From ab9e1f6edefe264c39447b271e7a45b967c78e5c Mon Sep 17 00:00:00 2001
From: "patrick.lambert" <patrick.mh.lambert@inrae.fr>
Date: Fri, 23 Apr 2021 08:56:39 +0200
Subject: [PATCH] correction for elegance
---
.../java/species/ReproduceWithDiagnose.java | 21 +++++++++----------
1 file changed, 10 insertions(+), 11 deletions(-)
diff --git a/src/main/java/species/ReproduceWithDiagnose.java b/src/main/java/species/ReproduceWithDiagnose.java
index e45c074..0eb64bb 100644
--- a/src/main/java/species/ReproduceWithDiagnose.java
+++ b/src/main/java/species/ReproduceWithDiagnose.java
@@ -25,7 +25,6 @@ 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 miscellaneous.Miscellaneous;
import miscellaneous.Trio;
import species.DiadromousFish.Gender;
@@ -83,12 +82,12 @@ public class ReproduceWithDiagnose extends AquaNismsGroupProcess<DiadromousFish,
private transient NormalGen genNormal;
- /**
- * the random numbers generator for binomial draws
- *
- * @unit --
- */
- private transient BinomialForSuperIndividualGen aleaGen;
+ // /**
+ // * the random numbers generator for binomial draws
+ // *
+ // * @unit --
+ // */
+ // private transient BinomialForSuperIndividualGen aleaGen;
private transient MortalityFunction mortalityFunction;
@@ -111,7 +110,7 @@ public class ReproduceWithDiagnose extends AquaNismsGroupProcess<DiadromousFish,
super.initTransientParameters(pilot);
genNormal = new NormalGen(pilot.getRandomStream(), new NormalDist(0., 1.));
- aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
+ // aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
mortalityFunction = new MortalityFunction();
stockRecruitmentRelationship = new StockRecruitmentRelationship();
@@ -205,11 +204,11 @@ public class ReproduceWithDiagnose extends AquaNismsGroupProcess<DiadromousFish,
amountPerSuperIndividual = alpha / maxNumberOfSuperIndividualPerReproduction;
// Compute the Allee effect parameters S95 and S50
- if (Soffset >= 0.) {// Allee effect independant of catchment size (including
+ if (Soffset >= 0.) {// Allee effect independant of catchment size (including no Allee Effect)
S95 = Soffset;
S50 = Soffset;
} else {
- S95 = eta * riverBasin.getAccessibleSurface(); // corresponds to S* in the rougier publication
+ S95 = eta * riverBasin.getAccessibleSurface(); // corresponds to S* in the rougier etal 2015
S50 = S95 / ratioS95_S50;
}
// initilisation of the stock recruitment relationship
@@ -535,7 +534,7 @@ class StockRecruitmentRelationship implements UnivariateFunction {
// BH Stock-Recruitment relationship with logistic depensation
double meanNumberOfRecruit = 0.;
double effectiveStock = getEffectiveStock(stock);
- if (stock > 0)
+ if (effectiveStock > 0)
meanNumberOfRecruit = Math.round(alpha * effectiveStock) / (beta + effectiveStock);
return meanNumberOfRecruit;
}
--
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