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SimAquaLife
GR3D
Commits
7e0f088b
Commit
7e0f088b
authored
Mar 24, 2021
by
patrick.lambert
Browse files
creation of analysis package
parent
6bf85149
Changes
21
Hide whitespace changes
Inline
Side-by-side
data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml
View file @
7e0f088b
...
...
@@ -283,18 +283,18 @@
<!--<species.WriteEffectiveAndBiomassImportFluxes> <synchronisationMode>ASYNCHRONOUS</synchronisationMode> <exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput> </species.WriteEffectiveAndBiomassImportFluxes> -->
<
specie
s.AnalyseSpawnerFeatures>
<
analysi
s.AnalyseSpawnerFeatures>
<synchronisationMode>
ASYNCHRONOUS
</synchronisationMode>
<analysisSeason>
SPRING
</analysisSeason>
<memorySize>
30
</memorySize>
</
specie
s.AnalyseSpawnerFeatures>
</
analysi
s.AnalyseSpawnerFeatures>
<
specie
s.AnalyseFishDistribution>
<
analysi
s.AnalyseFishDistribution>
<synchronisationMode>
ASYNCHRONOUS
</synchronisationMode>
<analysisSeason>
SPRING
</analysisSeason>
<memorySize>
30
</memorySize>
<minimumRecruitsForPopulatedBasin>
50
</minimumRecruitsForPopulatedBasin>
</
specie
s.AnalyseFishDistribution>
</
analysi
s.AnalyseFishDistribution>
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>
ASYNCHRONOUS
</synchronisationMode>
...
...
@@ -342,15 +342,15 @@
</processesEachStep>
<processesAtEnd>
<
specie
s.AnalyseLikelihoodOfPresence>
<
analysi
s.AnalyseLikelihoodOfPresence>
<synchronisationMode>
ASYNCHRONOUS
</synchronisationMode>
<presenceFileName>
data/input/northeastamerica/nea_presence.csv
</presenceFileName>
<period>
obs_1900_1950
</period>
<minimumRecruitsForPopulatedBasin>
50
</minimumRecruitsForPopulatedBasin>
<epsilon>
0.001
</epsilon>
</
specie
s.AnalyseLikelihoodOfPresence>
</
analysi
s.AnalyseLikelihoodOfPresence>
<
specie
s.IdentifyPopulation>
<
analysi
s.IdentifyPopulation>
<synchronisationMode>
ASYNCHRONOUS
</synchronisationMode>
<consoleDisplay>
false
</consoleDisplay>
<years>
...
...
@@ -358,7 +358,7 @@
</years>
<fluxesSeason>
SPRING
</fluxesSeason>
<fileNameOutput>
effectiveFluxes
</fileNameOutput>
</
specie
s.IdentifyPopulation>
</
analysi
s.IdentifyPopulation>
</processesAtEnd>
</processes>
<useCemetery>
false
</useCemetery>
...
...
src/main/java/
specie
s/AnalyseFishDistribution.java
→
src/main/java/
analysi
s/AnalyseFishDistribution.java
View file @
7e0f088b
...
...
@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package
specie
s
;
package
analysi
s
;
import
java.util.HashMap
;
import
java.util.Map
;
...
...
@@ -34,6 +34,8 @@ import fr.cemagref.simaqualife.pilot.Pilot;
import
miscellaneous.QueueMemory
;
import
miscellaneous.TreeMapForCentile
;
import
observer.ObservableRecord
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
/**
*
...
...
src/main/java/
specie
s/AnalyseLikelihoodOfPresence.java
→
src/main/java/
analysi
s/AnalyseLikelihoodOfPresence.java
View file @
7e0f088b
...
...
@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package
specie
s
;
package
analysi
s
;
import
java.io.FileReader
;
import
java.util.Locale
;
...
...
@@ -31,6 +31,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
import
environment.RiverBasin
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
fr.cemagref.simaqualife.pilot.Pilot
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
/**
*
...
...
src/main/java/
specie
s/AnalyseSpawnerFeatures.java
→
src/main/java/
analysi
s/AnalyseSpawnerFeatures.java
View file @
7e0f088b
...
...
