Commit 398b3be9 authored by patrick.lambert's avatar patrick.lambert
Browse files

Merge branch 'SpawnerRunAnalysis' into develop

parents a812cb2a 17b53021
......@@ -100,25 +100,28 @@ target
.classpath
.project
org.*
/src/main/java/environment/*.ucls
/src/main/java/environment/TestShape.java
/src/main/java/species/testAlea.java
/src/main/java/species/Essai.java
/src/main/java/miscellaneous/Essai.java
>>>>>>> master
/exploration/R/.Rhistory
/exploration/R/.RData
/outcmaesaxlen.dat
/outcmaesdisp.dat
/outcmaesfit.dat
/outcmaesstddev.dat
/outcmaesxmean.dat
/outcmaesxrecentbest.dat
/exploration/scriptR/BruchPrg.R.orig
# R: files
*.Rproj
*.Rhistory
*.RData
*.Rproj.user
*.~lock.*
# qgis file
*.qix
.Rproj.user
/exploration/scriptR/.RData
/exploration/scriptR/*.Rproj
/exploration/scriptR/.Rhistory
/exploration/scriptR/scriptR.Rproj
/exploration/scriptR/.Rproj.user/
/exploration/scriptR/.RData
/src/main/java/environment/*.ucls
/src/main/java/environment/TestShape.java
/src/main/java/species/testAlea.java
/data/input/northeastamerica/shape/*.qix
......@@ -275,11 +275,11 @@
<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
</species.Survive>
<species.WriteEffectiveAndBiomassFluxes>
<species.WriteEffectiveAndBiomassImportFluxes>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput>
</species.WriteEffectiveAndBiomassFluxes>
</species.WriteEffectiveAndBiomassImportFluxes>
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
......@@ -302,18 +302,12 @@
<displayFluxesOnConsole>false</displayFluxesOnConsole>
</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<species.WriteEffectiveAndBiomassFluxes>
<species.WriteEffectiveAndBiomassImportFluxes>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesAfterReproduction</fileNameOutput>
</species.WriteEffectiveAndBiomassFluxes>
<species.WriteEffectiveAndBiomassExportFluxes>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<fileName>effectiveAndBiomassExportFluxes</fileName>
<writeSeason>SUMMER</writeSeason>
</species.WriteEffectiveAndBiomassExportFluxes>
</species.WriteEffectiveAndBiomassImportFluxes>
<species.MigrateToSea>
<seaMigrationSeason>SUMMER</seaMigrationSeason>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
......
......@@ -61,12 +61,12 @@
</yAxisLabel>
<variableName>getFemaleSpawnerEffective</variableName>
</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
<miscellaneous.TemporalRangeSerieChart>
<observer.TemporalRangeSerieChart>
<title>Range distribution</title>
<xAxisLabel>Time (season)</xAxisLabel>
<yAxisLabel>latitude</yAxisLabel>
<variableName>getRangeDistributionWithLat</variableName>
</miscellaneous.TemporalRangeSerieChart>
</observer.TemporalRangeSerieChart>
<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
<graphType>LINE</graphType>
<title>Mean age at first reproduction for female</title>
......@@ -122,7 +122,7 @@
<java-class>environment.RiverBasin</java-class>
<fr.cemagref.observation.kernel.ObservablesHandler>
<observers>
<miscellaneous.TemporalSerieChartForBasin>
<observer.TemporalSerieChartForBasin>
<graphType>LINE</graphType>
<title>Number of juveniles</title>
<xAxisLabel>Time
......@@ -130,14 +130,14 @@
</xAxisLabel>
<yAxisLabel>number of juveniles</yAxisLabel>
<variableName>getJuvenileNumber</variableName>
</miscellaneous.TemporalSerieChartForBasin>
<miscellaneous.TemporalSerieChartForBasin>
</observer.TemporalSerieChartForBasin>
<observer.TemporalSerieChartForBasin>
<graphType>LINE</graphType>
<title>% Autochtone</title>
<xAxisLabel>Time (season)</xAxisLabel>
<yAxisLabel>% Autochtone</yAxisLabel>
<variableName>getLastPercentageOfAutochtone</variableName>
</miscellaneous.TemporalSerieChartForBasin>
</observer.TemporalSerieChartForBasin>
</observers>
</fr.cemagref.observation.kernel.ObservablesHandler>
</entry>
......
