fishRIOBasin_Sapidissima_Rjava.xml 11.7 KB
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<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>

		<fileNameInputForInitialObservation></fileNameInputForInitialObservation>
		<centileForRange>0.95</centileForRange>
		<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>45.0</lFirstMaturityForFemale>
		<lFirstMaturityForMale>40.0</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>3.0</tempMinGrow>
					<tempMaxGrow>26.0</tempMaxGrow>
					<tempOptGrow>17.0</tempOptGrow>
					<kOptForFemale>0.3236</kOptForFemale>
					<kOptForMale>0.2141</kOptForMale>
					<sigmaDeltaLVonBert>0.2</sigmaDeltaLVonBert>
				</species.Grow>

				<species.MigrateFromOffshoreToInshore>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<migrationSeasonToReachInshore>SPRING</migrationSeasonToReachInshore>
				</species.MigrateFromOffshoreToInshore>

				<species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<alpha0Rep>-2.9</alpha0Rep>
					<alpha1Rep>19.7</alpha1Rep>
					<alpha3Rep>0.0</alpha3Rep>
					<meanBvSurface>17351</meanBvSurface>
					<standardDeviationBvSurface>35594</standardDeviationBvSurface>
					<meanInterDistance>300.0</meanInterDistance>
					<standardDeviationInterDistance>978.0</standardDeviationInterDistance>
					<pHomingForReachEquil>0.97</pHomingForReachEquil>
					<pHomingAfterEquil>0.97</pHomingAfterEquil>
					<NbYearForInstallPop>0</NbYearForInstallPop>
					<riverMigrationSeason>SPRING</riverMigrationSeason>
					<alpha2Rep>0.0</alpha2Rep>
					<meanSpawnersLengthAtRepro>45.0</meanSpawnersLengthAtRepro>
					<standardDeviationOfSpawnersLengthAtRepro>2.0</standardDeviationOfSpawnersLengthAtRepro>
					<weightOfDeathBasin>0.4</weightOfDeathBasin>
				</species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>

				<species.Survive>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<tempMinSurvivalSpawnerInRiv>8</tempMinSurvivalSpawnerInRiv>
					<tempOptSurvivalSpawnerInRiv>17.0</tempOptSurvivalSpawnerInRiv>
					<tempMaxSurvivalSpawnerInRiv>26</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> -->

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				<analysis.AnalyseSpawnerFeatures>
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					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<analysisSeason>SPRING</analysisSeason>
					<memorySize>30</memorySize>
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				</analysis.AnalyseSpawnerFeatures>
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				<analysis.AnalyseFishDistribution>
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					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<analysisSeason>SPRING</analysisSeason>
					<memorySize>30</memorySize>
					<minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
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				</analysis.AnalyseFishDistribution>
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				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<reproductionSeason>SPRING</reproductionSeason>
					<tempMinRep>10</tempMinRep>
					<tempOptRep>17</tempOptRep>
					<tempMaxRep>30</tempMaxRep>
					<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>
					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
					<maxNumberOfSuperIndividualPerReproduction>100.0
					</maxNumberOfSuperIndividualPerReproduction>
					<withDiagnose>false</withDiagnose>
					<displayFluxesOnConsole>false</displayFluxesOnConsole>
				</species.ReproduceAndSurviveAfterReproductionWithDiagnose>

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				<species.MigrateFromRiverToInshore>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<migrationSeasonToReachInshore>SPRING</migrationSeasonToReachInshore>
					<displayFluxesOnConsole>false</displayFluxesOnConsole>
				</species.MigrateFromRiverToInshore>

				<species.MigrateToOffshore>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<migrationSeasonToReachSummeringOffshore>SPRING</migrationSeasonToReachSummeringOffshore>
				</species.MigrateToOffshore>

				<species.MigrateBetweenOffshores>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<migrationSeasonToReachWinteringOffshore>AUTOMN</migrationSeasonToReachWinteringOffshore>
					<migrationSeasonToReachSummeringOffshore>SPRING</migrationSeasonToReachSummeringOffshore>
				</species.MigrateBetweenOffshores>

				<environment.updateTemperatureInRIOBasin>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
				</environment.updateTemperatureInRIOBasin>
			</processesEachStep>

			<processesAtEnd>
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				<analysis.AnalyseLikelihoodOfPresence>
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					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
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					<presenceFileName>data/input/northeastamerica/nea_presence.csv</presenceFileName>
					<period>obs_1900_1950</period>
					<minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
					<epsilon>0.001</epsilon>
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				</analysis.AnalyseLikelihoodOfPresence>
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				<analysis.IdentifyPopulation>
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					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<consoleDisplay>false</consoleDisplay>
					<years>
						<long>1813</long>
					</years>
					<fluxesSeason>SPRING</fluxesSeason>
					<fileNameOutput>effectiveFluxes</fileNameOutput>
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				</analysis.IdentifyPopulation>
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			</processesAtEnd>
		</processes>
		<useCemetery>false</useCemetery>
	</species.DiadromousFishGroup>
</list>