Files in roliveros-ramos/osmose

Object Oriented Simulator of Marine Ecosystems

.Rbuildignore

.github/workflows/java-compile.yml

.github/workflows/r-compile.yml

.gitignore

.vscode/eclipse-formatter.xml

.vscode/launch.json

.vscode/settings.json

.vscode/tasks.json

CITATION.cff

DESCRIPTION

LICENSE

NAMESPACE

R/aaa-.R R/cacheManager.R R/deprecated.R R/ex_osmose-plot.R R/osmose-auxiliar.R R/osmose-class.R R/osmose-eco.R R/osmose-getVar.R R/osmose-internal.R R/osmose-main.R R/osmose-package.R R/osmose-plot-auxiliar.R R/osmose-plot-inDevel.R R/osmose-plot-util.R R/osmose-plot.R R/osmose-plot4d.R R/osmose-readConfiguration.R R/osmose-write_osmose.R R/osmose.config-class.R R/osmose.config-internal.R R/osmose.config-plot-auxiliar.R R/osmose.config-plot.R R/osmose.maps.R R/osmose.netcdf.R R/osmose2R.R R/osmose_init-auxiliar.R R/osmose_init-initialization.R R/osmose_init-process.R R/osmose_init-selectivity.R R/osmose_init-update_maps.R R/osmose_init.R R/update_config.R README.md RELEASE.md cran-comments.md

data-raw/calib_demo.zip

data-raw/gog.zip

data-raw/outputs.zip

demo/00Index

demo/osmose.config_class.R demo/osmose_class.R

doc/Makefile

doc/README.md

doc/_static/biblio.bib

doc/_static/css/hacks.css

doc/_static/logo-osmose.pdf

doc/_static/logo-osmose.svg

doc/_static/theme_overrides.css

doc/alias.rst

doc/astart.rst

doc/astart/_static/run_testconf.R

doc/astart/arch.rst

doc/astart/calib_inst.rst

doc/astart/compile_java.rst

doc/astart/down_java.rst

doc/astart/download_nc.rst

doc/astart/download_osm.rst

doc/astart/running.rst

doc/biblio.rst

doc/bioen_odd_des.rst

doc/bioen_odd_des/_static/energybudget.csv

doc/bioen_odd_des/_static/mermaid/scheduling.md

doc/bioen_odd_des/_static/oxygenfunction.csv

doc/bioen_odd_des/_static/school.csv

doc/bioen_odd_des/_static/species.csv

doc/bioen_odd_des/_static/tempfunction.csv

doc/bioen_odd_des/design_concepts.rst

doc/bioen_odd_des/statevar.rst

doc/bioen_odd_des/submodel.rst

doc/bioen_odd_des/submodel/_static/OCLTT_fig_FF.png

doc/bioen_odd_des/submodel/_static/plot_repfonct.py

doc/bioen_odd_des/submodel/_static/schema_resume_bioen.png

doc/bioen_odd_des/submodel/energy_uptake.rst

doc/bioen_odd_des/submodel/maintenance.rst

doc/bioen_odd_des/submodel/maturation.rst

doc/bioen_odd_des/submodel/mortality.rst

doc/bioen_odd_des/submodel/new_tissue.rst

doc/bioen_odd_des/submodel/reproduction.rst

doc/calib.rst

doc/calib/_static/democalib.R

doc/calib/calset.rst

doc/calib/dataprep.rst

doc/calib/dirarc.rst

doc/calib/run.rst

doc/calib/runcal.rst

doc/calib/runmod.rst

doc/calib/varcal.rst

doc/conf.py

doc/evo_odd_des.rst

doc/evo_odd_des/_static/mermaid/trait_variations.md

doc/evo_odd_des/design_concepts.rst

doc/evo_odd_des/init.rst

doc/evo_odd_des/submodel.rst

doc/evo_odd_des/submodel/genetic_inheritance.rst

doc/evo_odd_des/submodel/genetic_structure.rst

doc/evo_odd_des/submodel/trait_determinism.rst

doc/genindex.rst

doc/index.rst

doc/make.bat

doc/make_unique.py

doc/misc.rst

doc/misc/_static/datarmor/calibrate_MPI.R doc/misc/_static/datarmor/calibrate_OMP.R doc/misc/_static/datarmor/calibrate_SEQ.R

