From 3a1bbc49feac4d045aaf7d8cb3d2bb86e52dfe63 Mon Sep 17 00:00:00 2001
From: "camille.poulet" <camille.poulet@irstea.fr>
Date: Tue, 17 Sep 2019 10:43:35 +0200
Subject: [PATCH] Correction Temperature Effect on Survival
---
data/input/fishTryRealBV_CC.xml | 6 +-
.../java/miscellaneous/Miscellaneous.java | 72 +++++++++++--------
src/main/java/species/Survive.java | 9 +--
3 files changed, 49 insertions(+), 38 deletions(-)
diff --git a/data/input/fishTryRealBV_CC.xml b/data/input/fishTryRealBV_CC.xml
index f78f02e..b572f72 100644
--- a/data/input/fishTryRealBV_CC.xml
+++ b/data/input/fishTryRealBV_CC.xml
@@ -287,9 +287,9 @@
<species.Survive>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <tempMinMortGenInRiv>10.0</tempMinMortGenInRiv>
- <tempMaxMortGenInRiv>23.0</tempMaxMortGenInRiv>
- <tempOptMortGenInRiv>20.0</tempOptMortGenInRiv>
+ <tempMinSurvivalSpawnerInRiv>10.0</tempMinSurvivalSpawnerInRiv>
+ <tempMaxSurvivalSpawnerInRiv>23.0</tempMaxSurvivalSpawnerInRiv>
+ <!-- <tempOptSurvivalSpawnerInRiv>20.0</tempOptSurvivalSpawnerInRiv> -->
<survivalProbOptGenInRiv>1.0</survivalProbOptGenInRiv>
<mortalityRateInRiver>0.4</mortalityRateInRiver>
<mortalityRateInSea>0.4</mortalityRateInSea>
diff --git a/src/main/java/miscellaneous/Miscellaneous.java b/src/main/java/miscellaneous/Miscellaneous.java
index 8b36401..dcd7138 100644
--- a/src/main/java/miscellaneous/Miscellaneous.java
+++ b/src/main/java/miscellaneous/Miscellaneous.java
@@ -6,41 +6,51 @@ import umontreal.iro.lecuyer.randvar.UniformGen;
public class Miscellaneous {
- public static long binomialForSuperIndividual(Pilot pilot, long amount, double succesProba, long threshold) {
- long amountWithSuccess;
- if (amount > threshold) { // use a normal approximation for huge amount
+ public static long binomialForSuperIndividual(Pilot pilot, long amount, double succesProba, long threshold) {
+ long amountWithSuccess;
+ if (amount > threshold) { // use a normal approximation for huge amount
/* double p=-1.;
while (p<0 | p>1){
p = genAleaNormal.nextDouble() *
Math.sqrt(succesProba * (1 - succesProba) /amount) + succesProba;
}
amountWithSuccess = (long) Math.round(p* amount);*/
- amountWithSuccess = -1;
- while (amountWithSuccess < 0 | amountWithSuccess > amount) {
- amountWithSuccess = Math.round(NormalGen.nextDouble(pilot.getRandomStream(), 0., 1.) * Math.sqrt(succesProba * (1 - succesProba) * amount)
- + succesProba * amount);
- }
-
- } else {
- amountWithSuccess = 0;
- for (long i = 0; i < amount; i++) {
- if (UniformGen.nextDouble(pilot.getRandomStream(), 0, 1) < succesProba) {
- amountWithSuccess++;
- }
- }
- }
- return amountWithSuccess;
- }
-
- public static long binomialForSuperIndividual(Pilot pilot, long amount, double succesProba) {
- return binomialForSuperIndividual(pilot, amount, succesProba, 50);
- }
-
- static public double temperatureEffect(double T, double Tmin, double Topt, double Tmax) {
- if (T <= Tmin || T >= Tmax) {
- return 0;
- } else {
- return (T - Tmin) * (T - Tmax) / ((T - Tmin) * (T - Tmax) - ((T - Topt) * (T-Topt)));
- }
- }
