Skip to content

GitLab

Commit 10262818 authored by Poulet Camille's avatar Poulet Camille
Browse files

Try easyRun XML Allee Effect and Phom

parent a744b2a8
Hide whitespace changes
Inline Side-by-side
data/input/northeastamerica/fishRIOBasin_Sapidissima_Old.xml 0 → 100644
View file @ 10262818
<list>
<species.DiadromousFishGroup>
<name>species A</name>
<color>
<red>255</red>
<green>0</green>
<blue>0</blue>
<alpha>255</alpha>
</color>
<dMaxDisp>300.0</dMaxDisp>
<nutrientRoutine class="species.NutrientRoutine">
<nutrientsOfInterest>
<string>N</string>
<string>P</string>
</nutrientsOfInterest>
<residenceTime>30.0</residenceTime>
<excretionRate class="hashtable">
<entry>
<string>P</string>
<double>2.17E-6</double>
</entry>
<entry>
<string>N</string>
<double>2.471E-5</double>
</entry>
</excretionRate>
<fishFeaturesPreSpawning class="hashtable">
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>bLW_Gonad</string>
<double>3.3838</double>
</entry>
<entry>
<string>aLW_Gonad</string>
<double>-8.8744</double>
</entry>
<entry>
<string>bLW</string>
<double>3.2252</double>
</entry>
<entry>
<string>aLW</string>
<double>0.004095817237891344</double>
</entry>
</hashtable>
</entry>
<entry>
<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>bLW_Gonad</string>
<double>2.6729</double>
</entry>
<entry>
<string>aLW_Gonad</string>
<double>-5.2425</double>
</entry>
<entry>
<string>bLW</string>
<double>3.3429</double>
</entry>
<entry>
<string>aLW</string>
<double>0.002665367811305362</double>
</entry>
</hashtable>
</entry>
</fishFeaturesPreSpawning>
<fishFeaturesPostSpawning class="hashtable">
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>bLW_Gonad</string>
<double>3.8331</double>
</entry>
<entry>
<string>aLW_Gonad</string>
<double>-11.285</double>
</entry>
<entry>
<string>bLW</string>
<double>2.9973</double>
</entry>
<entry>
<string>aLW</string>
<double>0.010383887012522573</double>
</entry>
</hashtable>
</entry>
<entry>
<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>bLW_Gonad</string>
<double>2.8545</double>
</entry>
<entry>
<string>aLW_Gonad</string>
<double>-6.6234</double>
</entry>
<entry>
<string>bLW</string>
<double>2.9418</double>
</entry>
<entry>
<string>aLW</string>
<double>0.013199187556948952</double>
</entry>
</hashtable>
</entry>
</fishFeaturesPostSpawning>
<juvenileFeatures class="hashtable">
<entry>
<string>bLW</string>
<double>3.0306</double>
</entry>
<entry>
<string>aLW</string>
<double>0.006986429759979109</double>
</entry>
</juvenileFeatures>
<compoCarcassPreSpawning class="hashtable">
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>P</string>
<double>0.00666</double>
</entry>
<entry>
<string>N</string>
<double>0.02941</double>
</entry>
</hashtable>
</entry>
<entry>
<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>P</string>
<double>0.006730000000000001</double>
</entry>
<entry>
<string>N</string>
<double>0.029580000000000002</double>
</entry>
</hashtable>
</entry>
</compoCarcassPreSpawning>
<compoGametes class="hashtable">
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>P</string>
<double>0.00724</double>
</entry>
<entry>
<string>N</string>
<double>0.0325</double>
</entry>
</hashtable>
</entry>
<entry>
<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>P</string>
<double>0.0032</double>
</entry>
<entry>
<string>N</string>
<double>0.03242</double>
</entry>
</hashtable>
</entry>
</compoGametes>
<compoJuvenile class="hashtable">
<entry>
<string>P</string>
<double>0.00887</double>
</entry>
<entry>
<string>N</string>
<double>0.02803</double>
</entry>
</compoJuvenile>
</nutrientRoutine>
<parameterSetfileName></parameterSetfileName>
<parameterSetLine>0</parameterSetLine>
<yearOfTheUpdate>0</yearOfTheUpdate>