doc/misc/_static/datarmor/runCalib_MPI.pbs

doc/misc/_static/datarmor/runCalib_OMP.pbs

doc/misc/_static/datarmor/runCalib_SEQ.pbs

doc/misc/_static/fisheries/bycatch/fishingMatrix.csv

doc/misc/_static/fisheries/bycatch/plot_bycatch.py

doc/misc/_static/fisheries/select/plot_select.py

doc/misc/_static/fisheries/spatial/create_fmap_template.py

doc/misc/_static/fisheries/spatial/eec_lon_lat.nc

doc/misc/_static/fisheries/time/plot_timevar.py

doc/misc/datarmor.rst

doc/misc/datarmor/packload.txt

doc/misc/datarmor/runpar.txt

doc/misc/weights_calc.txt

doc/newconf/_static/create_grid.R

doc/newconf/geo.txt

doc/newconf/grid.txt

doc/newconf/ltl.txt

doc/odd_des.rst

doc/odd_des/_static/bkgschool.csv

doc/odd_des/_static/bkgspecies.csv

doc/odd_des/_static/grid.csv

doc/odd_des/_static/mermaid/init_biomass.md doc/odd_des/_static/mermaid/scheduling.md

doc/odd_des/_static/rscspecies.csv

doc/odd_des/_static/school.csv

doc/odd_des/_static/simu.csv

doc/odd_des/_static/species.csv

doc/odd_des/design_concepts.rst

doc/odd_des/init.rst

doc/odd_des/input.rst

doc/odd_des/proc_sche.rst

doc/odd_des/purpose.rst

doc/odd_des/statevar.rst

doc/odd_des/submodel.rst

doc/odd_des/submodel/_static/mermaid/influx.md doc/odd_des/submodel/_static/mermaid/init_influx.md