@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package
specie
s
;
package
analysi
s
;
import
java.util.HashMap
;
import
java.util.Map
;
...
...
@@ -31,6 +31,8 @@ import environment.Time.Season;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
fr.cemagref.simaqualife.pilot.Pilot
;
import
miscellaneous.QueueMemory
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
import
species.DiadromousFish.Gender
;
/**
...
...
src/main/java/
specie
s/AnalyseSpawnerRun.java
→
src/main/java/
analysi
s/AnalyseSpawnerRun.java
View file @
7e0f088b
...
...
@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package
specie
s
;
package
analysi
s
;
import
java.util.ArrayList
;
import
java.util.List
;
...
...
@@ -33,6 +33,8 @@ import fr.cemagref.observation.kernel.ObservablesHandler;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
fr.cemagref.simaqualife.pilot.Pilot
;
import
observer.ObservableRecord
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
/**
*
...
...
src/main/java/
specie
s/Calibrate.java
→
src/main/java/
analysi
s/Calibrate.java
View file @
7e0f088b
...
...
@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package
specie
s
;
package
analysi
s
;
import
java.io.IOException
;
...
...
src/main/java/
specie
s/ExportLenghtAgeDistribution.java
→
src/main/java/
analysi
s/ExportLenghtAgeDistribution.java
View file @
7e0f088b
...
...
@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package
specie
s
;
package
analysi
s
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
@@ -32,6 +32,8 @@ import environment.Time;
import
environment.Time.Season
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
fr.cemagref.simaqualife.pilot.Pilot
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
import
species.DiadromousFish.Stage
;
/**
...
...
src/main/java/
specie
s/ExportMeanRecruitment.java
→
src/main/java/
analysi
s/ExportMeanRecruitment.java
View file @
7e0f088b
package
specie
s
;
package
analysi
s
;
import
com.thoughtworks.xstream.XStream
;
import
com.thoughtworks.xstream.io.xml.DomDriver
;
...
...
@@ -9,6 +9,8 @@ import environment.Time;
import
environment.Time.Season
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
fr.cemagref.simaqualife.pilot.Pilot
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
src/main/java/
specie
s/ExportPopulationStatus.java
→
src/main/java/
analysi
s/ExportPopulationStatus.java
View file @
7e0f088b
package
specie
s
;
package
analysi
s
;
import
com.thoughtworks.xstream.XStream
;
import
com.thoughtworks.xstream.io.xml.DomDriver
;
...
...
@@ -9,6 +9,8 @@ import environment.Time;
import
environment.Time.Season
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
fr.cemagref.simaqualife.pilot.Pilot
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
src/main/java/
specie
s/ExportRecruitment.java
→
src/main/java/
analysi
s/ExportRecruitment.java
View file @
7e0f088b
package
specie
s
;
package
analysi
s
;
import
com.thoughtworks.xstream.XStream
;
import
com.thoughtworks.xstream.io.xml.DomDriver
;
...
...
@@ -9,6 +9,8 @@ import environment.Time;
import
environment.Time.Season
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
fr.cemagref.simaqualife.pilot.Pilot
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
src/main/java/
specie
s/ExportSpeciesRange.java
→
src/main/java/
analysi
s/ExportSpeciesRange.java
View file @
7e0f088b
...
...
@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package
specie
s
;
package
analysi
s
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
@@ -30,6 +30,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
import
environment.Time
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
fr.cemagref.simaqualife.pilot.Pilot
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
/**
*
...
...
src/main/java/
specie
s/IdentifyPopulation.java
→
src/main/java/
analysi
s/IdentifyPopulation.java
View file @
7e0f088b
...
...
@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package
specie
s
;
package
analysi
s
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
@@ -34,6 +34,8 @@ import environment.RiverBasin;
import
environment.Time
;
import
environment.Time.Season
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
/**
*
...
...
src/main/java/
specie
s/TypeTrajectoryCV.java
→
src/main/java/
analysi
s/TypeTrajectoryCV.java
View file @
7e0f088b
package
specie
s
;
package
analysi
s
;
import
com.thoughtworks.xstream.XStream
;
import
com.thoughtworks.xstream.io.xml.DomDriver
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
import
java.io.BufferedWriter
;
import
java.io.File
;
import
java.io.FileReader
;
...
