOfInterest,aResidenceTime, anExcretionRate, aFeaturePreSpawning, aFeaturePostSpawning, aGameteSpawned,
+ FishNutrient fn = new FishNutrient(nutrientsOfInterest,aResidenceTime, anExcretionRate, aFeaturePreSpawning, aFeaturePostSpawning,
aCompoCarcassPreSpawning, aCompoCarcassPostSpawning, aCompoGametes,
aJuvenileFeatures, aCompoJuveniles);
--
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