doc/odd_des/submodel/_static/plot_growth.py

doc/odd_des/submodel/_static/plot_random_dis.py

doc/odd_des/submodel/growth.rst

doc/odd_des/submodel/influx.rst

doc/odd_des/submodel/ltl-update.rst

doc/odd_des/submodel/mort.rst

doc/odd_des/submodel/mort/_static/fisheries/bycatch/fishingMatrix.csv

doc/odd_des/submodel/mort/_static/fisheries/bycatch/plot_bycatch.py

doc/odd_des/submodel/mort/_static/fisheries/select/plot_select.py

doc/odd_des/submodel/mort/_static/fisheries/spatial/create_fmap_template.py

doc/odd_des/submodel/mort/_static/fisheries/spatial/eec_lon_lat.nc

doc/odd_des/submodel/mort/_static/fisheries/time/plot_timevar.py

doc/odd_des/submodel/mort/_static/plot_fish_period.py

doc/odd_des/submodel/mort/_static/plot_size_ratios.py

doc/odd_des/submodel/mort/_static/predation-accessibility.csv

doc/odd_des/submodel/mort/_static/verif_fisheries0.png

doc/odd_des/submodel/mort/_static/verif_fisheries1.png

doc/odd_des/submodel/mort/_static/verif_fisheries2.png

doc/odd_des/submodel/mort/_static/verif_fisheries3.png

doc/odd_des/submodel/mort/_static/verif_fisheries4.png

doc/odd_des/submodel/mort/fish.rst

doc/odd_des/submodel/mort/migrat.rst

doc/odd_des/submodel/mort/pred.rst

doc/odd_des/submodel/mort/starv.rst

doc/odd_des/submodel/movement.rst

doc/odd_des/submodel/reprod.rst

doc/odd_des/submodel/school-init.rst

doc/old_params.txt

doc/osmose-econ.rst

doc/osmose-econ/calibration.rst

doc/osmose-econ/introduction.rst

doc/osmose-econ/output.rst

doc/osmose-econ/parameters.rst

doc/osmose.rst

doc/osmose/_static/compile.sh

doc/osmose/_static/plot_step_chart.tex

doc/osmose/bkg.rst

doc/osmose/forcing.rst

doc/osmose/grid.rst

doc/osmose/ltl.rst

doc/params/_static/config_files_des/fishingmort.csv

doc/params/_static/config_files_des/grid.csv

doc/params/_static/config_files_des/ltlgen.csv

doc/params/_static/config_files_des/ltlspe.csv

doc/params/_static/config_files_des/map.csv

doc/params/_static/config_files_des/mort.csv

doc/params/_static/config_files_des/movement.csv

doc/params/_static/config_files_des/mpa.csv

doc/params/_static/config_files_des/naturalmort.csv

doc/params/_static/config_files_des/output.csv

doc/params/_static/config_files_des/outputspe.csv

doc/params/_static/config_files_des/population.csv

doc/params/_static/config_files_des/predation.csv

doc/params/_static/config_files_des/run.csv

doc/params/_static/config_files_des/species.csv

doc/params/fishing.txt

doc/params/format.txt

doc/params/format.txt2

doc/params/grid.txt

doc/params/gruss.txt

doc/params/influx.txt

doc/params/listofparam.txt

doc/params/listofparam.txt2

doc/params/ltl.txt

doc/params/main.txt

doc/params/main.txt2

doc/params/migration.txt

doc/params/mnat.txt

doc/params/mortality.txt

doc/params/movement.txt

doc/params/mpa.txt

doc/params/naming_conv.txt

doc/params/popinit.txt

doc/params/predation.txt

doc/params/reprod.txt

doc/params/resource-forcing.txt

doc/params/species.txt

doc/rosmose.rst

doc/rosmose/_static/getVar.R doc/rosmose/_static/getVar2.R

doc/rosmose/_static/gogosm_mortalityRateDistribByAge-OctopusVulgaris_Simu0.nc

doc/rosmose/_static/package_loading.R doc/rosmose/_static/param_loading.R doc/rosmose/_static/plot_osmose_outputs.R doc/rosmose/_static/read_nc.R doc/rosmose/_static/read_osmose_outputs.R doc/rosmose/_static/runosmose.R