...
src/main/java/
specie
s/WriteBiomassFluxes.java
→
src/main/java/
analysi
s/WriteBiomassFluxes.java
View file @
7e0f088b
package
specie
s
;
package
analysi
s
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
@@ -15,6 +15,8 @@ import environment.Time;
import
environment.Time.Season
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
fr.cemagref.simaqualife.pilot.Pilot
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
import
species.DiadromousFish.Stage
;
/**
...
...
src/main/java/
specie
s/WriteCurrentNutrientExportFluxes.java
→
src/main/java/
analysi
s/WriteCurrentNutrientExportFluxes.java
View file @
7e0f088b
package
specie
s
;
package
analysi
s
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
@@ -12,6 +12,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
import
environment.Time
;
import
environment.Time.Season
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
public
class
WriteCurrentNutrientExportFluxes
extends
AquaNismsGroupProcess
<
DiadromousFish
,
DiadromousFishGroup
>
{
...
...
src/main/java/
specie
s/WriteCurrentNutrientImportFluxes.java
→
src/main/java/
analysi
s/WriteCurrentNutrientImportFluxes.java
View file @
7e0f088b
package
specie
s
;
package
analysi
s
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
@@ -12,6 +12,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
import
environment.Time
;
import
environment.Time.Season
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
public
class
WriteCurrentNutrientImportFluxes
extends
AquaNismsGroupProcess
<
DiadromousFish
,
DiadromousFishGroup
>
{
...
...
src/main/java/
specie
s/WriteEffectiveAndBiomassExportFluxes.java
→
src/main/java/
analysi
s/WriteEffectiveAndBiomassExportFluxes.java
View file @
7e0f088b
package
specie
s
;
package
analysi
s
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
@@ -17,6 +17,8 @@ import environment.RiverBasin;
import
environment.Time
;
import
environment.Time.Season
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
import
species.DiadromousFish.Stage
;
public
class
WriteEffectiveAndBiomassExportFluxes
extends
AquaNismsGroupProcess
<
DiadromousFish
,
DiadromousFishGroup
>
{
...
...
src/main/java/
specie
s/WriteEffectiveAndBiomassImportFluxes.java
→
src/main/java/
analysi
s/WriteEffectiveAndBiomassImportFluxes.java
View file @
7e0f088b
...
...
@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package
specie
s
;
package
analysi
s
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
@@ -34,6 +34,8 @@ import environment.Time;
import
environment.Time.Season
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
fr.cemagref.simaqualife.pilot.Pilot
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
import
species.DiadromousFish.Stage
;
/**
...
...
src/main/java/
specie
s/WriteEffectivesFluxes.java
→
src/main/java/
analysi
s/WriteEffectivesFluxes.java
View file @
7e0f088b
...
...
@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package
specie
s
;
package
analysi
s
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
@@ -34,7 +34,9 @@ import environment.Time;
import
environment.Time.Season
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
fr.cemagref.simaqualife.pilot.Pilot
;
import
species.DiadromousFish
;
import
species.DiadromousFish.Stage
;
import
species.DiadromousFishGroup
;
@Deprecated
/**
...
...
src/main/java/
specie
s/WriteNutrientExportFluxes.java
→
src/main/java/
analysi
s/WriteNutrientExportFluxes.java
View file @
7e0f088b
package
specie
s
;
package
analysi
s
;
import
java.io.BufferedWriter
;
import
java.io.File
;
...
...
@@ -13,13 +13,14 @@ import com.thoughtworks.xstream.XStream;
import
com.thoughtworks.xstream.io.xml.DomDriver
;
import
fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess
;
import
species.DiadromousFish
;
import
species.DiadromousFishGroup
;
@Deprecated
public
class
WriteNutrientExportFluxes
extends
AquaNismsGroupProcess
<
DiadromousFish
,
DiadromousFishGroup
>
{
private
String
fileName
=
"nutrientExportFluxes"
;
public
static
void
main
(
String
[]
args
)
{
System
.
out
.
println
((
new
XStream
(
new
DomDriver
())).
toXML
(
new
WriteNutrientExportFluxes
()));
...
...
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