+ amountWithSuccess = -1;
+ while (amountWithSuccess < 0 | amountWithSuccess > amount) {
+ amountWithSuccess = Math.round(NormalGen.nextDouble(pilot.getRandomStream(), 0., 1.) * Math.sqrt(succesProba * (1 - succesProba) * amount)
+ + succesProba * amount);
+ }
+
+ } else {
+ amountWithSuccess = 0;
+ for (long i = 0; i < amount; i++) {
+ if (UniformGen.nextDouble(pilot.getRandomStream(), 0, 1) < succesProba) {
+ amountWithSuccess++;
+ }
+ }
+ }
+ return amountWithSuccess;
+ }
+
+ public static long binomialForSuperIndividual(Pilot pilot, long amount, double succesProba) {
+ return binomialForSuperIndividual(pilot, amount, succesProba, 50);
+ }
+
+ static public double temperatureEffect(double T, double Tmin, double Topt, double Tmax) {
+ if (T <= Tmin || T >= Tmax) {
+ return 0;
+ } else {
+ return (T - Tmin) * (T - Tmax) / ((T - Tmin) * (T - Tmax) - ((T - Topt) * (T-Topt)));
+ }
+ }
+
+ static public double rectangularTemperatureEffect(double T, double Tmin, double Tmax) {
+ if (T <= Tmin || T >= Tmax) {
+ return 0;
+ } else {
+ return 1;
+ }
+ }
}
+
+
diff --git a/src/main/java/species/Survive.java b/src/main/java/species/Survive.java
index 2b6fc5a..214e038 100644
--- a/src/main/java/species/Survive.java
+++ b/src/main/java/species/Survive.java
@@ -19,9 +19,9 @@ import org.openide.util.lookup.ServiceProvider;
@ServiceProvider(service = AquaNismsGroupProcess.class)
public class Survive extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
- public double tempMinMortGenInRiv = 10.;
- public double tempMaxMortGenInRiv = 23.; // DEFINIR TROIS AUTRES POUR MORTALITE
- public double tempOptMortGenInRiv = 20.;
+ public double tempMinSurvivalSpawnerInRiv = 10.;
+ public double tempMaxSurvivalSpawnerInRiv = 23.; // DEFINIR TROIS AUTRES POUR MORTALITE
+ public double tempOptSurvivalSpawnerInRiv = 20.;
public double survivalProbOptGenInRiv = 1.;
public double mortalityRateInRiver = 0.4;
@@ -43,7 +43,8 @@ public class Survive extends AquaNismsGroupProcess<DiadromousFish, DiadromousFis
survivalProbability = 1.;
//Survive
if(fish.getPosition().getType() == TypeBassin.RIVER && fish.isMature()){
- double tempEffectSurv = Miscellaneous.temperatureEffect(fish.getPosition().getCurrentTemperature(group.getPilot()), tempMinMortGenInRiv, tempOptMortGenInRiv, tempMaxMortGenInRiv);
+ //double tempEffectSurv = Miscellaneous.temperatureEffect(fish.getPosition().getCurrentTemperature(group.getPilot()), tempMinSurvivalSpawnerInRiv, tempOptSurvivalSpawnerInRiv, tempMaxSurvivalSpawnerInRiv);
+ double tempEffectSurv = Miscellaneous.rectangularTemperatureEffect(fish.getPosition().getCurrentTemperature(group.getPilot()), tempMinSurvivalSpawnerInRiv, tempMaxSurvivalSpawnerInRiv);
if (tempEffectSurv == 0.){
survivalProbability = 0.;
//System.out.println("le poisson situ� dans le bassin " + fish.getPosition().getName() + " en " + Time.getSeason() +" a un coeff de mortalit� de " + fish.getMortalityRateInRiver() + " mais � cause de la temp�rature une prob de survie de " + survivalProbability);
--
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