doc/rosmose/fishing_data.txt

doc/rosmose/libload.rst

doc/rosmose/param_load.rst

doc/rosmose/plot_output.rst

doc/rosmose/read_output.rst

doc/rosmose/run_model.rst

doc/setup_newconfig.txt

git-osmose.Rproj

inst/java/lib.zip

inst/java/osmose_3.3.1.zip

inst/java/osmose_3.3.2.zip

inst/java/osmose_3.3.3.zip

inst/java/osmose_4.0.0.zip

inst/java/osmose_4.1.0.zip

inst/java/osmose_4.2.0.zip

inst/reports/osmose-report.Rmd java/local/README.md

java/local/ml/options/options/1.0.0/options-1.0.0.jar

java/local/ml/options/options/1.0.0/options-1.0.0.jar.md5

java/local/ml/options/options/1.0.0/options-1.0.0.jar.sha1

java/local/ml/options/options/1.0.0/options-1.0.0.pom

java/local/ml/options/options/1.0.0/options-1.0.0.pom.md5

java/local/ml/options/options/1.0.0/options-1.0.0.pom.sha1

java/local/ml/options/options/maven-metadata.xml

java/local/ml/options/options/maven-metadata.xml.md5

java/local/ml/options/options/maven-metadata.xml.sha1

java/src/main/java/fr/ird/osmose/AbstractSchool.java

java/src/main/java/fr/ird/osmose/Cell.java

java/src/main/java/fr/ird/osmose/Configuration.java

java/src/main/java/fr/ird/osmose/IAggregation.java

java/src/main/java/fr/ird/osmose/IMarineOrganism.java

java/src/main/java/fr/ird/osmose/ISpecies.java

java/src/main/java/fr/ird/osmose/Osmose.java

java/src/main/java/fr/ird/osmose/Prey.java

java/src/main/java/fr/ird/osmose/School.java

java/src/main/java/fr/ird/osmose/SchoolSet.java

java/src/main/java/fr/ird/osmose/Simulation.java

java/src/main/java/fr/ird/osmose/SimulationStep.java

java/src/main/java/fr/ird/osmose/Species.java

java/src/main/java/fr/ird/osmose/background/BackgroundSchool.java

java/src/main/java/fr/ird/osmose/background/BackgroundSchoolSet.java

java/src/main/java/fr/ird/osmose/background/BackgroundSpecies.java

java/src/main/java/fr/ird/osmose/eco/EconomicModule.java

java/src/main/java/fr/ird/osmose/grid/AbstractGrid.java

java/src/main/java/fr/ird/osmose/grid/NcGrid.java

java/src/main/java/fr/ird/osmose/netcdf/AbstractInputNetcdf.java

java/src/main/java/fr/ird/osmose/netcdf/FisheryAccessMatrixNetcdf.java

java/src/main/java/fr/ird/osmose/netcdf/PredationAccessMatrixNetcdf.java

java/src/main/java/fr/ird/osmose/output/AbstractDistribOutput.java

java/src/main/java/fr/ird/osmose/output/AbstractOutput.java

java/src/main/java/fr/ird/osmose/output/AbstractOutputRegion.java

java/src/main/java/fr/ird/osmose/output/AbundanceOutput_age1.java

java/src/main/java/fr/ird/osmose/output/AgeAtDeathOutput.java

java/src/main/java/fr/ird/osmose/output/BioenMaintOutput.java

java/src/main/java/fr/ird/osmose/output/BioenMeanEnergyNet.java

java/src/main/java/fr/ird/osmose/output/BioenRhoOutput.java

java/src/main/java/fr/ird/osmose/output/BioenSizeInfOutput.java

java/src/main/java/fr/ird/osmose/output/BiomassDietStageOutput.java

java/src/main/java/fr/ird/osmose/output/DietDistribOutput.java

java/src/main/java/fr/ird/osmose/output/DietOutput.java

java/src/main/java/fr/ird/osmose/output/DiscardOutput.java

java/src/main/java/fr/ird/osmose/output/DistribOutput.java

java/src/main/java/fr/ird/osmose/output/FisheryOutput.java

java/src/main/java/fr/ird/osmose/output/FisheryOutputDistrib.java

java/src/main/java/fr/ird/osmose/output/FishingAccessBiomassOutput.java

java/src/main/java/fr/ird/osmose/output/FishingHarvestedBiomassDistribOutput.java

java/src/main/java/fr/ird/osmose/output/FishingPriceAccessBiomassOutput.java

java/src/main/java/fr/ird/osmose/output/IOutput.java