<basinsToUpdateFile></basinsToUpdateFile>
<outputPath>data/output/northeastamerica/</outputPath>
<minYearToWrite>1800</minYearToWrite>
<fileNameFluxes></fileNameFluxes>
<lengthAtHatching>2.8</lengthAtHatching>
<linfVonBertForFemale>76.0</linfVonBertForFemale>
<linfVonBertForMale>76.0</linfVonBertForMale>
<lFirstMaturityForFemale>45</lFirstMaturityForFemale>
<lFirstMaturityForMale>40</lFirstMaturityForMale>
<processes>
<processesAtBegin>
</processesAtBegin>
<processesEachStep>
<environment.InformTime>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<consoleDisplay>true</consoleDisplay>
</environment.InformTime>
<species.PlopProcess>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<temporisation>0</temporisation>
</species.PlopProcess>
<species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<nbFishPerSI>100000</nbFishPerSI>
<initialLength>2.8</initialLength>
<etaPopulate>40.0</etaPopulate>
<timesOfPopulate>5</timesOfPopulate>
<populateSeason>SPRING</populateSeason>
</species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize>
<species.Age>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
</species.Age>
<species.Grow>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<tempMinGrow>3</tempMinGrow>
<tempMaxGrow>26</tempMaxGrow>
<tempOptGrow>17</tempOptGrow>
<kOptForFemale>0.3236</kOptForFemale>
<kOptForMale>0.2142</kOptForMale>
<sigmaDeltaLVonBert>0.2</sigmaDeltaLVonBert>
</species.Grow>
<species.MigrateFromOffshoreToInshore>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<migrationSeasonToReachInshore>SPRING</migrationSeasonToReachInshore>
</species.MigrateFromOffshoreToInshore>
<species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>
<riverMigrationSeason>SPRING</riverMigrationSeason>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<alpha0Rep>-40.8</alpha0Rep>
<alpha1Rep>35.8</alpha1Rep>
<alpha2Rep>0.0</alpha2Rep>
<alpha3Rep>0.0</alpha3Rep>
<meanBvSurface>15321</meanBvSurface>
<standardDeviationBvSurface>35594</standardDeviationBvSurface>
<meanInterDistance>1803.52</meanInterDistance>
<standardDeviationInterDistance>1460.38</standardDeviationInterDistance>
<meanSpawnersLengthAtRepro>45.0</meanSpawnersLengthAtRepro>
<standardDeviationOfSpawnersLengthAtRepro>2.0</standardDeviationOfSpawnersLengthAtRepro>
<weightOfDeathBasin>0.5</weightOfDeathBasin>
<pHomingForReachEquil>0.97</pHomingForReachEquil>
<pHomingAfterEquil>0.97</pHomingAfterEquil>
<NbYearForInstallPop>0</NbYearForInstallPop>
</species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>
<species.Survive>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<tempMinSurvivalSpawnerInRiv>5.4</tempMinSurvivalSpawnerInRiv>
<tempOptSurvivalSpawnerInRiv>16.7</tempOptSurvivalSpawnerInRiv>
<tempMaxSurvivalSpawnerInRiv>27.5</tempMaxSurvivalSpawnerInRiv>
<survivalProbOptSpawnerInRiv>1.0</survivalProbOptSpawnerInRiv>
<!--<mortalityRateInRiver>0.4</mortalityRateInRiver> -->
<mortalityRateInSea>0.4</mortalityRateInSea>
<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
</species.Survive>
<!--<species.WriteEffectiveAndBiomassImportFluxes> <synchronisationMode>ASYNCHRONOUS</synchronisationMode> <exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput> </species.WriteEffectiveAndBiomassImportFluxes> -->
<analysis.AnalyseSpawnerFeatures>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<analysisSeason>SPRING</analysisSeason>
<memorySize>30</memorySize>
</analysis.AnalyseSpawnerFeatures>
<analysis.AnalyseFishDistribution>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<centileForRange>0.95</centileForRange>
<minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
</analysis.AnalyseFishDistribution>
<species.ReproduceWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<reproductionSeason>SPRING</reproductionSeason>