......@@ -275,11 +275,11 @@
<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
</species.Survive>
<species.WriteEffectiveAndBiomassFluxes>
<species.WriteEffectiveAndBiomassImportFluxes>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput>
</species.WriteEffectiveAndBiomassFluxes>
</species.WriteEffectiveAndBiomassImportFluxes>
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
......
<environment.RIOBasinNetworkWithContinent>
<memorySize>10</memorySize>
<memorySizeLongQueue>30</memorySizeLongQueue>
<cVthresholdForFinalStates>5.0</cVthresholdForFinalStates>
<RecruitmentThresholdForFsAndKappa>50.0</RecruitmentThresholdForFsAndKappa>
<yearOfTheBegin>1801</yearOfTheBegin>
<riverBasinFile>data/input/northeastamerica/nea_riverbasins.csv</riverBasinFile>
<offshoreBasinFile>data/input/northeastamerica/nea_offshorebasins.csv</offshoreBasinFile>
<continentShpFile></continentShpFile>
<riverBasinShpFile>data/input/northeastamerica/shape/riverbasins.shp</riverBasinShpFile>
<inshoreBasinShpFile>data/input/northeastamerica/shape/inshorebasins.shp</inshoreBasinShpFile>
<offshoreBasinShpFile>data/input/northeastamerica/shape/offshorebasins.shp</offshoreBasinShpFile>
<continentPathName>PATH</continentPathName>
<riverBasinNameLabel>BASIN_NAME</riverBasinNameLabel>
<inshoreBasinNameLabel>BASIN_NAME</inshoreBasinNameLabel>
<offshoreBasinNameLabel>BASIN_NAME</offshoreBasinNameLabel>
<distanceGridFileName>data/input/northeastamerica/distanceGridNEA.csv</distanceGridFileName>
<basinConnectionFileName>data/input/northeastamerica/inshore_offshore_connections.csv</basinConnectionFileName>
<temperatureOffshoreFile>data/input/northeastamerica/observed_offshore_temperatures.csv</temperatureOffshoreFile>
<temperatureInshoreFile>data/input/northeastamerica/observed_inshore_temperatures.csv</temperatureInshoreFile>
<temperatureRiverFile>data/input/northeastamerica/observed_river_temperatures.csv</temperatureRiverFile>
<useRealPDam>false</useRealPDam>
</environment.RIOBasinNetworkWithContinent>
<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>
<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>data/input/reality/Obs1900.csv</fileNameInputForInitialObservation>
<centileForRange>0.95</centileForRange>
<parameterSetfileName>data/input/reality/parameterSet.csv</parameterSetfileName>
<parameterSetLine>0</parameterSetLine>
<yearOfTheUpdate>0</yearOfTheUpdate>
<basinsToUpdateFile>data/input/reality/basinsToUpdate.csv</basinsToUpdateFile>
<outputPath>data/output/northeastamerica/</outputPath>
<minYearToWrite>1900</minYearToWrite>
<fileNameFluxes>nutrientFluxes</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.AnalyseSpawnerRun>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<analysisSeason>SPRING</analysisSeason>
</species.AnalyseSpawnerRun>
<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> -->
<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>
<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>
<species.WriteNutrientImportFluxes>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<fileName>nutrientImportfFluxes</fileName>
</species.WriteNutrientImportFluxes>
<species.WriteNutrientExportFluxes>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<fileName>nutrientExportFluxes</fileName>
</species.WriteNutrientExportFluxes>
</processesAtEnd>
</processes>
<useCemetery>false</useCemetery>
</species.DiadromousFishGroup>
</list>
......@@ -66,12 +66,12 @@
</yAxisLabel>
<variableName>getFemaleSpawnerEffective</variableName>