java/src/main/java/fr/ird/osmose/output/MeanGenotypeOutput.java

java/src/main/java/fr/ird/osmose/output/ModularSchoolSetSnapshot.java

java/src/main/java/fr/ird/osmose/output/MortalityOutput.java

java/src/main/java/fr/ird/osmose/output/MortalitySpeciesOutput.java

java/src/main/java/fr/ird/osmose/output/NDeadSchoolDistribOutput.java

java/src/main/java/fr/ird/osmose/output/NDeadSchoolOutput.java

java/src/main/java/fr/ird/osmose/output/NSchoolDistribOutput.java

java/src/main/java/fr/ird/osmose/output/NSchoolOutput.java

java/src/main/java/fr/ird/osmose/output/NewSchoolOutput.java

java/src/main/java/fr/ird/osmose/output/OutputManager.java

java/src/main/java/fr/ird/osmose/output/OutputRegion.java

java/src/main/java/fr/ird/osmose/output/OutputWholeRegion.java

java/src/main/java/fr/ird/osmose/output/PredatorPressureDistribOutput.java

java/src/main/java/fr/ird/osmose/output/PredatorPressureOutput.java

java/src/main/java/fr/ird/osmose/output/ResourceOutput.java

java/src/main/java/fr/ird/osmose/output/SchoolSetGetter.java

java/src/main/java/fr/ird/osmose/output/SchoolSetSnapshot.java

java/src/main/java/fr/ird/osmose/output/SchoolVariableGetter.java

java/src/main/java/fr/ird/osmose/output/SpeciesOutput.java

java/src/main/java/fr/ird/osmose/output/Surveys.java

java/src/main/java/fr/ird/osmose/output/VariableTraitOutput.java

java/src/main/java/fr/ird/osmose/output/WeightedDistribOutput.java

java/src/main/java/fr/ird/osmose/output/WeightedSpeciesOutput.java

java/src/main/java/fr/ird/osmose/output/distribution/DistributionType.java

java/src/main/java/fr/ird/osmose/output/distribution/OutputDistribution.java

java/src/main/java/fr/ird/osmose/output/netcdf/AbstractDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/AbstractMeanDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/AbstractOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/AbundanceDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/AbundanceOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/AdditionalMortalityDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/AdditionalMortalityNDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/BiomassDietStageOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/BiomassDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/BiomassOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/DietDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/DietOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/MeanSizeCatchOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/MeanSizeDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/MeanSizeOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/MeanTrophicLevelCatchOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/MeanTrophicLevelDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/MeanTrophicLevelOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/MortalityOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/MortalitySpeciesOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/PredSuccessOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/PredatorPressureDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/PredatorPressureOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/YieldDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/YieldNDistribOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/YieldNOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/netcdf/YieldOutput_Netcdf.java