<tempMinRep>5.1</tempMinRep>
<tempOptRep>13.5</tempOptRep>
<tempMaxRep>24.3</tempMaxRep>
<Soffset>-1.0</Soffset>
<eta>2.4</eta>
<ratioS95__S50>1.9</ratioS95__S50>
<a>270000</a>
<delta__t>0.33</delta__t>
<survOptRep>0.0017</survOptRep>
<lambda>4.1E-4</lambda>
<proportionOfFemaleAtBirth>0.5</proportionOfFemaleAtBirth>
<initialLength>2.8</initialLength>
<sigmaRecruitment>0.2</sigmaRecruitment>
<maxNumberOfSuperIndividualPerReproduction>100.0
</maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>false</withDiagnose>
<displayFluxesOnConsole>false</displayFluxesOnConsole>
</species.ReproduceWithDiagnose>
<species.SurviveAfterReproduction>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<afterReproductionSeason>SUMMER</afterReproductionSeason>
<maximalSurvivalRate>0.18</maximalSurvivalRate>
<temperatureEffectSurvivalAfterReproduction class="temperatureEffect.LogitEffect">
<Tref>19.9</Tref>
<alpha>-0.58</alpha>
</temperatureEffectSurvivalAfterReproduction>
<!-- <temperatureEffectSurvivalAfterReproduction -->
<!-- class="temperatureEffect.NoEffect"> -->
<!-- </temperatureEffectSurvivalAfterReproduction> -->
</species.SurviveAfterReproduction>
<species.MigrateFromRiverToInshore>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<migrationSeasonToReachInshore>SUMMER</migrationSeasonToReachInshore>
<displayFluxesOnConsole>false</displayFluxesOnConsole>
</species.MigrateFromRiverToInshore>
<species.MigrateToOffshore>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<migrationSeasonToReachOffshore>AUTOMN</migrationSeasonToReachOffshore>
<offshoreDestination>WINTERING</offshoreDestination>
</species.MigrateToOffshore>
<species.MigrateBetweenOffshores>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<migrationSeasonToReachWinteringOffshore>AUTOMN</migrationSeasonToReachWinteringOffshore>
<migrationSeasonToReachSummeringOffshore>SPRING</migrationSeasonToReachSummeringOffshore>
</species.MigrateBetweenOffshores>
<environment.updateTemperatureInRIOBasin>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
</environment.updateTemperatureInRIOBasin>
</processesEachStep>
<processesAtEnd>
<analysis.AnalyseLikelihoodOfPresence>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<presenceFileName>data/input/northeastamerica/nea_presence.csv</presenceFileName>
<period>obs_1900_1950</period>
<minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
<epsilon>0.001</epsilon>
</analysis.AnalyseLikelihoodOfPresence>
<analysis.IdentifyPopulation>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<consoleDisplay>false</consoleDisplay>
<years>
<long>1813</long>
</years>
<fluxesSeason>SPRING</fluxesSeason>
<fileNameOutput>effectiveFluxes</fileNameOutput>
</analysis.IdentifyPopulation>
</processesAtEnd>
</processes>
<useCemetery>false</useCemetery>
</species.DiadromousFishGroup>
</list>
data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava_AE_constant.xml 0 → 100644
View file @ 10262818
<list>
<species.DiadromousFishGroup>
<name>species A</name>
<color>
<red>255</red>
<green>0</green>
<blue>0</blue>
<alpha>255</alpha>
</color>
<dMaxDisp>300.0</dMaxDisp>
<nutrientRoutine class="species.NutrientRoutine">
<nutrientsOfInterest>
<string>N</string>
<string>P</string>
</nutrientsOfInterest>
<residenceTime>30.0</residenceTime>
<excretionRate class="hashtable">
<entry>
<string>P</string>
<double>2.17E-6</double>
</entry>
<entry>
<string>N</string>
<double>2.471E-5</double>
</entry>
</excretionRate>
<fishFeaturesPreSpawning class="hashtable">
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>bLW_Gonad</string>
<double>3.3838</double>
</entry>
<entry>
<string>aLW_Gonad</string>
<double>-8.8744</double>
</entry>
<entry>
<string>bLW</string>
<double>3.2252</double>