</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
<miscellaneous.TemporalRangeSerieChart>
<observer.TemporalRangeSerieChart>
<title>Range distribution</title>
<xAxisLabel>Time (season)</xAxisLabel>
<yAxisLabel>latitude</yAxisLabel>
<variableName>getRangeDistributionWithLat</variableName>
</miscellaneous.TemporalRangeSerieChart>
</observer.TemporalRangeSerieChart>
<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
<graphType>LINE</graphType>
<title>Mean age at first reproduction for female</title>
......@@ -127,7 +127,7 @@
<java-class>environment.RiverBasin</java-class>
<fr.cemagref.observation.kernel.ObservablesHandler>
<observers>
<miscellaneous.TemporalSerieChartForBasin>
<observer.TemporalSerieChartForBasin>
<graphType>LINE</graphType>
<title>Number of juveniles</title>
<xAxisLabel>Time
......@@ -135,14 +135,14 @@
</xAxisLabel>
<yAxisLabel>number of juveniles</yAxisLabel>
<variableName>getJuvenileNumber</variableName>
</miscellaneous.TemporalSerieChartForBasin>
<miscellaneous.TemporalSerieChartForBasin>
</observer.TemporalSerieChartForBasin>
<observer.TemporalSerieChartForBasin>
<graphType>LINE</graphType>
<title>% Autochtone</title>
<xAxisLabel>Time (season)</xAxisLabel>
<yAxisLabel>% Autochtone</yAxisLabel>
<variableName>getLastPercentageOfAutochtone</variableName>
</miscellaneous.TemporalSerieChartForBasin>
</observer.TemporalSerieChartForBasin>
</observers>
</fr.cemagref.observation.kernel.ObservablesHandler>
</entry>
......
<hashtable>
</hashtable>
\ No newline at end of file
<hashtable>
<entry>
<!-- <java-class>fr.cemagref.simaqualife.kernel.AquaticWorld</java-class> -->
<java-class>environment.RIOBasinNetworkWithContinent</java-class>
<fr.cemagref.observation.kernel.ObservablesHandler>
<observers>
<environment.RIOBasinNetworkObserverWithContinent>
<title>North East America</title>
<threshold>1000000</threshold>
<colorScaleEnum>RedsScale</colorScaleEnum>
</environment.RIOBasinNetworkObserverWithContinent>
<environment.RIOBasinNetworkObserverPresence>
<title>Shad presence in North East America</title>
<presenceFileName>data/input/northeastamerica/nea_presence.csv</presenceFileName>
<period>obs_1900_1950</period>
</environment.RIOBasinNetworkObserverPresence>
</observers>
</fr.cemagref.observation.kernel.ObservablesHandler>
</entry>
<entry>
<java-class>species.AnalyseSpawnerRun</java-class>
<fr.cemagref.observation.kernel.ObservablesHandler>
<observers>
<observer.RecordDuoChart>
<graphType>POINT</graphType>
<variableName>iteroparityRatesPerLatitude</variableName>
<xName>latitude</xName>
<yName>iteroparityRate</yName>
<yLimitMin>0.</yLimitMin>
<yLimitMax>1.</yLimitMax>
</observer.RecordDuoChart>
<observer.RecordCSVObserver>
<separator>;</separator>
<variableName>iteroparityRateRecords</variableName>
<sysout>false</sysout>
<outputFile>data/output/northeastamerica/essai.csv</outputFile>
</observer.RecordCSVObserver>
</observers>
</fr.cemagref.observation.kernel.ObservablesHandler>
</entry>
</hashtable>
\ No newline at end of file
......@@ -280,8 +280,8 @@
<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
</species.Survive>
<!--<species.WriteEffectiveAndBiomassFluxes> <synchronisationMode>ASYNCHRONOUS</synchronisationMode> <exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput> </species.WriteEffectiveAndBiomassFluxes> -->
<!--<species.WriteEffectiveAndBiomassImportFluxes> <synchronisationMode>ASYNCHRONOUS</synchronisationMode> <exportSeason>SPRING</exportSeason>