java/src/main/java/fr/ird/osmose/output/spatial/AbstractSpatialOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialAbundanceOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialBiomassOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialEggOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialEnetOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialEnetOutputjuv.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialEnetOutputlarvae.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialMortaPredOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialMortaStarvOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialSizeOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialSizeSpeciesOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialTLOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialYieldNOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialYieldOutput.java

java/src/main/java/fr/ird/osmose/output/spatial/SpatialdGOutput.java

java/src/main/java/fr/ird/osmose/populator/AbstractPopulator.java

java/src/main/java/fr/ird/osmose/populator/NetcdfPopulator.java

java/src/main/java/fr/ird/osmose/populator/PopulatingProcess.java

java/src/main/java/fr/ird/osmose/populator/RelativeBiomassPopulator.java

java/src/main/java/fr/ird/osmose/process/AbstractProcess.java

java/src/main/java/fr/ird/osmose/process/GrowthProcess.java

java/src/main/java/fr/ird/osmose/process/IncomingFluxProcess.java

java/src/main/java/fr/ird/osmose/process/MortalityProcess.java

java/src/main/java/fr/ird/osmose/process/MovementProcess.java

java/src/main/java/fr/ird/osmose/process/ReproductionProcess.java

java/src/main/java/fr/ird/osmose/process/bioen/BioenPredationMortality.java

java/src/main/java/fr/ird/osmose/process/bioen/BioenReproductionProcess.java

java/src/main/java/fr/ird/osmose/process/bioen/BioenStarvationMortality.java

java/src/main/java/fr/ird/osmose/process/bioen/EnergyBudget.java

java/src/main/java/fr/ird/osmose/process/bioen/OxygenFunction.java

java/src/main/java/fr/ird/osmose/process/bioen/PhysicalData.java

java/src/main/java/fr/ird/osmose/process/bioen/TempFunction.java

java/src/main/java/fr/ird/osmose/process/bioen/WeightedRandomDraft.java

java/src/main/java/fr/ird/osmose/process/genet/Genotype.java

java/src/main/java/fr/ird/osmose/process/genet/Locus.java

java/src/main/java/fr/ird/osmose/process/genet/Trait.java

java/src/main/java/fr/ird/osmose/process/growth/AbstractGrowth.java

java/src/main/java/fr/ird/osmose/process/growth/GompertzGrowth.java

java/src/main/java/fr/ird/osmose/process/growth/VonBertalanffyGrowth.java

java/src/main/java/fr/ird/osmose/process/mortality/AbstractMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/AbstractMortalitySpecies.java

java/src/main/java/fr/ird/osmose/process/mortality/AdditionalMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/FishingGear.java

java/src/main/java/fr/ird/osmose/process/mortality/FishingMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/ForagingMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/MortalityCause.java

java/src/main/java/fr/ird/osmose/process/mortality/OutMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/PredationMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/StarvationMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/additional/AnnualAdditionalMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/additional/AnnualLarvaMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/additional/ByDtAdditionalMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/additional/ByDtByClassAdditionalMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/additional/ByDtLarvaMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/fishery/FisheryBase.java

java/src/main/java/fr/ird/osmose/process/mortality/fishery/FisheryMapSet.java

java/src/main/java/fr/ird/osmose/process/mortality/fishery/FisheryPeriod.java

java/src/main/java/fr/ird/osmose/process/mortality/fishery/FisherySeasonality.java

java/src/main/java/fr/ird/osmose/process/mortality/fishery/FisherySelectivity.java

java/src/main/java/fr/ird/osmose/process/mortality/fishing/AbstractFishingMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/fishing/CatchesByDtByClassFishingMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/fishing/CatchesBySeasonFishingMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/fishing/CatchesByYearBySeasonFishingMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/fishing/RateByDtByClassFishingMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/fishing/RateBySeasonFishingMortality.java

java/src/main/java/fr/ird/osmose/process/mortality/fishing/RateByYearBySeasonFishingMortality.java

java/src/main/java/fr/ird/osmose/process/movement/AbstractSpatialDistribution.java

java/src/main/java/fr/ird/osmose/process/movement/MapDistribution.java

java/src/main/java/fr/ird/osmose/process/movement/RandomDistribution.java

java/src/main/java/fr/ird/osmose/resource/Resource.java

java/src/main/java/fr/ird/osmose/resource/ResourceForcing.java

java/src/main/java/fr/ird/osmose/resource/ResourceSpecies.java

java/src/main/java/fr/ird/osmose/stage/ClassGetter.java

java/src/main/java/fr/ird/osmose/stage/SchoolStage.java

java/src/main/java/fr/ird/osmose/util/AccessibilityManager.java

java/src/main/java/fr/ird/osmose/util/FileManager.java

java/src/main/java/fr/ird/osmose/util/GridMap.java

java/src/main/java/fr/ird/osmose/util/GridPoint.java

java/src/main/java/fr/ird/osmose/util/MPA.java

java/src/main/java/fr/ird/osmose/util/MapSet.java

java/src/main/java/fr/ird/osmose/util/Matrix.java

java/src/main/java/fr/ird/osmose/util/OsmoseLinker.java

java/src/main/java/fr/ird/osmose/util/Properties.java

java/src/main/java/fr/ird/osmose/util/Separator.java

java/src/main/java/fr/ird/osmose/util/SimulationLinker.java

java/src/main/java/fr/ird/osmose/util/StepParameters.java

java/src/main/java/fr/ird/osmose/util/XSRandom.java

java/src/main/java/fr/ird/osmose/util/YearParameters.java

java/src/main/java/fr/ird/osmose/util/filter/AliveSchoolFilter.java

java/src/main/java/fr/ird/osmose/util/filter/DeadSchoolFilter.java

java/src/main/java/fr/ird/osmose/util/filter/FilteredSet.java

java/src/main/java/fr/ird/osmose/util/filter/FilteredSets.java

java/src/main/java/fr/ird/osmose/util/filter/IFilter.java

java/src/main/java/fr/ird/osmose/util/filter/OldSchoolFilter.java

java/src/main/java/fr/ird/osmose/util/filter/OutSchoolFilter.java

java/src/main/java/fr/ird/osmose/util/filter/PresentSchoolFilter.java

java/src/main/java/fr/ird/osmose/util/filter/SpeciesFilter.java

java/src/main/java/fr/ird/osmose/util/io/ForcingFile.java

java/src/main/java/fr/ird/osmose/util/io/ForcingFileCaching.java

java/src/main/java/fr/ird/osmose/util/io/IOTools.java

java/src/main/java/fr/ird/osmose/util/io/MetaFilenameFilter.java

java/src/main/java/fr/ird/osmose/util/logging/OLogger.java

java/src/main/java/fr/ird/osmose/util/logging/OsmoseLogFormatter.java

java/src/main/java/fr/ird/osmose/util/logging/StdoutHandler.java

java/src/main/java/fr/ird/osmose/util/timeseries/ByClassTimeSeries.java

java/src/main/java/fr/ird/osmose/util/timeseries/ByRegimeTimeSeries.java

java/src/main/java/fr/ird/osmose/util/timeseries/BySpeciesTimeSeries.java

java/src/main/java/fr/ird/osmose/util/timeseries/ByYearTimeSeries.java

java/src/main/java/fr/ird/osmose/util/timeseries/GenericTimeSeries.java

java/src/main/java/fr/ird/osmose/util/timeseries/SeasonTimeSeries.java

java/src/main/java/fr/ird/osmose/util/timeseries/SingleTimeSeries.java

java/src/main/java/fr/ird/osmose/util/version/Release.java

java/src/main/java/fr/ird/osmose/util/version/Releases.java

java/src/main/java/fr/ird/osmose/util/version/VersionManager.java

java/src/main/java/fr/ird/osmose/util/version/VersionNumber.java

java/src/main/resources/cmd-usage.txt

java/src/test/java/fr/ird/osmose/TestAccess.java

java/src/test/java/fr/ird/osmose/TestAdditionalMortality.java

java/src/test/java/fr/ird/osmose/TestFishingMapSet.java

java/src/test/java/fr/ird/osmose/TestHeaders.java

java/src/test/java/fr/ird/osmose/TestMPA.java

java/src/test/java/fr/ird/osmose/TestMapSets.java

java/src/test/java/fr/ird/osmose/TestNames.java

java/src/test/java/fr/ird/osmose/TestNcSteps.java

java/src/test/java/fr/ird/osmose/TestNetcdfFishingMapSet.java

java/src/test/java/fr/ird/osmose/TestNetcdfMapSets.java

java/src/test/java/fr/ird/osmose/TestParams.java

java/src/test/java/fr/ird/osmose/TestPredMatrix.java

java/src/test/java/fr/ird/osmose/TestSchoolDistribution.java

java/src/test/java/fr/ird/osmose/TestSchoolStage.java

java/src/test/java/fr/ird/osmose/TestSeasonSeries.java

java/src/test/java/fr/ird/osmose/TestWeightedRandomDraft.java

java/src/test/java/fr/ird/osmose/TestWritting.java

java/src/test/java/fr/ird/osmose/TestYearsParam.java

java/src/test/resources/osmose-eec/.gitattributes

java/src/test/resources/osmose-eec/create_movement_maps.py

java/src/test/resources/osmose-eec/eec_all-parameters.csv

java/src/test/resources/osmose-eec/eec_backgroundspecies_biomass.nc

java/src/test/resources/osmose-eec/eec_grid-mask.nc

java/src/test/resources/osmose-eec/eec_ltlbiomassTons.nc

java/src/test/resources/osmose-eec/eec_param-additional-mortality_2Phase.csv

java/src/test/resources/osmose-eec/eec_param-background.csv

java/src/test/resources/osmose-eec/eec_param-fishing_2Phase.csv

java/src/test/resources/osmose-eec/eec_param-grid.csv

java/src/test/resources/osmose-eec/eec_param-init-pop.csv

java/src/test/resources/osmose-eec/eec_param-ltl-papierTROPHIC.csv

java/src/test/resources/osmose-eec/eec_param-movement.csv

java/src/test/resources/osmose-eec/eec_param-out-mortality.csv

java/src/test/resources/osmose-eec/eec_param-output_papierTROPHIC.csv

java/src/test/resources/osmose-eec/eec_param-predation.csv

java/src/test/resources/osmose-eec/eec_param-reproduction.csv

java/src/test/resources/osmose-eec/eec_param-simulation-papierTROPHIC.csv

java/src/test/resources/osmose-eec/eec_param-species.csv

java/src/test/resources/osmose-eec/eec_param-starvation.csv

java/src/test/resources/osmose-eec/fishery-catchability.csv

java/src/test/resources/osmose-eec/fishery-discards.csv

java/src/test/resources/osmose-eec/fishing/fishing-distrib.csv

java/src/test/resources/osmose-eec/fishing/fishing-seasonality-horse-mackerel.csv

java/src/test/resources/osmose-eec/fishing/fishing-seasonality-squids.csv

java/src/test/resources/osmose-eec/get_classes.py

java/src/test/resources/osmose-eec/grid-mask.csv

java/src/test/resources/osmose-eec/maps/10chinchard_0.csv

java/src/test/resources/osmose-eec/maps/10chinchard_1plus.csv

java/src/test/resources/osmose-eec/maps/10chinchard_spawning.csv

java/src/test/resources/osmose-eec/maps/11maquereau_nurseries.csv

java/src/test/resources/osmose-eec/maps/11maquereau_plus.csv

java/src/test/resources/osmose-eec/maps/12Hareng.csv

java/src/test/resources/osmose-eec/maps/12Hareng_plus.csv

java/src/test/resources/osmose-eec/maps/12Hareng_spawning.csv

java/src/test/resources/osmose-eec/maps/13sardine.csv

java/src/test/resources/osmose-eec/maps/14encornets.csv

java/src/test/resources/osmose-eec/maps/1Roussette_01.csv

java/src/test/resources/osmose-eec/maps/1Roussette_2plus.csv

java/src/test/resources/osmose-eec/maps/2rouget_0.csv

java/src/test/resources/osmose-eec/maps/2rouget_1plus_ete.csv

java/src/test/resources/osmose-eec/maps/2rouget_1plus_oct.csv

java/src/test/resources/osmose-eec/maps/3tacaud_0.csv

java/src/test/resources/osmose-eec/maps/3tacaud_1plus_oct.csv

java/src/test/resources/osmose-eec/maps/3tacaud_spawners_printemps.csv

java/src/test/resources/osmose-eec/maps/4Merlan_1plus.csv

java/src/test/resources/osmose-eec/maps/4Merlan_nurseries.csv

java/src/test/resources/osmose-eec/maps/4Merlan_spawning.csv

java/src/test/resources/osmose-eec/maps/5ptitTacaud_01.csv

java/src/test/resources/osmose-eec/maps/5ptitTacaud_2plus.csv

java/src/test/resources/osmose-eec/maps/6cod_1plus.csv

java/src/test/resources/osmose-eec/maps/6cod_nurseries.csv

java/src/test/resources/osmose-eec/maps/6cod_spawning.csv

java/src/test/resources/osmose-eec/maps/7callio_juillet.csv

java/src/test/resources/osmose-eec/maps/7callio_octobre.csv

java/src/test/resources/osmose-eec/maps/8sole_1plus.csv

java/src/test/resources/osmose-eec/maps/8sole_nurseries.csv

java/src/test/resources/osmose-eec/maps/8sole_spawning.csv

java/src/test/resources/osmose-eec/maps/9plie_1nurseries.csv

java/src/test/resources/osmose-eec/maps/9plie_1plus.csv

java/src/test/resources/osmose-eec/maps/9plie_spawning.csv

java/src/test/resources/osmose-eec/maps/empty.csv

java/src/test/resources/osmose-eec/maps/movements_horseMackerel_initialAge_0_lastAge_1.nc

java/src/test/resources/osmose-eec/maps/movements_horseMackerel_initialAge_1_lastAge_4.nc

java/src/test/resources/osmose-eec/maps/movements_horseMackerel_initialAge_4_lastAge_16.nc

java/src/test/resources/osmose-eec/mpa/effort_map1.csv

java/src/test/resources/osmose-eec/mpa/full_mpa.csv

java/src/test/resources/osmose-eec/mpa/mpa_map3.csv

java/src/test/resources/osmose-eec/mpa/partial_mpa.csv

java/src/test/resources/osmose-eec/mpa/rate_map1.csv

java/src/test/resources/osmose-eec/mpa/rate_map2.csv

java/src/test/resources/osmose-eec/mpa/rate_map3.csv

java/src/test/resources/osmose-eec/predation-accessibility.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp0.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp1.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp10.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp11.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp12.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp13.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp2.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp3.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp4.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp5.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp6.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp7.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp8.csv

java/src/test/resources/osmose-eec/reproduction/reproduction-seasonality-sp9.csv

java/src/test/resources/osmose-eec/sort-access-matrix.py

java/src/test/resources/osmose-eec/sorted-predation-accessibility.csv

java/src/test/resources/osmose-eec/test_mpa_values.py

man/cacheManager.Rd man/configureCalibration.Rd man/dot-osmose.barplot.Rd man/dot-osmose.format_data_stacked.Rd man/dot-plot_osmose_dietMatrix.Rd man/dot-read_2D.Rd man/dot-read_osmose_ncdf.Rd man/get_var.Rd man/get_var.osmose.Rd man/get_var.osmose.config.Rd man/initialize_osmose.Rd man/osmose-package.Rd man/osmose_calib_demo.Rd man/osmose_demo.Rd man/osmose_grid.Rd man/plot.osmose.Rd man/plot.osmose.config.Rd man/print.osmose.Rd man/print.summary.osmose.Rd man/readOsmoseConfiguration.Rd man/readOsmoseFiles.Rd man/read_osmose.Rd man/report.Rd man/report.osmose.Rd man/run_osmose.Rd man/summary.osmose.Rd man/summary.osmose.dietMatrix.Rd man/summary.osmose.mortalityRate.Rd man/updateCache.Rd man/update_ltl.Rd man/update_maps.Rd man/update_osmose.Rd man/write_osmose.Rd

pom.xml

vignettes/bibliography.bib

vignettes/create_run_read.Rmd vignettes/plot_method.Rmd

roliveros-ramos/osmose documentation built on Feb. 19, 2023, 8:19 a.m.