</entry>
<entry>
<string>aLW</string>
<double>0.004095817237891344</double>
</entry>
</hashtable>
</entry>
<entry>
<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>bLW_Gonad</string>
<double>2.6729</double>
</entry>
<entry>
<string>aLW_Gonad</string>
<double>-5.2425</double>
</entry>
<entry>
<string>bLW</string>
<double>3.3429</double>
</entry>
<entry>
<string>aLW</string>
<double>0.002665367811305362</double>
</entry>
</hashtable>
</entry>
</fishFeaturesPreSpawning>
<fishFeaturesPostSpawning class="hashtable">
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>bLW_Gonad</string>
<double>3.8331</double>
</entry>
<entry>
<string>aLW_Gonad</string>
<double>-11.285</double>
</entry>
<entry>
<string>bLW</string>
<double>2.9973</double>
</entry>
<entry>
<string>aLW</string>
<double>0.010383887012522573</double>
</entry>
</hashtable>
</entry>
<entry>
<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>bLW_Gonad</string>
<double>2.8545</double>
</entry>
<entry>
<string>aLW_Gonad</string>
<double>-6.6234</double>
</entry>
<entry>
<string>bLW</string>
<double>2.9418</double>
</entry>
<entry>
<string>aLW</string>
<double>0.013199187556948952</double>
</entry>
</hashtable>
</entry>
</fishFeaturesPostSpawning>
<juvenileFeatures class="hashtable">
<entry>
<string>bLW</string>
<double>3.0306</double>
</entry>
<entry>
<string>aLW</string>
<double>0.006986429759979109</double>
</entry>
</juvenileFeatures>
<compoCarcassPreSpawning class="hashtable">
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>P</string>
<double>0.00666</double>
</entry>
<entry>
<string>N</string>
<double>0.02941</double>
</entry>
</hashtable>
</entry>
<entry>
<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>P</string>
<double>0.006730000000000001</double>
</entry>
<entry>
<string>N</string>
<double>0.029580000000000002</double>
</entry>
</hashtable>
</entry>
</compoCarcassPreSpawning>
<compoGametes class="hashtable">
<entry>
<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>P</string>
<double>0.00724</double>
</entry>
<entry>
<string>N</string>
<double>0.0325</double>
</entry>
</hashtable>
</entry>
<entry>
<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
<hashtable>
<entry>
<string>P</string>
<double>0.0032</double>
</entry>
<entry>
<string>N</string>
<double>0.03242</double>
</entry>
</hashtable>
</entry>
</compoGametes>
<compoJuvenile class="hashtable">
<entry>
<string>P</string>
<double>0.00887</double>
</entry>
<entry>
<string>N</string>
<double>0.02803</double>
</entry>
</compoJuvenile>
</nutrientRoutine>
<parameterSetfileName></parameterSetfileName>
<parameterSetLine>0</parameterSetLine>
<yearOfTheUpdate>0</yearOfTheUpdate>
<basinsToUpdateFile></basinsToUpdateFile>
<outputPath>data/output/northeastamerica/</outputPath>
<minYearToWrite>1800</minYearToWrite>
<fileNameFluxes></fileNameFluxes>
<lengthAtHatching>2.8</lengthAtHatching>
<linfVonBertForFemale>76.0</linfVonBertForFemale>
<linfVonBertForMale>76.0</linfVonBertForMale>
<lFirstMaturityForFemale>44.8</lFirstMaturityForFemale>
<lFirstMaturityForMale>40.2</lFirstMaturityForMale>
<processes>
<processesAtBegin>
</processesAtBegin>
<processesEachStep>
<environment.InformTime>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<consoleDisplay>true</consoleDisplay>
</environment.InformTime>
<species.PlopProcess>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<temporisation>0</temporisation>
</species.PlopProcess>
<species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<nbFishPerSI>100000</nbFishPerSI>
<initialLength>2.8</initialLength>
<etaPopulate>40.0</etaPopulate>
<timesOfPopulate>5</timesOfPopulate>
<populateSeason>SPRING</populateSeason>
</species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize>